bluuebunny/crossref_metadata_2025_split huggingface dataset:
A theoretical model of Polycomb/Trithorax action unites stable epigenetic memory and dynamic regulation
Authors: Reinig Jeannette , Ruge Frank , Howard Martin , Ringrose Leonie 
Published: September 2020

AbstractPolycomb and Trithorax group proteins maintain stable epigenetic memory of gene expression states for some genes, but many targets show highly dynamic regulation. Here we combine experiment and theory to examine the mechanistic basis of these different modes of regulation. We present a mathematical model comprising a Polycomb/Trithorax response element (PRE/TRE) coupled to a promoter and including Drosophila developmental timing. The model accurately recapitulates published studies of PRE/TRE mediated epigenetic memory of both silencing and activation. With minimal parameter changes, the same model can also recapitulate experimental data for a different PRE/TRE that allows dynamic regulation of its target gene. The model predicts that both cell cycle length and PRE/TRE identity are critical for determining whether the system gives stable memory or dynamic regulation. Our work provides a simple unifying framework for a rich repertoire of PRE/TRE functions, and thus provides insights into genome-wide Polycomb/Trithorax regulation.
Tracking historical changes in perceived trustworthiness in Western Europe using machine learning analyses of facial cues in paintings
Authors: Safra Lou , Chevallier Coralie , Grèzes Julie , Baumard Nicolas 
Published: September 2020

AbstractSocial trust is linked to a host of positive societal outcomes, including improved economic performance, lower crime rates and more inclusive institutions. Yet, the origins of trust remain elusive, partly because social trust is difficult to document in time. Building on recent advances in social cognition, we design an algorithm to automatically estimate ratings of perceived trustworthiness evaluations from specific facial cues (such as muscle contractions associated with smiling) detected in European portraits in large historical databases. We used this measure as a proxy of social trust in history. Our results show that estimated levels of perceived trustworthiness in portraits increased over the period 1500–2000. Further analyses suggest that this rise of perceived trustworthiness is associated with increased living standards.
Ultra-sensitive and rapid detection of nucleic acids and microorganisms in body fluids using single-molecule tethering
Authors: Cheng Wen-Chih , Horn Troy , Zayats Maya , Rizk Georges , Major Samuel , Zhu Hongying , Russell Joseph , Xu Zhiguang , Rothman Richard E. , Celedon Alfredo 
Published: September 2020

AbstractDetection of microbial nucleic acids in body fluids has become the preferred method for rapid diagnosis of many infectious diseases. However, culture-based diagnostics that are time-consuming remain the gold standard approach in certain cases, such as sepsis. New culture-free methods are urgently needed. Here, we describe Single MOLecule Tethering or SMOLT, an amplification-free and purification-free molecular assay that can detect microorganisms in body fluids with high sensitivity without the need of culturing. The signal of SMOLT is generated by the displacement of micron-size beads tethered by DNA probes that are between 1 and 7 microns long. The molecular extension of thousands of DNA probes is determined with sub-micron precision using a robust and rapid optical approach. We demonstrate that SMOLT can detect nucleic acids directly in blood, urine and sputum at sub-femtomolar concentrations, and microorganisms in blood at 1 CFU mL−1 (colony forming unit per milliliter) threefold faster, with higher multiplexing capacity and with a more straight-forward protocol than amplified methodologies. SMOLT’s clinical utility is further demonstrated by developing a multiplex assay for simultaneous detection of sepsis-causing Candida species directly in whole blood.
Mortality and risk of tuberculosis among people living with HIV in whom TB was initially ruled out
Authors: García Juan Ignacio , Mambuque Edson , Nguenha Dinis , Vilanculo Faustino , Sacoor Charfudin , Sequera Victor Guillermo , Fernández-Quevedo Manuel , Pierre Maxime Leroux-La , Chiconela Helio , Faife Luis A. , Respeito Durval , Saavedra Belén , Nhampossa Tacilta , López-Varela Elisa , Garcia-Basteiro Alberto L. 
Published: September 2020

AbstractTuberculosis (TB) misdiagnosis remains a public health concern, especially among people living with HIV (PLHIV), given the high mortality associated with missed TB diagnoses. The main objective of this study was to describe the all-cause mortality, TB incidence rates and their associated risk factors in a cohort of PLHIV with presumptive TB in whom TB was initially ruled out. We retrospectively followed a cohort of PLHIV with presumptive TB over a 2 year-period in a rural district in Southern Mozambique. During the study period 382 PLHIV were followed-up. Mortality rate was 6.8/100 person-years (PYs) (95% CI 5.2–9.2) and TB incidence rate was 5.4/100 PYs (95% CI 3.9–7.5). Thirty-six percent of deaths and 43% of TB incident cases occurred in the first 12 months of the follow up. Mortality and TB incidence rates in the 2-year period after TB was initially ruled out was very high. The TB diagnostic work-up and linkage to HIV care should be strengthened to decrease TB burden and all-cause mortality among PLHIV with presumptive TB.
Mitogenomic architecture of the multivalent endemic black clam (Villorita cyprinoides) and its phylogenetic implications
Authors: Rahuman Summaya , Jeena N. S. , Asokan P. K. , Vidya R. , Vijayagopal P. 
Published: September 2020

AbstractThe Indian black clamVillorita cyprinoides(Family: Cyrenidae), an extractive commercially exploited species with aquaculture importance contributing more than 70% of clam fishery in India, is endemic to the Indian peninsula. Currently, there is very sparse information, especially on the molecular data ofVillorita. The present study aims to provide a comprehensive knowledge of mitogenome architecture and assess the phylogenetic status of Cyrenidae. This has resulted in reporting the first complete mitogenome ofV. cyprinoidesusing next-generation sequencing technology. The A+T circular mitogenome was 15,880 bp long, exhibiting 13 protein-coding genes (PCGs) including ATP8 (absent in several bivalves), 22 transfer RNA, and two ribosomal RNA genes residing in the heavy strand in a clockwise orientation and a gene order akin toCorbicula fluminea. The molecular phylogeny inferred from a concatenated multi-gene sequence [14 mitochondrial (12 PCGs,rrnS andrrnL) and two nuclear genes (Histone H3, 18S rRNA)] from 47 representative species of superorder Imparidentia, clusteredV. cyprinoidesand Cyrenid clams to a single clade supporting the monophyly of Cyrenidae. The subsequent mitochondrial gene order analysis substantiates the close relationship ofV. cyprinoidesandC. fluminea,analogous to phylogenetic output. The multilocus tree topology calibrated with verified fossil data deciphered the origin and diversification of Cyrenid clams during late Triassic-early Jurassic. The data derived from this study shall contribute remarkably for further insights on cryptic species identification, molecular characterization of bivalve mitogenomes and mitochondrial evolutionary history of genusVillorita. Moreover, complete mitogenome can aid in potential marker development for assessing the genetic health of black clam populations.
Screening participation after a false positive result in organized cervical cancer screening: a nationwide register-based cohort study
Authors: Larsen Pernille Thordal , Jørgensen Susanne Fogh , Tranberg Mette , Njor Sisse Helle 
Published: September 2020

AbstractOur aim was to investigate whether receiving a false positive (FP) cervical cytology result affected subsequent cervical cancer screening participation. This Danish nationwide register-based cohort study included 502,380 women aged 22.5–45 attending cervical cancer screening in 2012–2014 with a normal (n = 501,003) or FP (n = 1,377) cytology screening result. A FP result was defined as a cervical cytology showing high grade cytological abnormalities followed by a normal or ‘Cervical Intraepithelial Neoplasia grade 1’ biopsy result. Women were categorized as subsequent participants if they had a cervical cytology within 24–42 months after their last screening or surveillance test. We compared subsequent participation among women with a normal versus a FP result, using odds ratios including 95% confidence intervals. Participation was slightly higher among women with FP results than among women with normal results (71.5% vs. 69.2%, p = 0.058). After adjustment for age and screening history, women with FP results participated significantly more than women with normal results (OR: 1.19, 95% CI 1.06–1.35). Women receiving a FP result did not participate less in subsequent cervical cancer screening than women receiving a normal result. In fact, the use of opportunistic screening seemed to be increased among women receiving a FP result.
Isotopic systematics point to wild origin of mummified birds in Ancient Egypt
Authors: Linglin Marie , Amiot Romain , Richardin Pascale , Porcier Stéphanie , Antheaume Ingrid , Berthet Didier , Grossi Vincent , Fourel François , Flandrois Jean-Pierre , Louchart Antoine , Martin Jeremy E. , Lécuyer Christophe 
Published: September 2020

AbstractMillions of mummified birds serving for religious purpose have been discovered from archeological sites along the Nile Valley of Egypt, in majority ibises. Whether these birds were industrially raised or massively hunted is a matter of heavy debate as it would have a significant impact on the economy related to their supply and cult, and if hunted it would have represented an ecological burden on the birds populations. Here we have measured and analysed the stable oxygen, carbon and radiogenic strontium isotope compositions as well as calcium and barium content of bones along with the stable carbon, nitrogen and sulfur isotope composition of feathers from 20 mummified ibises and birds of prey recovered from various archeological sites of Ancient Egypt. If these migratory birds were locally bred, their stable oxygen, radiogenic strontium and stable sulfur isotopic compositions would be similar to that of coexisting Egyptians, and their stable carbon, nitrogen and oxygen isotope variance would be close, or lower than that of Egyptians. On one hand, isotopic values show that ibises ingested food from the Nile valley but with a higher isotopic scattering than observed for the diet of ancient Egyptians. On the other hand, birds of prey have exotic isotopic values compatible with their migratory behaviour. We therefore propose that most mummified ibises and all the birds of prey analysed here were wild animals hunted for religious practice.
Perceptual Learning and Production Practice Differentially Affect How Children Produce Novel Words
Authors: Richtsmeier Peter T. , Moore Michelle W. 
Published: September 2020

Purpose
Perceptual learning and production practice are basic mechanisms that children depend on to acquire adult levels of speech accuracy. In this study, we examined perceptual learning and production practice as they contributed to changes in speech accuracy in 3- and 4-year-old children. Our primary focus was manipulating the order of perceptual learning and production practice to better understand when and how these learning mechanisms interact.

Method
Sixty-five typically developing children between the ages of 3 and 4 years were included in the study. Children were asked to produce CVCCVC (C = consonant, V = vowel) nonwords like /bozjəm/ and /tʌvtʃəp/ that were described as the names of make-believe animals. All children completed two separate experimental blocks: a control block in which participants heard each nonword once and repeated it, and a test block in which the perceptual input frequency of each nonword varied between 1 and 10. Half of the participants completed a control–test order; half completed a test–control order.

Results
Greater accuracy was observed for nonwords produced in the second experimental block, reflecting a production practice effect. Perceptual learning resulted in greater accuracy during the test for nonwords that participants heard 3 times or more. However, perceptual learning did not carry over to control productions in the test–control design, suggesting that it reflects a kind of temporary priming. Finally, a post hoc analysis suggested that the size of the production practice effect depended on the age of acquisition of the consonants that comprised the nonwords.

Conclusions
The study provides new details about how perceptual learning and production practice interact with each other and with phonological aspects of the nonwords, resulting in complex effects on speech accuracy and learning of form-referent pairs. These findings may ultimately help speech-language pathologists maximize their clients' improvement in therapy.

Supplemental Material

https://doi.org/10.23641/asha.12971411
Using HCO+ isotopologues as tracers of gas depletion in protoplanetary disk gaps
Authors: Smirnov-Pinchukov Grigorii V. , Semenov Dmitry A. , Akimkin Vitaly V. , Henning Thomas 
Published: September 2020

Context. The widespread rings and gaps seen in the dust continuum in protoplanetary disks are sometimes accompanied by similar substructures seen in molecular line emission. One example is the outer gap at ~100 au in AS 209, which shows that the H13CO+ and C18O emission intensities decrease along with the continuum in the gap, while the DCO+ emission increases inside the gap.
Aims. We aim to study the behavior of DCO+/H13CO+ and DCO+/HCO+ ratios in protoplanetary disk gaps assuming the two scenarios: (A) the gas depletion follows the dust depletion and (B) only the dust is depleted.
Methods. We first modeled the physical disk structure using the thermo-chemical model ANDES. This 1+1D steady-state disk model calculates the thermal balance of gas and dust and includes the far ultraviolet, X-rays, cosmic rays, and other ionization sources together with the reduced chemical network for molecular coolants. Afterward, this physical structure was adopted for calculations of molecular abundances with the extended gas-grain chemical network with deuterium fractionation. Ideal synthetic spectra and 0th-moment maps were produced with the LIne Modeling Engine.
Results. We are able to qualitatively reproduce the increase in the DCO+ intensity and the decrease in the H13CO+ and C18O intensities inside the disk gap, which is qualitatively similar to what is observed in the outer AS 209 gap. The corresponding disk model (A) assumes that both the gas and dust are depleted in the gap. The model (B) with the gas-rich gap, where only the dust is depleted, produces emission that is too bright in all HCO+ isotopologues and C18O.
Conclusions. The DCO+/H13CO+ line ratio can be used to probe gas depletion in dust continuum gaps outside of the CO snow line. The DCO+/C18O line ratio shows a similar, albeit weaker, effect; however, these species can be observed simultaneously with a single (sub)mm interferometer setup.
K0SΣ0 photoproduction at the BGO-OD experiment
Authors: Kohl Katrin , Alef Stefan , Bauer Patrick , Beck Reinhard , Braghieri Alessandro , Cole Philip , Di Salvo Rachele , Elsner Daniel , Fantini Alessia , Freyermuth Oliver , Oliver Francesco , Gridnev Anatoly , Hammann Daniel , Hannappel Jürgen , Jude Thomas , Kozlenko Nikolay , Lapik Alexander , Levi Sandri Paolo , Lisin Valery , Mandaglio Giuseppe , Messi Roberto , Moricciani Dario , Nedorezov Vladimir , Novinsky Dmitry , Pedroni Paolo , Polonski Andrei , Reitz Björn-Eric , Romaniuk Mariia , Scheluchin Georg , Schmieden Hartmut , Sumachev Victorin , Tarakanov Viacheslav , Tillmanns Christian 
Published: September 2020

The BGO-OD experiment at the ELSA accelerator facility uses an energy tagged bremsstrahlung photon beam to investigate the excitation structure of the nucleon via meson photoproduction.
The setup with a BGO calorimeter surrounding the target and an open dipole spectrometer covering the for ward region is ideally suited for investigating low momentum transfer processes, in particular in strangeness photoproduction.
The associated photoproduction of K0S and hyperons is essential to understand the role of K* exchange mech anisms. A cusp-like structure observed in the yp → K0SΣ+ reaction at the K* threshold is described by models including dynamically generated resonances from vector meson-baryon interactions. Such interactions are pre dicted to give a peak like structure in K0SΣ0 photoproduction off the neutron. A very preliminary cross section is determined and compared to the prediction, the results appear to support the model
K+Λ(1405) photoproduction at the BGO-OD experiment
Authors: Scheluchin Georg , Alef Stefan , Bauer Patrick , Beck Reinhard , Braghieri Alessandro , Cole Philip , Di Salvo Rachele , Elsner Daniel , Fantini Alessia , Freyermuth Oliver , Ghio Francesco , Gridnev Anatoly , Hammann Daniel , Hannappel Jürgen , Jude Thomas , Kohl Katrin , Kozlenko Nikolay , Lapik Alexander , Sandri Paolo Levi , Lisin Valery , Mandaglio Giuseppe , Messi Roberto , Moricciani Dario , Nedorezov Vladimir , Novinsky Dmitry , Pedroni Paolo , Polonski Andrei , Reitz Björn-Eric , Romaniuk Mariia , Schmieden Hartmut , Sumachev Victorin , Tarakanov Viacheslav , Tillmanns Christian 
Published: September 2020

Since the discovery of the Λ(1405), it remains poorly described by conventional constituent quark models, and it is a candidate for having an “exotic” meson-baryon or “penta-quark” structure, similar to states recently reported in the hidden charm sector.The Λ(1405) can be produced in the reactionγpK+Λ(1405). The pure I=0 decay mode into Σ0π0is prohibited for the mass-overlapping Σ(1385). Combining a large aperture forward magnetic spectrometer and a central BGO crystal calorimeter, the BGO-OD experiment is ideally suited to measure this decay with theK+in the forward direction. Preliminary results are presented.*Supported by DFG (PN 388979758, 405882627)
Interpretation and adherence to the updated risk-stratified guideline for colonoscopy surveillance after polypectomy – a nationwide survey
Authors: van der Meulen Miriam P. , Korfage Ida J. , van Heijningen Else-Mariëtte B. , de Koning Harry J. , van Leerdam Monique E. , Dekker Evelien , Lansdorp-Vogelaar Iris ,   on behalf of the working group on the guideline for colonoscopy surveillance
Published: September 2020

Abstract
Background and study aims Low adherence to the Dutch guideline for colonoscopy surveillance after polypectomy led to release of a new guideline in 2013. This new guideline was risk-stratified at a more detailed level than the previous one to achieve more efficient use of colonoscopy resources. This study assessed the feasibility of the risk-stratified guideline by evaluating correct interpretation of and adherence to this guideline.
Methods Based on semi-structured interviews with 10 gastroenterologists, we developed an online survey to evaluate gastroenterologists’ recommendations for surveillance in 15 example cases of patients with polyps. If recommended intervals differed from the new guideline, respondents were asked to indicate their motives for doing so.
Results Ninety-one of 592 (15.4 %) invited gastroenterologists responded to at least one case, of whom 84 (14.2 %) completed the survey. Gastroenterologists gave a correct recommendation in a median of 10 of 15 cases and adherence per case ranged from 14 % to 95 % (median case 76 %). The two cases that addressed management of serrated polyps were least often answered correctly (14 % and 28 % correct answers). Discrepancies were mainly due to misinterpretation of the guideline with respect to serrated polyps (48 %) or misreading of the questions (30 %).
Conclusions Median adherence to the updated colonoscopy surveillance guideline of 76 % seems reasonable, and is higher than adherence to the previous guideline (range: 22 %-80 %, median 59 %). This shows that detailed (more complex) risk stratification for designation of a surveillance interval is feasible. Adherence could potentially be improved by clarifying correct interpretation of serrated polyps.
Kneipp-Therapie in Senioreneinrichtungen
Authors: Ortiz Miriam 
Published: September 2020

SummaryImmer mehr Einrichtungen der stationärenAltenpflege in Deutschland setzen in derPflege und Therapie ihrer Bewohner* konzeptionellnaturheilkundliche Maßnahmenunter Bezug auf Sebastian Kneipp ein. Diewissenschaftliche Evidenz dieser Verfahrenhinsichtlich krankheitspräventiver Effektewird zurzeit erforscht. Ein Pilotprojekt zurEvaluation zeigte jedoch vielversprechendeErgebnisse für die Gesundheit und Lebensqualitätder Bewohner und der Pflegekräfte.
Improving assessment and management of large non-pedunculated colorectal lesions in a Western center over 10 years: lessons learned and clinical impact
Authors: Vanella Giuseppe , Coluccio Chiara , Antonelli Giulio , Angeletti Stefano , Micheli Federica , Barbato Antonio , De Rossi Gaia , Marchetti Alessandro , Mereu Elena , Pepe Paola , Corleto Vito Domenico , D’Ambra Giancarlo , Ruggeri Maurizio , Di Giulio Emilio 
Published: September 2020

Abstract
Background and study aims Outcomes of endoscopic assessment and management of large colorectal (CR) non-pedunculated lesions (LNPLs) are still under evaluation, especially in Western settings. We analyzed the clinical impact of changes in LNPL management over the last decade in a European center.
Patients and methods All consecutive LNPLs ≥ 20 mm endoscopically assessed (2008–2019) were retrospectively included. Lesion, patient, and resection characteristics were compared among clinically relevant subgroups. Multivariate logistic regression (for predictors of submucosal invasion [SMI] and recurrence), Kaplan-Meier curves and ROC curves (for temporal cut-offs in trends analyses) were used.
Results A total of 395 LNPLs were included (30 mm [range 20–40]; SMI = 9.6 %; primary endoscopic resection [ER] = 88.4 %). Pseudo-depression and JNET classification independently predicted SMI beyond single morphologies/location. After complete ER, involvement of ileocecal valve/dentate line, piece-meal resection and high-grade dysplasia independently predicted recurrence. Rates of 5-year recurrence-free, surgery-free and cancer-free survival were 77.5 %, 98.6 % and 100 %, respectively, with 93.8 % recurrences endoscopically managed and no death attributable to ER or CR cancer (versus 3.4 % primary surgery mortality).ROC curves identified the period ≥ 2015 (following Endoscopic Submucosal Dissection [ESD] introduction and education on pre-resective lesion assessment) as associated with improved lesions’ characterization, increased en-bloc resection of SMI lesions (87.5 % vs 37.5 %; p = 0.0455), reduced primary surgery (7.5 % vs 16.7 %; p = 0.0072), surgical referral of benign lesions (5.1 % vs 14.8 %; p = 0.0019), and recurrences.
Conclusions ESD introduction and educational interventions allowed ER of more complex lesions, offset by increased complementary surgery for complications or intrinsic histological risk. Nevertheless, overall, they have reduced surgery demand and increased appropriateness and safety of LNPL management in our center.