bluuebunny/crossref_metadata_2025_split huggingface dataset:
Network Dynamics in the Developing Piriform Cortex of Unanesthetized Rats
Authors: Zhang Zihao , Collins Donald Chad , Maier Joost X 
Published: September 2020

Abstract
The time course of changes in functional cortical activity during early development has been extensively studied in the rodent visual system. A key period in this process is the time of eye opening, which marks the onset of patterned visual input and active vision. However, vision differs from other systems in that it receives limited patterned sensory input before eye opening, and it remains unclear how findings from vision relate to other systems. Here, we focus on the development of cortical network activity in the olfactory system—which is crucial for survival at birth—by recording field potential and spiking activity from piriform cortex of unanesthetized rat pups from birth (P0) to P21. Our results demonstrate that odors evoke stable 10–15 Hz oscillations in piriform cortex from birth to P15, after which cortical responses undergo rapid changes. This transition is coincident with the emergence of gamma oscillations and fast sniffing behavior and preceded by an increase in spontaneous activity. Neonatal network oscillations and their developmental dynamics exhibit striking similarities with those previously observed in the visual, auditory, and somatosensory systems, providing insight into the network-level mechanisms underlying the development of sensory cortex in general and olfactory processing in particular.
Coronavirus Disease 2019 (COVID-19) Transmission in the United States Before Versus After Relaxation of Statewide Social Distancing Measures
Authors: Tsai Alexander C , Harling Guy , Reynolds Zahra , Gilbert Rebecca F , Siedner Mark J 
Published: September 2020

AbstractBackgroundWeeks after issuing social distancing orders to suppress severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission and reduce growth in cases of severe coronavirus disease 2019 (COVID-19), all US states and the District of Columbia partially or fully relaxed these measures.MethodsWe identified all statewide social distancing measures that were implemented and/or relaxed in the United States between 10 March and 15 July 2020, triangulating data from state government and third-party sources. Using segmented linear regression, we estimated the extent to which relaxation of social distancing affected epidemic control, as indicated by the time-varying, state-specific effective reproduction number (Rt).ResultsIn the 8 weeks prior to relaxation, mean Rt declined by 0.012 units per day (95% confidence interval [CI], −.013 to −.012), and 46/51 jurisdictions achieved Rt &lt; 1.0 by the date of relaxation. After relaxation of social distancing, Rt reversed course and began increasing by 0.007 units per day (95% CI, .006–.007), reaching a mean Rt of 1.16. Eight weeks later, the mean Rt was 1.16 and only 9/51 jurisdictions were maintaining an Rt &lt; 1.0. Parallel models showed similar reversals in the growth of COVID-19 cases and deaths. Indicators often used to motivate relaxation at the time of relaxation (eg, test positivity rate &lt;5%) predicted greater postrelaxation epidemic growth.ConclusionsWe detected an immediate and significant reversal in SARS-CoV-2 epidemic suppression after relaxation of social distancing measures across the United States. Premature relaxation of social distancing measures undermined the country’s ability to control the disease burden associated with COVID-19.
Estrogen Deficiency and Colonic Function: Surgical Menopause and Sex Differences in Angiotensin and Dopamine Receptor Interaction
Authors: Garrido-Gil Pablo , Rodriguez-Perez Ana I , Lage Lucia , Labandeira-Garcia Jose L 
Published: September 2020

Abstract
The physiopathological mechanisms that regulate menopausal and sex differences in colonic transit, inflammatory processes, and efficacy of treatments have not been clarified. The dopaminergic system and renin–angiotensin system coexist in the gut and regulate different processes such as motility, absorption/secretion, and inflammation. We investigated the changes in expression of major angiotensin and dopamine receptors in the colon of male, female, and ovariectomized female mice. Possible interaction between both systems was investigated using male and female mice deficient (ko) for major angiotensin and dopamine receptors. In wild-type mice, colonic tissue from females showed lower angiotensin type 1/angiotensin type 2 ratio (an index of pro-inflammatory/anti-inflammatory renin–angiotensin system balance), lower dopamine D1 and D2 receptor expression, and lower levels of pro-inflammatory and pro-oxidative markers relative to males. Interestingly, ovariectomy increased the expression of pro-inflammatory angiotensin type 1 receptor expression and decreased anti-inflammatory angiotensin type 2 receptor expression, increased D1 and D2 receptor expression, and increased the levels of pro-inflammatory and pro-oxidative markers. Ovariectomy-induced changes were blocked by estrogen replacement. The present results suggest a mutual regulation between colonic angiotensin and dopamine receptors and sex differences in this mutual regulation. Estrogen regulates changes in both angiotensin and dopamine receptor expression, which may be involved in sex- and surgical menopause-related effects on gut motility, permeability, and vulnerability to inflammatory processes.
National Profiles of Coronavirus Disease 2019 Mortality Risks by Age Structure and Preexisting Health Conditions
Authors: Verdery Ashton M , Newmyer Lauren , Wagner Brandon , Margolis Rachel 
Published: September 2020

Abstract

Background and Objectives
Although individual age and preexisting health conditions are well-documented risk factors for coronavirus disease 2019 (COVID-19) mortality, it is unclear whether these 2 factors capture unique dimensions of risk for epidemic severity at the national level. In addition, no studies have examined whether national distributions of these factors are associated with epidemic experiences to date.

Research Design and Methods
Drawing on surveys of older adults from 42 countries and estimated case fatality ratios by age and preexisting health conditions, we document and compare national profiles of COVID-19 mortality risks among older adults. We develop 2 measures of national risk profiles: one based on age structures and another based on distributions of preexisting health conditions. Our analysis compares these constructs and documents their associations with national COVID-19 mortality rates.

Results
National profiles of COVID-19 mortality risk based on age structure and preexisting health conditions are moderately uncorrelated, capturing different aspects of risk. Both types of national risk profiles correlate meaningfully with countries’ COVID-19 mortality experiences to date.

Discussion and Implications
Measures of population age structure are readily available for every country in the world, while cross-national measures of older adult population health are more limited. In the COVID-19 crisis, these factors give different pictures of the countries with high and low risks of COVID-19 mortality. Moreover, our results suggest that both types of national risk profiles based on population health reflect current COVID-19 mortality severity in several countries, highlighting the need for more cross-national comparative data on older adult population health.
The Limit Point of the Pentagram Map and Infinitesimal Monodromy
Authors: Aboud Quinton , Izosimov Anton 
Published: September 2020

Abstract
The pentagram map takes a planar polygon $P$ to a polygon $P^{\prime }$ whose vertices are the intersection points of the consecutive shortest diagonals of $P$. The orbit of a convex polygon under this map is a sequence of polygons that converges exponentially to a point. Furthermore, as recently proved by Glick, coordinates of that limit point can be computed as an eigenvector of a certain operator associated with the polygon. In the present paper, we show that Glick’s operator can be interpreted as the infinitesimal monodromy of the polygon. Namely, there exists a certain natural infinitesimal perturbation of a polygon, which is again a polygon but in general not closed; what Glick’s operator measures is the extent to which this perturbed polygon does not close up.
A Dual-Antigen Enzyme-Linked Immunosorbent Assay Allows the Assessment of Severe Acute Respiratory Syndrome Coronavirus 2 Antibody Seroprevalence in a Low-Transmission Setting
Authors: Hicks Sarah M , Pohl Kai , Neeman Teresa , McNamara Hayley A , Parsons Kate M , He Jin-shu , Ali Sidra A , Nazir Samina , Rowntree Louise C , Nguyen Thi H O , Kedzierska Katherine , Doolan Denise L , Vinuesa Carola G , Cook Matthew C , Coatsworth Nicholas , Myles Paul S , Kurth Florian , Sander Leif E , Mann Graham J , Gruen Russell L , George Amee J , Gardiner Elizabeth E , Cockburn Ian A ,   SARS-CoV-2 Testing in Elective Surgery Collaborators
Published: September 2020

Abstract
Estimates of seroprevalence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibodies have been hampered by inadequate assay sensitivity and specificity. Using an enzyme-linked immunosorbent assay–based approach that combines data about immunoglobulin G responses to both the nucleocapsid and spike receptor binding domain antigens, we show that excellent sensitivity and specificity can be achieved. We used this assay to assess the frequency of virus-specific antibodies in a cohort of elective surgery patients in Australia and estimated seroprevalence in Australia to be 0.28% (95% Confidence Interval, 0–1.15%). These data confirm the low level of transmission of SARS-CoV-2 in Australia before July 2020 and validate the specificity of our assay.
Translating an evidence-based clinical pathway into shareable CDS: developing a systematic process using publicly available tools
Authors: Michel Jeremy J , Flores Emilia J , Dutcher Lauren , Mull Nikhil K , Tsou Amy Y 
Published: September 2020

Abstract

Objective
To develop a process for translating semi-structured clinical decision support (CDS) into shareable, computer-readable CDS.

Materials and Methods
We developed a systematic and transparent process using publicly available tools (eGLIA, GEM Cutter, VSAC, and the CDS Authoring Tool) to translate an evidence-based clinical pathway (CP) into a Clinical Quality Language (CQL)-encoded CDS artifact.

Results
We produced a 4-phase process for translating a CP into a CQL-based CDS artifact. CP content was extracted using GEM into discrete clinical concepts, encoded using standard terminologies into value sets on VSAC, evaluated against workflows using a wireframe, and finally structured as a computer readable CDS artifact using CQL. This process included a quality control step and intermediate products to support transparency and reuse by other CDS developers.

Discussion
Translating a CP into a shareable, computer-readable CDS artifact was accomplished through a systematic process. Our process identified areas of ambiguity and gaps in the CP, which generated improvements in the CP. Collaboration with clinical subject experts and the CP development team was essential for translation. Publicly available tools were sufficient to support most translation steps, but expression of certain complex concepts required manual encoding.

Conclusion
Standardized development of CDS from a CP is feasible using a systematic 4-phase process. CPs represent a potential reservoir for developers of evidence-based CDS. Aspects of CP development simplified portions of the CDS translation process. Publicly available tools can facilitate CDS development; however, enhanced tool features are needed to model complex CDS statements.
Validation Study of BioSystems® Y15 Histamine Dehydrogenase Kit for the Detection of Histamine in Fish and Fishery Products: AOAC Performance Tested MethodSM 072001
Authors: Tobeña Andreu , Dueñas Sabina , Boix Mercè 
Published: September 2020

Abstract

Background
BioSystems has developed a histamine kit for automated procedure, through the use of a Y15 analyzer, for quantification of histamine in fish and fishery products.

Objective
Validate the method under the specific guidelines of the AOAC Research Institute Performance Tested MethodSM (PTM) program.

Method
Samples are extracted with boiling water. The enzymatic method is based on histamine dehydrogenase that catalyzes the oxidation of histamine in the presence of an electron mediator that reduces a dye that is measured at 420 nm. The increase of absorbance is proportional to the histamine concentration. Dispensing of reagents and sample, absorbance readings, calibration, and calculation of results are performed automatically in the analyzer BioSystems Y15.

Results
The linearity ranges from 0 to 200 mg/kg (r2 &gt; 0.99). The LOQ is 10 mg/kg in all the matrixes. Recoveries range from 75 to 107% at concentrations from 5 to 200 mg/kg, with repeatability precision values between 0.8 and 5.5%. Comparisons with the HPLC reference method shows a good correlation. Cross-reactivity of the assay is negligible for all biogenic amines tested except for agmatine (6.3%). Product consistency was verified by validating lot-to-lot variations and variations within the same lot. Shelf life was verified by real-time stability testing during 40 months at 2–8°C. No differences in histamine detection were observed in robustness testing, in which minor changes are introduced to the assay protocol.

Conclusions
The automated, simple, and rapid BioSystems Y15 Histamine Dehydrogenase Kit has been successfully validated.

Highlights
The method is qualified for PTM certification No. 072001.
Insights into the Decontamination of Cocaine-Positive Hair Samples
Authors: Erne Robert , Baumgartner Markus R , Kraemer Thomas 
Published: September 2020

Abstract
A highly discussed step in hair sample preparation for forensic analytics is the applied decontamination. The here presented investigations aim to gain insight and give recommendations on how to conduct this decontamination for the analysis of cocaine consumption in hair. Key insights were gained from the investigation of cocaine consumer hair, which was artificially contaminated in a humid atmosphere with 13C6 labelled cocaine and from cocaine powder contaminated hair. Several decontamination protocols were investigated, whereby the usage of a decontamination protocol consisting of multiple short repetitive washes allowed to visualize the wash out of (13C6-) cocaine. Multiple methanol washes proved to be an efficient and simple decontamination approach. Our findings showed that decontamination protocols can successfully wash out recent cocaine contaminations. They were observed to be rather quickly washed out, whereas cocaine from consumption or “older” cocaine contaminations were shown to eliminate both at a constant rate (from inner hair compartments). Thus, the usage of decontamination protocols to differentiate between consumption and contamination was shown to be limited. As contamination can happen any time at any level, only the application of elaborated decision trees, based on cocaine metabolite ratios and thresholds, can provide the distinction between consumption and contamination. Thus, the authors highly recommend the usage of such tools on all hair samples analyzed for cocaine consumption.
A histone H4 gene prevents drought-induced bolting in Chinese cabbage by attenuating the expression of flowering genes
Authors: Xin Xiaoyun , Su Tongbing , Li Peirong , Wang Weihong , Zhao Xiuyun , Yu Yangjun , Zhang Deshuang , Yu Shuancang , Zhang Fenglan 
Published: September 2020

Abstract
Flowering is an important trait in Chinese cabbage, because premature flowering reduces yield and quality of the harvested products. Water deficit, caused by drought or other environmental conditions, induces early flowering. Drought resistance involves global reprogramming of transcription, hormone signaling, and chromatin modification. We show that a histone H4 protein, BrHIS4.A04, physically interacts with a homeodomain protein BrVIN3.1, which was selected during the domestication of late-bolting Chinese cabbage. Over-expression of BrHIS4.A04 resulted in premature flowering under normal growth conditions, but prevented further premature bolting in response to drought. We show that the expression of key abscisic acid (ABA) signaling genes, and also photoperiodic flowering genes was attenuated in BrHIS4.A04-overexpressing (BrHIS4.A04OE) plants under drought conditions. Furthermore, the relative change in H4-acetylation at these gene loci was reduced in BrHIS4.A04OE plants. We suggest that BrHIS4.A04 prevents premature bolting by attenuating the expression of photoperiodic flowering genes under drought conditions, through the ABA signaling pathway. Since BrHIS4.A04OE plants displayed no phenotype related to vegetative or reproductive development under laboratory-induced drought conditions, our findings contribute to the potential fine-tuning of flowering time in crops through genetic engineering without any growth penalty, although more data are necessary under field drought conditions.
Swift-XRT follow-up of gravitational wave triggers during the third aLIGO/Virgo observing run
Authors: Page K L , Evans P A , Tohuvavohu A , Kennea J A , Klingler N J , Cenko S B , Oates S R , Ambrosi E , Barthelmy S D , Beardmore A P , Bernardini M G , Breeveld A A , Brown P J , Burrows D N , Campana S , Caputo R , Cusumano G , D’Aì A , D’Avanzo P , D’Elia V , De Pasquale M , Emery S W K , Giommi P , Gronwall C , Hartmann D H , Krimm H A , Kuin N P M , Malesani D B , Marshall F E , Melandri A , Nousek J A , O’Brien P T , Osborne J P , Pagani C , Page M J , Palmer D M , Perri M , Racusin J L , Sakamoto T , Sbarufatti B , Schlieder J E , Siegel M H , Tagliaferri G , Troja E 
Published: September 2020

ABSTRACT
The Neil Gehrels Swift Observatory followed up 18 gravitational wave (GW) triggers from the LIGO/Virgo collaboration during the O3 observing run in 2019/2020, performing approximately 6500 pointings in total. Of these events, four were finally classified (if real) as binary black hole (BH) triggers, six as binary neutron star (NS) events, two each of NSBH and Mass Gap triggers, one an unmodelled (Burst) trigger, and the remaining three were subsequently retracted. Thus far, four of these O3 triggers have been formally confirmed as real gravitational wave events. While no likely electromagnetic counterparts to any of these GW events have been identified in the X-ray data (to an average upper limit of 3.60 × 10−12 erg cm−2 s−1 over 0.3–10 keV), or at other wavelengths, we present a summary of all the Swift-XRT observations performed during O3, together with typical upper limits for each trigger observed. The majority of X-ray sources detected during O3 were previously uncatalogued; while some of these will be new (transient) sources, others are simply too faint to have been detected by earlier survey missions such as ROSAT. The all-sky survey currently being performed by eROSITA will be a very useful comparison for future observing runs, reducing the number of apparent candidate X-ray counterparts by up to 95 per cent.
A novel xeno-organoid approach: exploring the crosstalk between human iPSC-derived PGC-like and rat testicular cells
Authors: Mall E M , Rotte N , Yoon J , Sandhowe-Klaverkamp R , Röpke A , Wistuba J , Hübner K , Schöler H R , Schlatt S 
Published: September 2020

Abstract
Specification of germ cell-like cells from induced pluripotent stem cells has become a clinically relevant tool for research. Research on initial embryonic processes is often limited by the access to foetal tissue, and in humans, the molecular events resulting in primordial germ cell (PGC) specification and sex determination remain to be elucidated. A deeper understanding of the underlying processes is crucial to describe pathomechanisms leading to impaired reproductive function. Several protocols have been established for the specification of human pluripotent stem cell towards early PGC-like cells (PGCLC), currently representing the best model to mimic early human germline developmental processes in vitro. Further sex determination towards the male lineage depends on somatic gonadal cells providing the necessary molecular cues. By establishing a culture system characterized by the re-organization of somatic cells from postnatal rat testes into cord-like structures and optimizing efficient PGCLC specification protocols, we facilitated the co-culture of human germ cell-like cells within a surrogate testicular microenvironment. Specified conditions allowed the survival of rat somatic testicular and human PGCLCs for 14 days. Human cells maintained the characteristic expression of octamer-binding transcription factor 4, SRY-box transcription factor 17, and transcription factor AP-2 gamma and were recovered from the xeno-organoids by cell sorting. This novel xeno-organoid approach will allow the in vitro exploration of early sex determination of human PGCLCs.
Stable gene expression for normalisation and single-sample scoring
Authors: Bhuva Dharmesh D , Cursons Joseph , Davis Melissa J 
Published: September 2020

Abstract
Gene expression signatures have been critical in defining the molecular phenotypes of cells, tissues, and patient samples. Their most notable and widespread clinical application is stratification of breast cancer patients into molecular (PAM50) subtypes. The cost and relatively large amounts of fresh starting material required for whole-transcriptome sequencing has limited clinical application of thousands of existing gene signatures captured in repositories such as the Molecular Signature Database. We identified genes with stable expression across a range of abundances, and with a preserved relative ordering across thousands of samples, allowing signature scoring and supporting general data normalisation for transcriptomic data. Our new method, stingscore, quantifies and summarises relative expression levels of signature genes from individual samples through the inclusion of these ‘stably-expressed genes’. We show that our list of stable genes has better stability across cancer and normal tissue data than previously proposed gene sets. Additionally, we show that signature scores computed from targeted transcript measurements using stingscore can predict docetaxel response in breast cancer patients. This new approach to gene expression signature analysis will facilitate the development of panel-type tests for gene expression signatures, thus supporting clinical translation of the powerful insights gained from cancer transcriptomic studies.
DualSeqDB: the host–pathogen dual RNA sequencing database for infection processes
Authors: Macho Rendón Javier , Lang Benjamin , Ramos Llorens Marc , Gaetano Tartaglia Gian , Torrent Burgas Marc 
Published: September 2020

Abstract
Despite antibiotic resistance being a matter of growing concern worldwide, the bacterial mechanisms of pathogenesis remain underexplored, restraining our ability to develop new antimicrobials. The rise of high-throughput sequencing technology has made available a massive amount of transcriptomic data that could help elucidate the mechanisms underlying bacterial infection. Here, we introduce the DualSeqDB database, a resource that helps the identification of gene transcriptional changes in both pathogenic bacteria and their natural hosts upon infection. DualSeqDB comprises nearly 300 000 entries from eight different studies, with information on bacterial and host differential gene expression under in vivo and in vitro conditions. Expression data values were calculated entirely from raw data and analyzed through a standardized pipeline to ensure consistency between different studies. It includes information on seven different strains of pathogenic bacteria and a variety of cell types and tissues in Homo sapiens, Mus musculus and Macaca fascicularis at different time points. We envisage that DualSeqDB can help the research community in the systematic characterization of genes involved in host infection and help the development and tailoring of new molecules against infectious diseases. DualSeqDB is freely available at http://www.tartaglialab.com/dualseq.