bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Psychopathology and Neuroanatomical Markers of Depression in Early Psychosis
Authors: Upthegrove Rachel , Lalousis Paris , Mallikarjun Pavan , Chisholm Katharine , Griffiths Sian Lowri , Iqbal Mariam , Pelton Mirabel , Reniers Renate , Stainton Alexandra , Rosen Marlene , Ruef Anne , Dwyer Dominic B , Surman Marian , Haidl Theresa , Penzel Nora , Kambeitz-llankovic Lana , Bertolino Alessandro , Brambilla Paolo , Borgwardt Stefan , Kambeitz Joseph , Lencer Rebekka , Pantelis Christos , Ruhrmann Stephan , Schultze-Lutter Frauke , Salokangas Raimo K R , Meisenzahl Eva , Wood Stephen J , Koutsouleris Nikolaos ,   PRONIA Consortium
Published: June 2020

Abstract
Depression frequently occurs in first-episode psychosis (FEP) and predicts longer-term negative outcomes. It is possible that this depression is seen primarily in a distinct subgroup, which if identified could allow targeted treatments. We hypothesize that patients with recent-onset psychosis (ROP) and comorbid depression would be identifiable by symptoms and neuroanatomical features similar to those seen in recent-onset depression (ROD). Data were extracted from the multisite PRONIA study: 154 ROP patients (FEP within 3 months of treatment onset), of whom 83 were depressed (ROP+D) and 71 who were not depressed (ROP−D), 146 ROD patients, and 265 healthy controls (HC). Analyses included a (1) principal component analysis that established the similar symptom structure of depression in ROD and ROP+D, (2) supervised machine learning (ML) classification with repeated nested cross-validation based on depressive symptoms separating ROD vs ROP+D, which achieved a balanced accuracy (BAC) of 51%, and (3) neuroanatomical ML-based classification, using regions of interest generated from ROD subjects, which identified BAC of 50% (no better than chance) for separation of ROP+D vs ROP−D. We conclude that depression at a symptom level is broadly similar with or without psychosis status in recent-onset disorders; however, this is not driven by a separable depressed subgroup in FEP. Depression may be intrinsic to early stages of psychotic disorder, and thus treating depression could produce widespread benefit.
Sensitivity analysis of the effects of non-pharmaceutical interventions on COVID-19 in Europe
Authors: Soltesz Kristian , Gustafsson Fredrik , Timpka Toomas , Jaldén Joakim , Jidling Carl , Heimerson Albin , Schön Thomas B. , Spreco Armin , Ekberg Joakim , Dahlström Örjan , Carlson Fredrik Bagge , Jöud Anna , Bernhardsson Bo 
Published: June 2020

AbstractThe role of non-pharmaceutical interventions (NPIs) on the spread of SARS-CoV-2 has drawn significant attention, both scientific and political. Particularly, an article by the Imperial College COVID-19 Response Team (ICCRT), published online in Nature on June 8, 2020, evaluates the efficiency of 5 NPIs. Based on mortality data up to early May, it concludes that only one of the interventions, lockdown, has been efficient in 10 out of 11 studied European countries.We show, via simulations using the ICCRT model code, that conclusions regarding the effectiveness of individual NPIs are not justified. Our analysis focuses on the 11th country, Sweden, an outlier in that no lockdown was effectuated. The new simulations show that estimated NPI efficiencies across all 11 countries change drastically unless the model is adapted to give the Swedish data special treatment. While stated otherwise in the Nature article, such adaptation has been done in the model code reproducing its results: An ungrounded country-specific parameter said to have been introduced in all 11 countries, is in the code only activated for Sweden. This parameter de facto provides a new NPI category, only present in Sweden, and with an impact comparable to that of a lockdown.While the considered NPIs have unarguably contributed to reduce virus spread, our analysis reveals that their individual efficiency cannot be reliably quantified by the ICCRT model, provided mortality data up to early May.
On the Colijn-Plazzotta numbering scheme for unlabeled binary rooted trees
Authors: Rosenberg Noah A. 
Published: June 2020

AbstractColijn & Plazzotta (Syst. Biol.67:113-126, 2018) introduced a scheme for bijectively associating the unlabeled binary rooted trees with the positive integers. First, the rank 1 is associated with the 1-leaf tree. Proceeding recursively, ordered pair (k1,k2),k1⩾k2⩾ 1, is then associated with the tree whose left subtree has rankk1and whose right subtree has rankk2. Following dictionary order on ordered pairs, the tree whose left and right subtrees have the ordered pair of ranks (k1,k2) is assigned rankk1(k1− 1)/2 + 1 +k2. With this ranking, given a number of leavesn, we determine recursions foran, the smallest rank assigned to some tree withnleaves, andbn, the largest rank assigned to some tree withnleaves. Fornequal to a power of 2, the value ofanis seen to increase exponentially with 2αnfor a constantα≈ 1.24602; more generally, we show it is boundedan< 1.5n. The value ofbnis seen to increase withfor a constantβ≈ 1.05653. The great difference in the rates of increase foranandbnindicates that as the indexvis incremented, the number of leaves for the tree associated with rankvquickly traverses a wide range of values. We interpret the results in relation to applications in evolutionary biology.Mathematics subject classification05C05, 92B10, 92D15
Augmenting Signaling Pathway Reconstructions
Authors: Rubel Tobias , Ritz Anna 
Published: June 2020

AbstractSignaling pathways drive cellular response, and understanding such pathways is fundamental to molecular systems biology. A mounting volume of experimental protein interaction data has motivated the development of algorithms to computationally reconstruct signaling pathways. However, existing methods suffer from low recall in recovering protein interactions in ground truth pathways, limiting our confidence in any new predictions for experimental validation. We present the Pathway Reconstruction AUGmenter (PRAUG), a higher-order function for producing high-quality pathway reconstruction algorithms. PRAUG modifies any existing pathway reconstruction method, resulting in augmented algorithms that outperform their un-augmented counterparts for six different algorithms across twenty-nine diverse signaling pathways. The algorithms produced by PRAUG collectively reveal potential new proteins and interactions involved in the Wnt and Notch signaling pathways. PRAUG offers a valuable framework for signaling pathway prediction and discovery.
First proof of the capability of wastewater surveillance for COVID-19 in India through detection of genetic material of SARS-CoV-2
Authors: Kumar Manish , Patel Arbind Kumar , Shah Anil V , Raval Janvi , Rajpara Neha , Joshi Madhvi , Joshi Chaitanya G 
Published: June 2020

ABSTRACTwe made the first ever successful effort from India to detect the genetic material of SARS-CoV-2 viruses to understand the capability and application of WBE surveillance in India. Sampling was carried out on 8 and 27 May, 2020 from Old Pirana Waste Water Treatment Plant (WWTP) at Ahmedabad, Gujarat with 106 million liters per day (MLD) capacity receiving effluent of Civil Hospital treating COVID-19 patient. All three i.e. ORF1ab, N and S genes of SARS-CoV-2 were discerned in the influents with no gene spotted in the effluent collected on 8 and 27 May 2020. Temporal difference between 8 and 27 May 2020 samples was of 10x in gene copy loading with corresponding change of 2x in the number active COVID-19 patient in the city. Number of gene copies was found comparable to that reported in the untreated wastewaters of Australia, China and Turkey and lower than that of the USA, France and Spain. This study, being the first from India and probably among the first ten reports in the world of gene detection of SARS-CoV-2 in the environmental samples, aims to assist concerned authorities and policymakers to formulate and/or upgrade the COVID-19 surveillance to have explicit picture of phase of the pandemic. While infectious SARS-CoV-2 has yet to be identified in the aquatic environment, the virus potentially enters the wastewater stream from patient excretions and thus can be a great tool for pandemic monitoring.HIGHLIGHTS□First ever report of the presence of gene of SARS-CoV-2 in the wastewater in India.□CT value is explicitly indicative of the increase of COVID-19 patient in the vicinity.□All three i.e. ORF1ab, N and S genes of SARS-CoV-2 were discerned in the influents.□None of three genes were spotted in the effluent collected on 8 and 27 May 2020.□Wastewater surveillance conclusively specified temporal difference in COVID-19 load.□Temporal difference was 10x and 2x in gene copies and COVID-19 patient, respectively.
Tbr2-expressing retinal ganglion cells are ipRGCs
Authors: Mao Chai-An , Chen Ching-Kang , Kiyama Takae , Weber Nicole , Whitaker Christopher M. , Pan Ping , Badea Tudor C. , Massey Stephen C. 
Published: June 2020

AbstractThe mammalian retina contains more than 40 retinal ganglion cell (RGC) subtypes based on their unique morphologies, functions, and molecular profiles. Among them, intrinsically photosensitive RGCs (ipRGCs) are the first specified RGC type that emerged from a common pool of retinal progenitor cells. Previous work has shown that T-box transcription factorT-brain 2(Tbr2) is essential for the formation and maintenance of ipRGCs, and Tbr2-expressing RGCs activateOpn4expression upon native ipRGC loss, suggesting that Tbr2+RGCs can serve as a reservoir for ipRGCs. However, the identity of Tbr2+RGCs has not been fully vetted, and the developmental and molecular mechanisms underlying the formation of native and reservoir ipRGCs remain unclear. Here, we showed that Tbr2-expressing retinal neurons include RGCs and GABAergic displaced amacrine cells (dACs). Using genetic sparse labeling, we demonstrated that the majority of Tbr2+RGCs are intrinsically photosensitive and morphologically indistinguishable from known ipRGC types and have identical retinofugal projections. Additionally, we found a minor fraction of Pou4f1-expressing Tbr2+RGCs marks a unique OFF RGC subtype. Most of the Tbr2+RGCs can be ablated by anti-melanopsin-SAP toxin in adult retinas, supporting that Tbr2+RGCs contain reservoir ipRGCs that express melanopsin at varying levels. WhenTbr2is deleted in adult retinas,Opn4expression is diminished followed by the death ofTbr2-deficient cells, suggesting that Tbr2 is essential for bothOpn4expression and ipRGC survival. Finally, Tbr2 extensively occupies multipleT-elements in theOpn4locus, indicating a direct regulatory role for Tbr2 onOpn4transcription.Significance statementMelanopsin/Opn4-expressing intrinsically photosensitive retinal ganglion cells (ipRGCs) play fundamental roles in non-image forming vision. Previously we identifiedTbr2as the key transcription regulator for the development and maintenance of ipRGCs. To reveal the full identity of Tbr2-expressing retinal neurons and how Tbr2 acts, we generated a novel mouse line to genetically label and study Tbr2-expressing cells. Our in-depth characterizations firmly established that most Tbr2+RGCs are indeed ipRGCs and that Tbr2 regulatesOpn4transcription, thus place Tbr2-Opn4 transcription regulatory hierarchy as the primary component in the development and maintenance of the non-image forming visual system.
Holder Pasteurization Inactivates SARS-CoV-2 in Human Breast Milk
Authors: Conzelmann Carina , Groß Rüdiger , Meister Toni Luise , Todt Daniel , Krawczyk Adalbert , Dittmer Ulf , Stenger Steffen , Münch Jan , Steinmann Eike , Müller Janis A , Pfaender Stephanie 
Published: June 2020

AbstractSARS-CoV-2 RNA has been detected in the human breast milk of infected mothers, raising concerns regarding the safety of breastfeeding upon infection. We here show that holder pasteurization inactivates SARS-CoV-2 and provides an alternative and safe option for infected mothers to continue feeding breast milk to their infants.
Ambient noise from ocean surf drives frequency shifts in non-passerine bird song
Authors: Sebastianelli Matteo , Blumstein Daniel T. , Kirschel Alexander N. G. 
Published: June 2020

AbstractEffective communication in birds is often hampered by background noise, with many recent studies focusing on the effect of anthropogenic noise on passerine bird song. Continuous low-frequency natural noise is predicted to drive changes in both frequency and temporal patterning of bird vocalizations, but the extent to which these effects may also affect birds that lack vocal learning is not yet fully understood. Here we use a gradient of exposure to natural low-frequency noise to assess whether it exerts selective pressure on vocalizations in a species whose songs are innate. We tested whether three species ofPogoniulustinkerbirds adapt their song when exposed to a source of continuous low-frequency noise from ocean surf. We show that dominant frequency increases the closer birds are to the coast in all the three species, and in line with higher noise levels, indicating that ocean surf sound may apply a selective pressure on tinkerbird songs. As a consequence, tinkerbirds adapt their songs with an increase in frequency to avoid the masking effect due to overlapping frequencies with ambient noise, therefore improving long-range communication with intended receivers. Our study provides for the first time, compelling evidence that natural ambient noise affects vocalizations in birds whose songs are developed innately. We believe that our results can also be extrapolated in the context of anthropogenic noise pollution, hence providing a baseline for the study of the effects of low-frequency ambient noise on birds that lack vocal learning.Significance StatementBirdsong is constantly under selection as it mediates key interactions such as mate attraction, competition with same-sex individuals for reproduction and competition with heterospecifics for space-related resources. Any phenomenon that interferes with communication can therefore have a profound impact on individual fitness. Passerines are more likely to avoid the masking effect of background noise because of their higher vocal flexibility. Many non-passerine species lacking such flexibility might therefore be more vulnerable to the negative effects on their fitness of exposure to low-frequency background noise. Species incapable of adapting their signals to background noise are predicted to disappear from noisy areas. Despite this, we show that species that lack song learning may show an adaptive response to natural noise which may develop over evolutionary timescales.
Optimisation of functional network resources when learning behavioural strategies for performing complex tasks
Authors: Daws Richard E. , Scott Gregory , Soreq Eyal , Leech Robert , Hellyer Peter J. , Hampshire Adam 
Published: June 2020

AbstractWe developed two novel self-ordered switching (SOS) fMRI paradigms to investigate how human behaviour and underlying network resources are optimised when learning to perform complex tasks with multiple goals. SOS was performed with detailed feedback and minimal pretraining (study 1) or with minimal feedback and substantial pretraining (study 2). In study 1, multiple-demand (MD) system activation became less responsive to routine trial demands but more responsive to the executive switching events with practice. Default Mode Network (DMN) activation showed the opposite relationship. Concomitantly, reaction time learning curves correlated with increased connectivity between functional brain networks and subcortical regions. This ‘fine-tuning’ of network resources correlated with progressively more routine and lower complexity behavioural structure. Furthermore, overall task performance was superior for people who applied structured behavioural routines with low algorithmic complexity. These behavioural and network signatures of learning were less evident in study 2, where task structure was established prior to entering the scanner. Together, these studies demonstrate how detailed feedback monitoring enables network resources to be progressively redeployed in order to efficiently manage concurrent demands.HighlightsWe examine the optimisation of behaviour and brain-network resources during a novel “self-ordered switching” (SOS) paradigm.Task performance depended on generating behavioural routines with low algorithmic complexity (i.e., structured behaviours).Behaviour became more structured and reaction time decreased as SOS was practised.As behaviour became more structured, activation in multiple-demand regions decreased for simple trial events but increased for executive switching eventsIncreases in between-network functional connectivity correlate with reaction time decreases.
A COVID Moonshot: assessment of ligand binding to the SARS-CoV-2 main protease by saturation transfer difference NMR spectroscopy
Authors: Kantsadi Anastassia L. , Cattermole Emma , Matsoukas Minos-Timotheos , Spyroulias Georgios A. , Vakonakis Ioannis 
Published: June 2020

AbstractSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiological cause of the coronavirus disease 2019, for which no effective therapeutics are available. The SARS-CoV-2 main protease (Mpro) is essential for viral replication and constitutes a promising therapeutic target. Many efforts aimed at deriving effective Mproinhibitors are currently underway, including an international open-science discovery project, codenamed COVID Moonshot. As part of COVID Moonshot, we used saturation transfer difference nuclear magnetic resonance (STD-NMR) spectroscopy to assess the binding of putative Mproligands to the viral protease, including molecules identified by crystallographic fragment screening and novel compounds designed as Mproinhibitors. In this manner, we aimed to complement enzymatic activity assays of Mproperformed by other groups with information on ligand affinity. We have made the MproSTD-NMR data publicly available. Here, we provide detailed information on the NMR protocols used and challenges faced, thereby placing these data into context. Our goal is to assist the interpretation of MproSTD-NMR data, thereby accelerating ongoing drug design efforts.
A D-amino acid produced by plant-bacteria metabolic crosstalk empowers interspecies competition
Authors: Aliashkevich Alena , Howell Matthew , Endre Gabriella , Kondorosi Eva , Brown Pamela J.B. , Cava Felipe 
Published: June 2020

AbstractThe bacterial cell wall is made of peptidoglycan (PG), a polymer that is essential for maintenance of cell shape and survival. Many bacteria alter their PG chemistry as a strategy to adapt their cell wall to environmental challenges. Therefore, identifying these factors is important to better understand the interplay between microbes and their habitat. Here we used the soil bacteriumPseudomonas putidato uncover cell wall modulators from plant extracts and found canavanine (CAN), a non-proteinogenic amino acid. We demonstrated that cell wall chemical editing by CAN is licensed byP. putidaBsrP, a broad-spectrum racemase which catalyzes production of D-CAN. Remarkably, D-CAN alters dramatically the PG structure of Rhizobiales (e.g.Agrobacterium tumefaciens, Sinorhizobium meliloti), impairing PG synthesis, crosslinkage and cell division. UsingA. tumefacienswe demonstrated that the detrimental effect of D-CAN is suppressed by a single amino acid substitution in the cell division PG transpeptidase penicillin binding protein 3a. Collectively, this work provides a fascinating example of how interspecies metabolic crosstalk can be a source of novel cell wall regulatory molecules to govern microbial biodiversity.
Characterization of basal forebrain glutamate neurons suggests a role in control of arousal and avoidance behavior
Authors: McKenna James T. , Yang Chun , Bellio Thomas , Anderson-Chernishof Marissa B. , Gamble Mackenzie C. , Hulverson Abigail , McCoy John G. , Winston Stuart , McNally James M. , Basheer Radhika , Brown Ritchie E. 
Published: June 2020

ABSTRACTThe basal forebrain (BF) is involved in arousal, attention, and reward processing but the role of individual BF subtypes is still being uncovered. Glutamatergic neurons are the least well-understood of the three major BF neurotransmitter phenotypes. Here we analyzed the distribution, size, calcium-binding protein content and projections of the major group of BF glutamate neurons expressing the vesicular glutamate transporter subtype 2 (vGluT2) and tested the functional effect of activating them. Mice expressing Cre recombinase under control of the vGluT2 promoter were crossed with a reporter strain expressing the red fluorescent protein, tdTomato, to generate vGluT2-cre-tdTomato mice. Immunohistochemical staining for choline acetyltransferase and a cross with mice expressing green fluorescent protein selectively in GABAergic neurons confirmed cholinergic, GABAergic and vGluT2+ neurons represent separate BF subpopulations. Subsets of BF vGluT2+ neurons expressed the calcium binding proteins calbindin or calretinin, suggesting that multiple subtypes of BF vGluT2+ neurons exist. Anterograde tracing using adeno-associated viral vectors expressing channelrhodopsin2- enhanced yellow fluorescent fusion proteins revealed major projections of BF vGluT2+ neurons to neighboring BF cholinergic and parvalbumin neurons, as well as to extra-BF areas involved in the control of arousal and regions responding to aversive or rewarding stimuli such as the lateral habenula and ventral tegmental area. Optogenetic activation of BF vGluT2 neurons in a place preference paradigm elicited a striking avoidance of the area where stimulation was given. Together with previous optogenetic findings suggesting an arousal-promoting role, our findings suggest BF vGluT2 neurons play a dual role in promoting wakefulness and avoidance behavior.
Perceived Challenges of COVID-19 Infection Prevention and Control Preparedness: A Multinational Survey
Authors: Tartari Ermira , Hopman Joost , Allegranzi Benedetta , Gao Bin , Widmer Andreas , Cheng Vincent Chi-Chung , Wong Shuk Ching , Marimuthu Kalisvar , Ogunsola Folasade , Voss Andreas 
Published: June 2020

AbstractObjectivesImplementation of effective infection prevention and control (IPC) measures is needed to support global capacity building to limit transmission of coronavirus disease 2019 (COVID-19) and mitigate its impact on health systems. We assessed the perceptions of healthcare workers on the current global IPC preparedness measures for COVID-19.MethodsA cross-sectional survey using an electronic survey was circulated between February 26, 2020, and March 20, 2020, to IPC professionals during COVID-19 pandemic. The survey addressed the presence of COVID-19 guidelines as well as specific IPC preparedness activities in response to the outbreak.FindingsIn total, 339 IPC professionals spanning 63 countries in all 6 World Health Organization (WHO) regions, mostly from tertiary care centres participated. Of all participants, 66·6% were aware of the existence of national guidelines to prevent COVID-19. A shortage of PPE supplies was reported by 48% (ranging from 64·2% in low-income countries to 27·4% in high-income countries); 41·5% of respondents considered that the media had an impact on guideline development and 63·6% believed that guidelines were based on maximum security rather than on evidence-based analyses. 58·5% and 72·7% of participants believed that healthcare facilities and community settings respectively were not sufficiently prepared.ConclusionResults revealed lack of guidelines and concerns over insufficient PPE supply in both high- and low-income countries. Our findings should alert national health authorities to ramp up the implementation of IPC measures and focus on long-term preparedness and readiness for future pandemics, likely requiring government funds rather than reliance on healthcare institutions.