bluuebunny/crossref_metadata_2025_split huggingface dataset:
Morphological complexity affects the diversity of marine microbiomes
Authors: Lemay Matthew A , Chen Melissa Y , Mazel Florent , Hind Katharine R , Starko Samuel , Keeling Patrick J , Martone Patrick T , Parfrey Laura Wegener 
Published: December 2020

Abstract
Large eukaryotes support diverse communities of microbes on their surface—epibiota—that profoundly influence their biology. Alternate factors known to structure complex patterns of microbial diversity—host evolutionary history and ecology, environmental conditions and stochasticity—do not act independently and it is challenging to disentangle their relative effects. Here, we surveyed the epibiota from 38 sympatric seaweed species that span diverse clades and have convergent morphology, which strongly influences seaweed ecology. Host identity explains most of the variation in epibiont communities and deeper host phylogenetic relationships (e.g., genus level) explain a small but significant portion of epibiont community variation. Strikingly, epibiota community composition is significantly influenced by host morphology and epibiota richness increases with morphological complexity of the seaweed host. This effect is robust after controlling for phylogenetic non-independence and is strongest for crustose seaweeds. We experimentally validated the effect of host morphology by quantifying bacterial community assembly on latex sheets cut to resemble three seaweed morphologies. The patterns match those observed in our field survey. Thus, biodiversity increases with habitat complexity in host-associated microbial communities, mirroring patterns observed in animal communities. We suggest that host morphology and structural complexity are underexplored mechanisms structuring microbial communities.
Une expérience subjective du soin psychique
Authors: Leong Shirley 
Published: December 2020

Comment offrir une écoute et des paroles aux patients en soins intensifs ? Comment soutenir les proches ? Ces questionnements fréquents chez tous les soignants de réanimation s’accompagnent de celle non moins cruciale de l’accompagnement des équipes.
Partant de l’écriture comme outil à penser, de paroles et de lectures qui en découlent, des ateliers ont été proposés à 4 promotions d’externes pendant leur stage en réanimation.
« Mixés » avec les outils des ateliers d’écriture littéraire et thérapeutique, de la médecine narrative et des groupes Balint, proposant des lectures variées (auteurs classiques ou non, dans l’univers médical ou non – Saint-Exupéry, Brainard, Masaoka...) et l’appui de consignes d’écriture, ces interventions ont permis aux jeunes soignants d’écrire et d’ouvrir leur imagination, tout en restant dans l’univers hospitalier, les éloignant du verbe médical non pas pour les en détourner mais pour l’enrichir. Les thématiques abordées dans une logique processuelle (illusion groupale, autoportrait, expérience personnelle de la maladie, expérience vécue d’une relation soignant-soigné) ont permis des échanges variés et la participation de chacun.
Une création coopérative s’est élaborée et chaque groupe apportant une critique constructive a pu améliorer le projet initial.
Electronic properties of carbon nanotubes as detected by photoemission and inverse photoemission
Authors: Soncini Cristian , Bondino Federica , Magnano Elena , Bhardwaj Sunil , Kumar Manvendra , Cepek Cinzia , Pedio Maddalena 
Published: December 2020

Abstract
The relation between morphology and energy level alignment in carbon nanotubes (CNT) is a crucial information for the optimization of applications in nanoelectronics, optics, mechanics and (bio)chemistry. Here we present a study of the relation between the electronic properties and the morphology of single wall CNT (SWCNT), aligned multi wall CNT (MWCNT) and unaligned MWCNT. The CNT were synthesized via catalytic chemical vapor deposition in ultra-high vacuum conditions. Combined ultraviolet photoemission and inverse photoemission (IPES) spectra reveal a high sensitivity to the nanotube morphology. In the case of unaligned SWCNT the distinctive unoccupied Van Hove singularities (vHs) features are observed in the high resolution IPES spectra. Those features are assigned to semiconducting and metallic SWCNT states, according to calculated vHs DOS. The two MWCNT samples are similar in the diameter of the tube (about 15 nm) and present similar filled and empty electronic states, although the measured features in the aligned MWCNT are more defined. Noteworthy, interlayer states are also revealed. Their intensities are directly related to the MWCNT alignment. Focussing and geometrical effects associated to the MWCNT alignment are discussed to account the spectral differences.
The Quantum Efficiency and Diffractive Image Artifacts of Si:As IBC mid-IR Detector Arrays at 5–10 μm: Implications for the JWST/MIRI Detectors
Authors: Gáspár András , Rieke George H. , Guillard Pierre , Dicken Daniel , Gastaud René , Alberts Stacey , Morrison Jane , Ressler Michael E. , Argyriou Ioannis , Glasse Alistair 
Published: December 2020

Abstract
Arsenic doped back illuminated blocked impurity band (BIBIB) silicon detectors have advanced near and mid-IR astronomy for over thirty years; they have high quantum efficiency (QE), especially at wavelengths longer than 10 μm, and a large spectral range. Their radiation hardness is also an asset for space based instruments. Three examples of Si:As BIBIB arrays are used in the Mid-InfraRed Instrument (MIRI) of the James Webb Space Telescope (JWST), observing between 5 and 28 μm. In this paper, we analyze the parameters leading to high quantum efficiency (up to ∼60%) for the MIRI devices between 5 and 10 μm. We also model the cross-shaped artifact that was first noticed in the 5.7 and 7.8 μm Spitzer/IRAC images and has since also been imaged at shorter wavelength (≤10 μm) laboratory tests of the MIRI detectors. The artifact is a result of internal reflective diffraction off the pixel-defining metallic contacts to the readout detector circuit. The low absorption in the arrays at the shorter wavelengths enables photons diffracted to wide angles to cross the detectors and substrates multiple times. This is related to similar behavior in other back illuminated solid-state detectors with poor absorption, such as conventional CCDs operating near 1 μm. We investigate the properties of the artifact and its dependence on the detector architecture with a quantum-electrodynamic (QED) model of the probabilities of various photon paths. Knowledge of the artifact properties will be especially important for observations with the MIRI LRS and MRS spectroscopic modes.
Climate change mitigation through dietary change: a systematic review of empirical and modelling studies on the environmental footprints and health effects of ‘sustainable diets’
Authors: Jarmul Stephanie , Dangour Alan D , Green Rosemary , Liew Zara , Haines Andy , Scheelbeek Pauline FD 
Published: December 2020

Abstract
The adoption of healthy diets with low environmental impact has been widely promoted as an important climate change mitigation strategy. Typically, these diets are high in plant-sourced and low in animal-sourced and processed foods. Despite the fact that their environmental impacts vary, they are often referred to as ‘sustainable diets’. Here we systematically review the available published evidence on the effect of ‘sustainable diets’ on environmental footprints and human health. Eight databases (OvidSP-Medline, OvidSP-Embase, EBSCO-GreenFILE, Web of Science Core Collection, Scopus, OvidSP-CAB-Abstracts, OvidSP-AGRIS, and OvidSP-Global Health) were searched to identify literature (published 1999–2019) reporting health effects and environmental footprints of ‘sustainable diets’. Available evidence was mapped and pooled analysis was conducted by unique combinations of diet pattern, health and environmental outcome. Eighteen studies (412 measurements) met our inclusion criteria, distinguishing twelve non-mutually exclusive sustainable diet patterns, six environmental outcomes, and seven health outcomes. In 87% of measurements (n = 151) positive health outcomes were reported from ‘sustainable diets’ (average relative health improvement: 4.09% [95% CI −0.10–8.29]) when comparing ‘sustainable diets’ to current/baseline consumption patterns. Greenhouse gas emissions associated with ‘sustainable diets’ were on average 25.8%[95%CI −27.0 to −14.6] lower than current/baseline consumption patterns, with vegan diets reporting the largest reduction in GHG-emissions (−70.3% [95% CI: −90.2 to −50.4]), however, water use was frequently reported to be higher than current/baseline diets. Multiple benefits for both health and the environment were reported in the majority (n = 315[76%]) of measurements. We identified consistent evidence of both positive health effects and reduced environmental footprints accruing from ‘sustainable diets’. The notable exception of increased water use associated with ‘sustainable diets’ identifies that co-benefits are not universal and some trade-offs are likely. When carefully designed, evidence-based, and adapted to contextual factors, dietary change could play a pivotal role in climate change mitigation, sustainable food systems, and future population health.
Subsea permafrost carbon stocks and climate change sensitivity estimated by expert assessment
Authors: Sayedi Sayedeh Sara , Abbott Benjamin W , Thornton Brett F , Frederick Jennifer M , Vonk Jorien E , Overduin Paul , Schädel Christina , Schuur Edward A G , Bourbonnais Annie , Demidov Nikita , Gavrilov Anatoly , He Shengping , Hugelius Gustaf , Jakobsson Martin , Jones Miriam C , Joung DongJoo , Kraev Gleb , Macdonald Robie W , David McGuire A , Mu Cuicui , O’Regan Matt , Schreiner Kathryn M , Stranne Christian , Pizhankova Elena , Vasiliev Alexander , Westermann Sebastian , Zarnetske Jay P , Zhang Tingjun , Ghandehari Mehran , Baeumler Sarah , Brown Brian C , Frei Rebecca J 
Published: December 2020

Abstract
The continental shelves of the Arctic Ocean and surrounding seas contain large stocks of organic matter (OM) and methane (CH4), representing a potential ecosystem feedback to climate change not included in international climate agreements. We performed a structured expert assessment with 25 permafrost researchers to combine quantitative estimates of the stocks and sensitivity of organic carbon in the subsea permafrost domain (i.e. unglaciated portions of the continental shelves exposed during the last glacial period). Experts estimated that the subsea permafrost domain contains ∼560 gigatons carbon (GtC; 170–740, 90% confidence interval) in OM and 45 GtC (10–110) in CH4. Current fluxes of CH4 and carbon dioxide (CO2) to the water column were estimated at 18 (2–34) and 38 (13–110) megatons C yr−1, respectively. Under Representative Concentration Pathway (RCP) RCP8.5, the subsea permafrost domain could release 43 Gt CO2-equivalent (CO2e) by 2100 (14–110) and 190 Gt CO2e by 2300 (45–590), with ∼30% fewer emissions under RCP2.6. The range of uncertainty demonstrates a serious knowledge gap but provides initial estimates of the magnitude and timing of the subsea permafrost climate feedback.
B-Lymphoblastic Leukemia With Aberrant CD5 Expression
Authors: Ye Matthew T , Zhu Jia , Luo David X , Wang Yi , Chen Zehui , Yang Yaling , Tian Chen , Zhang Yizhuo , You M James 
Published: December 2020

AbstractObjectivesB-acute lymphoblastic leukemia (B-ALL) is a neoplasm of precursor lymphoid cells committed to the B-lineage. Expression of CD5 is rare in B-ALL.MethodsWe studied the clinicopathologic, immunophenotypic, and molecular genetic features of 10 cases of B-ALL with aberrant CD5 expression, and compared with CD5–B-ALL.ResultsB-ALL with aberrant CD5 expression is rare and predominantly affects men. Patients with CD5+ B-ALL had shorter median overall survival (21 vs 45 months, P = .0003). Expression of CD5 imposed a challenge in the differential diagnoses between B-ALL and other CD5+ B-cell lymphomas with blastic morphology. Dim CD20 and CD45, lack of surface immunoglobulin, expression of CD34 and TdT, negative immunostain for cyclin D1, and absence of t(11;14)(q13;q32) support a diagnosis of B-ALL.ConclusionsCD5 expression is rare in B-ALL and associated with poor clinical outcome. CD5+ B-ALL represents a distinct entity that needs to be considered in the differential diagnoses of CD5+ B-cell lymphoproliferative disorders.
Repurposing approved drugs for cancer therapy
Authors: Schein Catherine H 
Published: December 2020

AbstractBackgroundMany drugs approved for other indications can control the growth of tumor cells and limit adverse events (AE).Data sourcesLiterature searches with keywords ‘repurposing and cancer’ books, websites: https://clinicaltrials.gov/, for drug structures: https://pubchem.ncbi.nlm.nih.gov/Areas of agreementIntroducing approved drugs, such as those developed to treat diabetes (Metformin) or inflammation (Thalidomide), identified to have cytostatic activity, can enhance chemotherapy or even replace more cytotoxic drugs. Also, anti-inflammatory compounds, cytokines and inhibitors of proteolysis can be used to control the side effects of chemo- and immuno-therapies or as second-line treatments for tumors resistant to kinase inhibitors (KI). Drugs specifically developed for cancer therapy, such as interferons (IFN), the tyrosine KI abivertinib TKI (tyrosine kinase inhibitor) and interleukin-6 (IL-6) receptor inhibitors, may help control symptoms of Covid-19.Areas of controversyBetter knowledge of mechanisms of drug activities is essential for repurposing. Chemotherapies induce ER stress and enhance mutation rates and chromosome alterations, leading to resistance that cannot always be related to mutations in the target gene. Metformin, thalidomide and cytokines (IFN, tumor necrosis factor (TNF), interleukin-2 (IL-2) and others) have pleiomorphic activities, some of which can enhance tumorigenesis. The small and fragile patient pools available for clinical trials can cloud the data on the usefulness of cotreatments.Growing pointsBetter understanding of drug metabolism and mechanisms should aid in repurposing drugs for primary, adjuvant and adjunct treatments.Areas timely for developing researchOptimizing drug combinations, reducing cytotoxicity of chemotherapeutics and controlling associated inflammation.
Closed-loop stimulation of the medial septum terminates epileptic seizures
Authors: Takeuchi Yuichi , Harangozó Márk , Pedraza Lizeth , Földi Tamás , Kozák Gábor , Li Qun , Berényi Antal 
Published: December 2020

Abstract
Temporal lobe epilepsy with distributed hippocampal seizure foci is often intractable and its secondary generalization might lead to sudden death. Early termination through spatially extensive hippocampal intervention is not feasible directly, because of the large size and irregular shape of the hippocampus. In contrast, the medial septum is a promising target to govern hippocampal oscillations through its divergent connections to both hippocampi. Combining this ‘proxy intervention’ concept and precisely timed stimulation, we report here that closed-loop medial septum electrical stimulation can quickly terminate intrahippocampal seizures and suppress secondary generalization in a rat kindling model. Precise stimulus timing governed by internal seizure rhythms was essential. Cell type-specific stimulation revealed that the precisely timed activation of medial septum GABAergic neurons underlaid the effects. Our concept of time-targeted proxy stimulation for intervening pathological oscillations can be extrapolated to other neurological and psychiatric disorders, and has potential for clinical translation.
Connectome-Based Predictive Modeling of Individual Anxiety
Authors: Wang Zhihao , Goerlich Katharina S , Ai Hui , Aleman André , Luo Yue-jia , Xu Pengfei 
Published: December 2020

AbstractAnxiety-related illnesses are highly prevalent in human society. Being able to identify neurobiological markers signaling high trait anxiety could aid the assessment of individuals with high risk for mental illness. Here, we applied connectome-based predictive modeling (CPM) to whole-brain resting-state functional connectivity (rsFC) data to predict the degree of trait anxiety in 76 healthy participants. Using a computational “lesion” approach in CPM, we then examined the weights of the identified main brain areas as well as their connectivity. Results showed that the CPM successfully predicted individual anxiety based on whole-brain rsFC, especially the rsFC between limbic areas and prefrontal cortex. The prediction power of the model significantly decreased from simulated lesions of limbic areas, lesions of the connectivity within limbic areas, and lesions of the connectivity between limbic areas and prefrontal cortex. Importantly, this neural model generalized to an independent large sample (n = 501). These findings highlight important roles of the limbic system and prefrontal cortex in anxiety prediction. Our work provides evidence for the usefulness of connectome-based modeling in predicting individual personality differences and indicates its potential for identifying personality factors at risk for psychopathology.
Influenza Vaccine Effectiveness Against All-Cause Mortality Following Laboratory-Confirmed Influenza in Older Adults, 2010–2011 to 2015–2016 Seasons in Ontario, Canada
Authors: Chung Hannah , Buchan Sarah A , Campigotto Aaron , Campitelli Michael A , Crowcroft Natasha S , Dubey Vinita , Gubbay Jonathan B , Karnauchow Timothy , Katz Kevin , McGeer Allison J , McNally J Dayre , Mubareka Samira , Murti Michelle , Richardson David C , Rosella Laura C , Schwartz Kevin L , Smieja Marek , Zahariadis George , Kwong Jeffrey C 
Published: December 2020

Abstract

Background
Older adults are at increased risk of mortality from influenza infections. We estimated influenza vaccine effectiveness (VE) against mortality following laboratory-confirmed influenza.

Methods
Using a test-negative design study and linked laboratory and health administrative databases in Ontario, Canada, we estimated VE against all-cause mortality following laboratory-confirmed influenza for community-dwelling adults aged &gt;65 years during the 2010–2011 to 2015–2016 influenza seasons.

Results
Among 54 116 older adults tested for influenza across the 6 seasons, 6837 died within 30 days of specimen collection. Thirteen percent (925 individuals) tested positive for influenza, and 50.6% were considered vaccinated for that season. Only 23.2% of influenza test-positive cases had influenza recorded as their underlying cause of death. Before and after multivariable adjustment, we estimated VE against all-cause mortality following laboratory-confirmed influenza to be 20% (95% confidence interval [CI], 8%–30%) and 20% (95% CI, 7%–30%), respectively. This estimate increased to 34% after correcting for influenza vaccination exposure misclassification. We observed significant VE against deaths following influenza confirmation during 2014–2015 (VE = 26% [95% CI, 5%–42%]). We also observed significant VE against deaths following confirmation of influenza A/H1N1 and A/H3N2, and against deaths with COPD as the underlying cause.

Conclusions
These results support the importance of influenza vaccination in older adults, who account for most influenza-associated deaths annually.
Influence of Intramuscular Depot Medroxyprogesterone Acetate Initiation on Vaginal Microbiota in the Postpartum Period
Authors: Whitney Bridget M , Srinivasan Sujatha , Tapia Kenneth , Muriuki Eric Munene , Chohan Bhavna H , Wallis Jacqueline M , Liu Congzhou , Guthrie Brandon L , McClelland R Scott , Hoffman Noah G , Fredricks David N , Roxby Alison C 
Published: December 2020

Abstract

Background
The vaginal microbiome plays a key role in women’s reproductive health. Use of exogenous hormones, such as intramuscular depot medroxyprogesterone acetate (DMPA-IM), may alter the composition of vaginal bacterial community.

Methods
Vaginal swab samples were collected from postpartum Kenyan women initiating DMPA-IM or nonhormonal contraception (non-HC). Bacterial vaginosis was assessed by Nugent score (Nugent-BV) and bacterial community composition was evaluated using broad-range 16S ribosomal RNA gene polymerase chain reaction with high-throughput sequencing. Changes in Nugent score, alpha diversity (Shannon diversity index), and total bacterial load between contraceptive groups from enrollment to 3 months after initiation were estimated using multivariable linear mixed effects regression.

Results
Among 54 human immunodeficiency virus–negative women, 33 choosing DMPA-IM and 21 choosing non-HC, Nugent-BV was more common among DMPA-IM users at enrollment. At follow-up, Nugent score had decreased significantly among DMPA-IM users (change, −1.89; 95% confidence interval [CI], −3.53 to −.25; P = .02) while alpha diversity remained stable (0.03; −.24 to .30; P = .83). Conversely, Nugent score remained relatively stable among non-HC users (change, −0.73; 95% CI, −2.18 to .73; P = .33) while alpha diversity decreased (−0.34; −.67 to −.001; P = .05). The total bacterial load decreased slightly in DMPA-IM users and increased slightly among non-HC users, resulting in a significant difference in change between the contraceptive groups (difference, −0.64 log10 gene copies per swab sample; 95% CI, −1.19 to −.08; P = .02). While significant changes in Nugent score and alpha diversity were observed within contraceptive groups, changes between groups were not significantly different.

Conclusions
Postpartum vaginal bacterial diversity did not change in DMPA-IM users despite a reduction in Nugent-BV, but it decreased significantly among women using non-HC. Choice of contraception may influence Lactobacillus recovery in postpartum women.
Outbreak of Pseudomonas aeruginosa Infections from a Contaminated Gastroscope Detected by Whole Genome Sequencing Surveillance
Authors: Sundermann Alexander J , Chen Jieshi , Miller James K , Saul Melissa I , Shutt Kathleen A , Griffith Marissa P , Mustapha Mustapha M , Ezeonwuka Chinelo , Waggle Kady , Srinivasa Vatsala , Kumar Praveen , Pasculle A William , Ayres Ashley M , Snyder Graham M , Cooper Vaughn S , Van Tyne Daria , Marsh Jane W , Dubrawski Artur W , Harrison Lee H 
Published: December 2020

Abstract

Background
Traditional methods of outbreak investigations utilize reactive whole genome sequencing (WGS) to confirm or refute the outbreak. We have implemented WGS surveillance and a machine learning (ML) algorithm for the electronic health record (EHR) to retrospectively detect previously unidentified outbreaks and to determine the responsible transmission routes.

Methods
We performed WGS surveillance to identify and characterize clusters of genetically-related Pseudomonas aeruginosa infections during a 24-month period. ML of the EHR was used to identify potential transmission routes. A manual review of the EHR was performed by an infection preventionist to determine the most likely route and results were compared to the ML algorithm.

Results
We identified a cluster of 6 genetically related P. aeruginosa cases that occurred during a 7-month period. The ML algorithm identified gastroscopy as a potential transmission route for 4 of the 6 patients. Manual EHR review confirmed gastroscopy as the most likely route for 5 patients. This transmission route was confirmed by identification of a genetically-related P. aeruginosa incidentally cultured from a gastroscope used on 4of the 5 patients. Three infections, 2 of which were blood stream infections, could have been prevented if the ML algorithm had been running in real-time.

Conclusions
WGS surveillance combined with a ML algorithm of the EHR identified a previously undetected outbreak of gastroscope-associated P. aeruginosa infections. These results underscore the value of WGS surveillance and ML of the EHR for enhancing outbreak detection in hospitals and preventing serious infections.