bluuebunny/crossref_metadata_2025_split huggingface dataset:
S5.5a Standing up FungiNet: Genomic epidemiology and surveillance of fungal diseases
Authors: Chow Nancy , Parnell Lindsay , Escandon Patricia , Govender Nelesh , Chiller Tom 
Published: September 2022

Abstract

S5.5 Genomic Epidemiology of Fungal Infections, September 22, 2022, 3:00 PM - 4:30 PM

Objectives
With the advent of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing, the public health landscape for genomic epidemiology and surveillance has transformed for a variety of pathogens. For fungal diseases, the U.S. Centers for Disease Control and Prevention (CDC) is working with global partners to stand up FungiNet, a network that aims to equip scientists with laboratory, bioinformatics, and informatics resources to harness genomic data. FungiNet partners will use genomic and epidemiologic data to detect outbreaks, identify introductions, and characterize transmission of fungal infections. In 2022, FungiNet aims to onboard nine state and local health departments in the United States and two global partners, the Instituto Nacional de Salud in Colombia and the National Institute for Communicable Diseases in South Africa, with a focus on Candida auris.

Methods
To streamline the onboarding process, CDC generated standardized operating procedures (SOPs) specific to C. auris. For DNA extraction, SOPs were created for workflows using the Zymo Research Quick-DNA™ (ZR) Fungal/Bacterial Miniprep, Qiagen Dneasy Blood and Tissue, and Epicentre (Illumina) MasterPure Yeast DNA Purification kits. For library preparation and Illumina sequencing, PulseNet methods used for foodborne pathogens were validated for C. auris. For NCBI data submissions, required data elements were defined. For SNP and phylogenetic analyses, the bioinformatics workflow MycoSNP was adapted to use Nextflow software and the Terra platform. For visualization with epidemiologic data, guidance documents and tutorials for Microreact were created. Finally, for data reporting, processes are being designed in REDCap and in laboratory information management systems to rapidly share genomic-related data.

Results
To date, 11 partners have committed to building capacity for C. auris genomic sequencing and analysis as a FungiNet partner. Of these, seven have validated methods for DNA extraction, and nine have generated high-quality sequencing data. Only one partner has installed and locally run MycoSNP, and none have submitted raw sequence data to NCBI.

Conclusions
Currently, 11 FungiNet partners are working to onboard C. auris genomic sequencing and bioinformatics analysis in 2022. This process is complex, requiring several laboratories, bioinformatics, and informatics workflows. For many partners, bioinformatics analysis and NCBI submission are the most challenging activities with the installation of MycoSNP and the ability to batch upload data to NCBI as the main barriers. Next steps will focus on the validation of informatics methods to link genomic and epidemiologic data.
S6.2d Dermatophytosis due to Trichophyton erinacei caused by contact with African hedgehogs as family pets
Authors: Bonifaz Alexandro , Araiza Javier , de la Cruz Helena Vidaurri , Morales-Peña Neredi , Treviño-Rangel Rogelio , González Gloria 
Published: September 2022

Abstract

S6.2 Resurgence of dermatophytic infections, September 22, 2022, 4:45 PM - 6:15 PM

Objective
To present a series of cases of various types of dermatophytosis caused by Trichophyton erinacei, caused by contact with African hedgehogs.

Methods
Patients with clinical suspicion of ringworm caused by T. erinacei were included in the study. Each patient underwent a mycological study, with direct examinations (KOH), cultures in Sabouraud dextrose agar medium with and without antibiotics. With the cultures obtained, molecular identification was made using the PCR technique and Matrix Assisted Laser Desorption Ionization Time of Flight (MALDI-TOF) proteomics. Once confirmed, the patients were given treatment and follow-up. When the pets (hedgehogs) were accessible, they were cultured with a cytobrush and the quills removed.

Results
In a period of 3.5 years, 16 verified cases were incorporated, 13 were females (72%) and 3 males (18%), the average age was 18.2 years, with the smallest case being 8 years old and the oldest 45 years old. The tineas manifested as follows: tinea manus 11 cases (68.7%); 2 respective cases of tinea corporis and tinea capitis (18.1 respectively) and one case of Majocchi's granuloma. The average evolution was 1.5 months with the case older than 3 months and the younger 15 days. All cases were given terbinafine at variable times and doses (according to weight and age) and clinical and mycological cure was obtained.

Discussion
Tineas can have epidemiological changes that are favored by a variety of factors, in general, pet ringworms are due to common domestic animals such as dogs and cats. Due to changing fashions, children and adolescents in recent years have changed pets such as hamsters, and recently hedgehogs, especially African variety (Atelerix albiventris) the latter may have T. erinacei as part of their skin microbiota, a similar dermatophyte or that was part of the T. mentagrophyes complex, in general of low virulence, however, its antigenic variants are little recognized by humans, which makes them present in a very inflammatory form, particularly in the hands, due to the handling of the animal, as well as the deeper inoculation (in the dermis) by the spikes left by the inoculum. So, they can generate deep tineas such as Majocchi's granuloma. In general, they respond well to systemic antifungals such as terbinafine and itraconazole, and sometimes the use of topical or systemic steroids is necessary.

Conclusions
This series of cases is a good example of how a change of habits when having pets can introduce new etiological agents that are poorly recognized antigenically, which give rise to more inflammatory and sometimes profound tineas.
Gusts in the headwind: uncertainties in direct dark matter detection
Authors: Lawrence Grace E , Duffy Alan R , Blake Chris A , Hopkins Philip F 
Published: September 2022

ABSTRACT
We use high-resolution, hydrodynamic, galaxy simulations from the Latte suite of FIRE-2 simulations to investigate the inherent variation of dark matter in sub-sampled regions around the Solar Circle of a Milky Way-type analogue galaxy and its impact on direct dark matter detection. These simulations show that the baryonic back reaction, as well as the assembly history of substructures, has lasting impacts on the dark matter’s spatial and velocity distributions. These are experienced as ‘gusts’ of dark matter wind around the Solar Circle, potentially complicating interpretations of direct detection experiments on Earth. We find that the velocity distribution function in the galactocentric frame shows strong deviations from the Maxwell Boltzmann form typically assumed in the fiducial Standard Halo Model, indicating the presence of high-velocity substructures. By introducing a new numerical integration technique that removes any dependencies on the Standard Halo Model, we generate event-rate predictions for both single-element Germanium and compound Sodium Iodide detectors, and explore how the variability of dark matter around the Solar Circle influences annual modulation signal predictions. We find that these velocity substructures contribute additional astrophysical uncertainty to the interpretation of event rates, although their impact on summary statistics, such as the peak day of annual modulation, is generally low.
Harvesting the Ly α forest with convolutional neural networks
Authors: Cheng Ting-Yun , Cooke Ryan J , Rudie Gwen 
Published: September 2022

ABSTRACT
We develop a machine learning based algorithm using a convolutional neural network (CNN) to identify low H i column density Ly α absorption systems (log NH i/cm−2 &lt; 17) in the Ly α forest, and predict their physical properties, such as their H i column density (log NH i/cm−2), redshift (zH i), and Doppler width (bH i). Our CNN models are trained using simulated spectra (S/N ≃ 10), and we test their performance on high quality spectra of quasars at redshift z ∼ 2.5−2.9 observed with the High Resolution Echelle Spectrometer on the Keck I telescope. We find that ${\sim}78{{\ \rm per\ cent}}$ of the systems identified by our algorithm are listed in the manual Voigt profile fitting catalogue. We demonstrate that the performance of our CNN is stable and consistent for all simulated and observed spectra with S/N ≳ 10. Our model can therefore be consistently used to analyse the enormous number of both low and high S/N data available with current and future facilities. Our CNN provides state-of-the-art predictions within the range 12.5 ≤ log NH i/cm−2 &lt; 15.5 with a mean absolute error of Δ(log NH i/cm−2) = 0.13, Δ(zH i) = 2.7 × 10−5, and Δ(bH i) = 4.1 km s−1. The CNN prediction costs &lt; 3 min per model per spectrum with a size of 120 000 pixels using a laptop computer. We demonstrate that CNNs can significantly increase the efficiency of analysing Ly α forest spectra, and thereby greatly increase the statistics of Ly α absorbers.
Chandrasekhar-mass white dwarfs are the progenitors of a small fraction of Type Ia supernovae according to nucleosythesis constraints
Authors: Bravo Eduardo , Piersanti Luciano , Blondin Stéphane , Domínguez Inma , Straniero Oscar , Cristallo Sergio 
Published: September 2022

ABSTRACT
The precise progenitor system of type Ia supernovae (SNe Ia), whether it is a white dwarf (WD) close to the Chandrasekhar limit or substantially less massive, has been a matter of debate for decades. Recent research by our group on the accretion and simmering phases preceding the explosion of a massive WD has shown that the central density at thermal runaway lies in the range 3.6 − 6.3 × 109 g cm−3 for reasonable choices of accretion rate on to the WD and progenitor metallicity. In this work, we have computed one-dimensional simulations of the explosion of such WDs, with special emphasis on the chemical composition of the ejecta, which in all cases is extremely rich in neutronized isotopes of chromium (54Cr) and titanium (50Ti). We show that, in order to reconcile such a nucleosynthesis with the isotopic abundances of the Solar system, Chandrasekhar-mass WDs can account for at most 26 per cent of normal-luminosity SNe Ia, or at most 20 per cent of all SNe Ia.
The Heterogeneity in the Landscape of Gene Dominance in Maize is Accompanied by Unique Chromatin Environments
Authors: Yin Liangwei , Xu Gen , Yang Jinliang , Zhao Meixia 
Published: September 2022

Abstract
Subgenome dominance after whole-genome duplication (WGD) has been observed in many plant species. However, the degree to which the chromatin environment affects this bias has not been explored. Here, we compared the dominant subgenome (maize1) and the recessive subgenome (maize2) with respect to patterns of sequence substitutions, genes expression, transposable element accumulation, small interfering RNAs, DNA methylation, histone modifications, and accessible chromatin regions (ACRs). Our data show that the degree of bias between subgenomes for all the measured variables does not vary significantly when both of the WGD genes are located in pericentromeric regions. Our data further indicate that the location of maize1 genes in chromosomal arms is pivotal for maize1 to maintain its dominance, but location has a less effect on maize2 homoeologs. In addition to homoeologous genes, we compared ACRs, which often harbor cis-regulatory elements, between the two subgenomes and demonstrate that maize1 ACRs have a higher level of chromatin accessibility, a lower level of sequence substitution, and are enriched in chromosomal arms. Furthermore, we find that a loss of maize1 ACRs near their nearby genes is associated with a reduction in purifying selection and expression of maize1 genes relative to their maize2 homoeologs. Taken together, our data suggest that chromatin environment and cis-regulatory elements are important determinants shaping the divergence and evolution of duplicated genes.
The high mobility group protein HMG20A cooperates with the histone reader PHF14 to modulate TGFβ and Hippo pathways
Authors: Gómez-Marín Elena , Posavec-Marjanović Melanija , Zarzuela Laura , Basurto-Cayuela Laura , Guerrero-Martínez José A , Arribas Gonzalo , Yerbes Rosario , Ceballos-Chávez María , Rodríguez-Paredes Manuel , Tomé Mercedes , Durán Raúl V , Buschbeck Marcus , Reyes José C 
Published: September 2022

Abstract
High mobility group (HMG) proteins are chromatin regulators with essential functions in development, cell differentiation and cell proliferation. The protein HMG20A is predicted by the AlphaFold2 software to contain three distinct structural elements, which we have functionally characterized: i) an amino-terminal, intrinsically disordered domain with transactivation activity; ii) an HMG box with higher binding affinity for double-stranded, four-way-junction DNA than for linear DNA; and iii) a long coiled-coil domain. Our proteomic study followed by a deletion analysis and structural modeling demonstrates that HMG20A forms a complex with the histone reader PHF14, via the establishment of a two-stranded alpha-helical coiled-coil structure. siRNA-mediated knockdown of either PHF14 or HMG20A in MDA-MB-231 cells causes similar defects in cell migration, invasion and homotypic cell–cell adhesion ability, but neither affects proliferation. Transcriptomic analyses demonstrate that PHF14 and HMG20A share a large subset of targets. We show that the PHF14-HMG20A complex modulates the Hippo pathway through a direct interaction with the TEAD1 transcription factor. PHF14 or HMG20A deficiency increases epithelial markers, including E-cadherin and the epithelial master regulator TP63 and impaired normal TGFβ-trigged epithelial-to-mesenchymal transition. Taken together, these data indicate that PHF14 and HMG20A cooperate in regulating several pathways involved in epithelial–mesenchymal plasticity.
Crystallographic analysis of engineered polymerases synthesizing phosphonomethylthreosyl nucleic acid
Authors: Hajjar Mohammad , Chim Nicholas , Liu Chao , Herdewijn Piet , Chaput John C 
Published: September 2022

Abstract
Xeno-nucleic acids (XNAs) are synthetic genetic polymers with backbone structures composed of non-ribose or non-deoxyribose sugars. Phosphonomethylthreosyl nucleic acid (pTNA), a type of XNA that does not base pair with DNA or RNA, has been suggested as a possible genetic material for storing synthetic biology information in cells. A critical step in this process is the synthesis of XNA episomes using laboratory-evolved polymerases to copy DNA information into XNA. Here, we investigate the polymerase recognition of pTNA nucleotides using X-ray crystallography to capture the post-catalytic complex of engineered polymerases following the sequential addition of two pTNA nucleotides onto the 3′-end of a DNA primer. High-resolution crystal structures reveal that the polymerase mediates Watson–Crick base pairing between the extended pTNA adducts and the DNA template. Comparative analysis studies demonstrate that the sugar conformation and backbone position of pTNA are structurally more similar to threose nucleic acid than DNA even though pTNA and DNA share the same six-atom backbone repeat length. Collectively, these findings provide new insight into the structural determinants that guide the enzymatic synthesis of an orthogonal genetic polymer, and may lead to the discovery of new variants that function with enhanced activity.
Integrated longitudinal analysis of adult grade 4 diffuse gliomas with long-term relapse interval revealed upregulation of TGF-β signaling in recurrent tumors
Authors: Kashani Elham , Schnidrig Désirée , Gheinani Ali Hashemi , Ninck Martina Selina , Zens Philipp , Maragkou Theoni , Baumgartner Ulrich , Schucht Philippe , Rätsch Gunnar , Rubin Mark A ,   SOCIBP consortium, Benjak Andrej , Bruggmann Rémy , Comoglio Federico , Kahles André , Keller Irene , K Y Ng Charlotte , Piscuoglio Salvatore , Prélot Laurie , Rätsch Gunnar , A Rubin Mark , Schnidrig Désirée , Selimovic-Hamza Senija , Thomas Tinu M , Berezowska Sabina , Ng Charlotte K Y , Vassella Erik 
Published: September 2022

AbstractBackgroundAdult-type diffuse gliomas, CNS WHO grade 4 are the most aggressive primary brain tumors and represent a particular challenge for therapeutic intervention.MethodsIn a single-center retrospective study of matched pairs of initial and post-therapeutic glioma cases with a recurrence period greater than 1 year, we performed whole exome sequencing combined with mRNA and microRNA expression profiling to identify processes that are altered in recurrent gliomas.ResultsMutational analysis of recurrent gliomas revealed early branching evolution in 75% of the patients. High plasticity was confirmed at the mRNA and miRNA levels. SBS1 signature was reduced and SBS11 was elevated, demonstrating the effect of alkylating agent therapy on the mutational landscape. There was no evidence for secondary genomic alterations driving therapy resistance. ALK7/ACVR1C and LTBP1 were upregulated, whereas LEFTY2 was downregulated, pointing towards enhanced Tumor Growth Factor β (TGF-β) signaling in recurrent gliomas. Consistently, altered microRNA expression profiles pointed towards enhanced Nuclear Factor Kappa B and Wnt signaling that, cooperatively with TGF-β, induces epithelial to mesenchymal transition (EMT), migration, and stemness. TGF-β-induced expression of pro-apoptotic proteins and repression of antiapoptotic proteins were uncoupled in the recurrent tumor.ConclusionsOur results suggest an important role of TGF-β signaling in recurrent gliomas. This may have clinical implications since TGF-β inhibitors have entered clinical phase studies and may potentially be used in combination therapy to interfere with chemoradiation resistance. Recurrent gliomas show high incidence of early branching evolution. High tumor plasticity is confirmed at the level of microRNA and mRNA expression profiles.
The Short-Term and Long-Term Associations Between Receiving Tobacco Discounts or Coupons and Smoking Cessation Among U.S. Adult Cigarette Smokers With Intention to Quit
Authors: Wang Yu , Duan Zongshuan , Weaver Scott R , Self-Brown Shannon R , Ashley David L , Emery Sherry L , Huang Jidong 
Published: September 2022

AbstractIntroductionTo examine the associations between baseline receipt of cigarette and non-cigarette tobacco discounts or coupons and smoking cessation at follow-up among US adult cigarette smokers with the intention to quit at baseline.Aims and MethodsData were from the Population Assessment of Tobacco and Health (PATH) study wave 3 (October 2015–October 2016), wave 4 (December 2016–January 2018), and wave 5 (December 2018–November 2019) surveys. Two separate sets of analyses were conducted using wave 3–4 data (N = 3707) and wave 4–5 data (N = 6251). Specifically, wave 4 was used as the 1-year follow-up of wave 3 to examine the short-term association, and wave 5 was used as the 2-year follow-up of wave 4 to examine the longer-term association. Study population were current established cigarette smokers with the intention to quit (within 1 year for wave 3–4 data) at baseline. Exposure was self-reported past 12-month receipt of discounts or coupons for cigarettes and non-cigarette tobacco products at baseline, and outcome was self-reported completely quitting cigarette smoking at follow-up. Baseline single-wave weights were applied, and multivariate logistic regressions were used to estimate the adjusted associations.ResultsParticipants who received cigarette discounts or coupons at baseline were less likely to quit completely for both 1-year follow-up (aOR = 0.66, 95% CI: 0.48 to 0.90) and 2-year follow-up (aOR = 0.74, 95% CI: 0.61 to 0.90). Baseline receipt of discounts or coupons for non-cigarette tobacco products were not consistently associated with cigarette smoking cessation at follow-up.ConclusionsReceipt of cigarette discounts or coupons was associated with a reduced likelihood of successful quitting among cigarette smokers with intention to quit. Policies restricting cigarette coupons may help them quit completely.ImplicationsThis study found that among baseline current established cigarette smokers with intention to quit in the United States, baseline receipt of cigarette discounts or coupons was negatively associated with cigarette smoking cessation for both 1-year follow-up and 2-year follow-up. Baseline receipt of discounts or coupons for e-cigarettes, cigars, and other tobacco products were not consistently significantly associated with cigarette smoking cessation at follow-up. Our study results indicated that policies restricting cigarette coupons may help increase the likelihood of successful smoking cessation for smokers with intention to quit.
Impact of a Multistep Bundles Intervention in the Management and Outcome of Gram-Negative Bloodstream Infections: A Single-Center “Proof-of-Concept” Study
Authors: Bavaro Davide Fiore , Diella Lucia , Belati Alessandra , De Gennaro Nicolò , Fiordelisi Deborah , Papagni Roberta , Guido Giacomo , De Vita Elda , Frallonardo Luisa , Camporeale Michele , Pellegrino Carmen , Denicolò Sofia , Ranieri Enrica , Mariani Michele Fabiano , Brindicci Gaetano , Ronga Luigi , Di Gennaro Francesco , Mosca Adriana , Saracino Annalisa 
Published: September 2022

Abstract

Background
This is a “proof-of-concept” study aiming to evaluate the impact of a multistep bundles intervention in the management and outcomes of patients with gram-negative bloodstream infections (GN-BSIs).

Methods
This was a single-center, quasi-experimental design study. In the pre-phase (January 2019 to May 2020), patients were retrospectively enrolled. During the post-phase (June 2020 to September 2021), all patients were prospectively enrolled in a nonmandatory 3-step bundles intervention arm including (i) step 1: imaging to detect deep foci of infection, follow-up blood cultures and procalcitonin monitoring; (ii) step 2: early targeted antibiotic treatment and surgical source control; (iii) step 3: discontinuation of antibiotics within 7–10 days in case of uncomplicated BSI. Patients were followed up to 28 days from BSI onset. The primary outcome was 28-day mortality.

Results
A total of 271 patients were enrolled: 127 and 144 in the pre- vs post-phase, respectively. Full application of step 1 (67% vs 42%; P &lt; .001), step 2 (83% vs 72%; P = .031), and step 3 (54% vs 2%; P &lt; .001) increased in the post-phase. Overall, the intervention reduced 28-day mortality (22% vs 35%, respectively; P = .016) and the median duration of total (11 vs 15 days; P &lt; .001) and targeted (8 vs 12 days; P = .001) antibiotic therapy. Finally, the multivariate Cox regression confirmed the independent protective effect of adherence to step 1 (adjusted hazard ratio [aHR], 0.36; 95% CI, 0.20–0.63) and step 2 (aHR, 0.48; 95% CI, 0.29–0.81) on risk of 28-day mortality.

Conclusions
Clinical management and outcomes of patients with GN-BSIs may be improved by providing a pre-established multistep bundles intervention.