bluuebunny/crossref_metadata_2025_split huggingface dataset:
In silico approach to predict pancreatic β-cells classically secreted proteins
Authors: Pinheiro-Machado Erika , Milkewitz Sandberg Tatiana Orli , PIHL Celina , Hägglund Per Mårten , Marzec Michal Tomasz 
Published: January 2020

Abstract
Pancreatic β-cells, residents of the islets of Langerhans, are the unique insulin-producers in the body. Their physiology is a topic of intensive studies aiming to understand the biology of insulin production and its role in diabetes pathology. However, investigations about these cells’ subset of secreted proteins, the secretome, are surprisingly scarce and a list describing islet/β-cell secretome upon glucose-stimulation is not yet available. In silico predictions of secretomes are an interesting approach that can be employed to forecast proteins likely to be secreted. In this context, using the rationale behind classical secretion of proteins through the secretory pathway, a Python tool capable of predicting classically secreted proteins was developed. This tool was applied to different available proteomic data (human and rodent islets, isolated β-cells, β-cell secretory granules, and β-cells supernatant), filtering them in order to selectively list only classically secreted proteins. The method presented here can retrieve, organize, search and filter proteomic lists using UniProtKB as a central database. It provides analysis by overlaying different sets of information, filtering out potential contaminants and clustering the identified proteins into functional groups. A range of 70–92% of the original proteomes analyzed was reduced generating predicted secretomes. Islet and β-cell signal peptide-containing proteins, and endoplasmic reticulum-resident proteins were identified and quantified. From the predicted secretomes, exemplary conservational patterns were inferred, as well as the signaling pathways enriched within them. Such a technique proves to be an effective approach to reduce the horizon of plausible targets for drug development or biomarkers identification.
Classifying Disfluencies in Preschool- and School-Age Spanish–English Bilinguals Who Do Not Stutter: An Exploratory Study
Authors: Rojas Raúl , Irani Farzan 
Published: January 2020

Purpose
This exploratory study examined the language skills and the type and frequency of disfluencies in the spoken narrative production of Spanish–English bilingual children who do not stutter.

Method
A cross-sectional sample of 29 bilingual students (16 boys and 13 girls) enrolled in grades prekindergarten through Grade 4 produced a total of 58 narrative retell language samples in English and Spanish. Key outcome measures in each language included the percentage of normal (%ND) and stuttering-like (%SLD) disfluencies, percentage of words in mazes (%MzWds), number of total words, number of different words, and mean length of utterance in words.

Results
Cross-linguistic, pairwise comparisons revealed significant differences with medium effect sizes for %ND and %MzWds (both lower for English) as well as for number of different words (lower for Spanish). On average, the total percentage of mazed words was higher than 10% in both languages, a pattern driven primarily by %ND; %SLDs were below 1% in both languages. Multiple linear regression models for %ND and %SLD in each language indicated that %MzWds was the primary predictor across languages beyond other language measures and demographic variables.

Conclusions
The findings extend the evidence base with regard to the frequency and type of disfluencies that can be expected in bilingual children who do not stutter in grades prekindergarten to Grade 4. The data indicate that %MzWds and %ND can similarly index the normal disfluencies of bilingual children during narrative production. The potential clinical implications of the findings from this study are discussed.
Galactic archaeology with asteroseismic ages
Authors: Spitoni E. , Verma K. , Silva Aguirre V. , Calura F. 
Published: January 2020

Context. With the wealth of information from large surveys and observational campaigns in the contemporary era, it is critical to properly exploit the data to constrain the parameters of Galactic chemical evolution models and quantify the associated uncertainties.
Aims. We aim to constrain the two-infall chemical evolution models for the solar annulus using the measured chemical abundance ratios and seismically inferred age of stars in the APOKASC sample. Recently, in revised two-infall chemical evolution models, a significant delay of ∼4.3 Gyr has been invoked between the two episodes of gas accretion. In this work, we wish to test its robustness and statistically confirm and quantify the delay.
Methods. We took a novel approach, using Bayesian framework based on Markov chain Monte Carlo methods to fit the two-infall chemical evolution models to the data.
Results. In addition to fitting the data for stars in the APOKASC sample, our best fit models also reproduce other important observational constraints of the chemical evolution of the disk: i) present day stellar surface density; ii) present-day supernova and star formation rates; iii) the metallicity distribution function; and iv) solar abundance values. We find a significant delay between the two gas accretion episodes for various models explored with different values for the star formation efficiencies. The values for the delay lie in the range 4.5−5.5 Gyr.
Conclusions. The results suggest that the APOKASC sample carries the signature of a delayed gas-rich merger, with dilution being the main process determining the shape of low-α stars in the abundance ratios space.
Detailed reproduction of the neutron emission from the compact DT neutron generator used as an in-situ 14 MeV calibration neutron source at JET
Authors: Čufar Aljaž , Batistoni Paola , Ghani Zamir , Giacomelli Luca , Lengar Igor , Loreti Stefano , Milocco Alberto , Popovichev Sergey , Pillon Mario , Rigamonti Davide , Rebai Marica , Tardocchi Marco , Snoj Luka ,   JET contributors
Published: January 2020

A compact DT neutron generator (NG) based on the mixed-beam operation was used as a calibration neutron source in the latest in-situ calibration of neutron detectors at the Joint European Torus (JET). In order to meet the requirement for the total uncertainty of the neutron detector calibration below ±10 %, the neutron emission properties had to be experimentally characterized and reproduced through detailed modelling of the neutron source characteristics and geometry of the neutron generator.
The detailed neutronics simulations were an essential part of both NG characterization and JET neutron detector calibration. The complex neutron emission properties of the NG were reproduced through a combination of simulations and highresolution neutron spectroscopy measurements. This meant that six different DT neutron source components resulting from NG's mixed beam operation were explicitly simulated and their relative intensities scaled based on experimentally obtained neutron spectrum measurements. Furthermore, the detailed model of the NG's geometry was produced based on information from the supplier of the NG and images from a computer tomography (CT) scan. Finally, the positioning of the neutron source inside the JET tokamak during in-situ calibration was reproduced based on the information from the remote handling system (RHS) at JET, the system responsible for the positioning of the source during the calibration experiment.
The extensive effort presented in the paper significantly contributed to the total uncertainties of the calibration factors well within the target value of ±10 %.
Gamma-heating and gamma flux measurements in the JSI TRIGA reactor, results and prospects
Authors: Gruel A. , Ambrožič K. , Destouches C. , Radulović V. , Sardet A. , Snoj L. 
Published: January 2020

The neutron field of various irradiation positions of the TRIGA Mark II reactor of the Jožef Stefan Institute has been thoroughly characterized by neutron activation dosimetry and miniature fission chambers techniques. In order to have a fully validated calculation scheme to analyze and plan experiments, the gamma field also has to be experimentally validated. The 10-year long collaboration between CEA and JSI is a perfect framework to carry out such a study, and measurements of the gamma field started in late 2016. Several measurement techniques were investigated in in-core and ex-core positions.
On-line measurements were carried out using miniature ionization chambers manufactured by the CEA and PTW Farmer ionization chambers. Positional dependence was studied, showing a decrease in the delayed gamma contribution to the total gamma flux with increasing distance from the reactor core center.
To characterize the gamma dose in the core, as well as in the periphery, thermo- and optically stimulated luminescent detectors were tested. These detectors are commonly used at CEA to measure the gamma dose in a given material in order to study the nuclear heating in various core elements (control rod, baffle, structural material). Different filters were used in order to assess an integrated dose ranging from a few Gy up to several kGy. The feasibility of such measurements demonstrates the complementarity between measurements with dosimetry and ionization chambers from low to very high gamma-dose environment, such as in material testing reactors.
Künstliche Intelligenz zur Detektion, Quantifizierung und Charakterisierung des metastasierten Prostatakarzinoms in der PSMA-PET/CT – Wo stehen wir?
Authors: Afshar-Oromieh Ali , Rominger Axel , Shi Kuangyu 
Published: January 2020

ZusammenfassungDas Prostatakarzinom (PCa) ist der weltweit häufigste maligne Tumor bei Männern. Seit ihrer klinischen Einführung im Jahr 2011 hat sich sowohl die PET/CT als auch die Radioligandentherapie mit PSMA-Liganden zur Diagnostik bzw. Therapie des PCa weltweit rasch ausgebreitet. Obwohl die PSMA-PET/CT als ein signifikanter Durchbruch in der Diagnostik des PCa gilt, stellt die Evaluation und Kontrolle aller Tumorherde inklusive ihrer Volumina und Charakteristiken bei fortgeschrittenem, multimetastatischem PCa nach wie vor eine große Herausforderung dar. Diese gilt es zu bewältigen, um beispielsweise eine Optimierung der Endoradiotherapie mit PSMA-Liganden zu erreichen. In diesem Kontext könnte die künstliche Intelligenz, die in den letzten Jahren signifikante Fortschritte erzielt hat, in der nahen Zukunft eine wichtige Rolle spielen. Die Artificial Intelligence (AI) hat bereits demonstriert, dass sie den menschlichen Fähigkeiten zur Datenverarbeitung überlegen sein kann und bietet damit großes Potenzial zur Verbesserung der Detektion, Quantifizierung und Charakterisierung von PCa-Herden in der PSMA-PET/CT.Die hier vorliegende Schrift befasst sich mit den aktuellen Entwicklungen der künstlichen Intelligenz für den Einsatz in der PSMA-PET/CT und den sich daraus bietenden Möglichkeiten.
Practical considerations for establishing writing groups in interdisciplinary programs
Authors: Bergen Nicole , Hudani Alzahra , Khan Selim , Montgomery Natalie D. , O’Sullivan Tracey 
Published: January 2020

AbstractAcademic writing capabilities are a cornerstone of success in doctoral programs, yet prove to be a point of anxiety and apprehension for many students. Providing support for academic writing within interdisciplinary programs poses special considerations, as students in these programs are called upon to transcend single disciplinary perspectives to address a central area of research, and to integrate multiple different disciplinary perspectives that may be conflicting or overlapping. When treated as a social practice, writing can serve as a common interest that draws doctoral students to convene and develop in their learning. This article describes the development of a student writing group in an interdisciplinary doctoral program, considering how the characteristics and activities of the group create an environment that enables and encourages enhanced interdisciplinary learning. The article argues that, when delivered successfully, student writing groups have the potential to strengthen student writing skills and outputs, as well as deepen interdisciplinary learning. Drawing from Lattuca’s four aspects of interdisciplinary learning (relational, mediated, transformative and situated), the article illustrates ways that the writing group helped to promote each aspect of learning and benefit the overall student experience in the program. Reflecting on these experiences, the authors propose six practical considerations for establishing writing groups in interdisciplinary programs: vision and purpose; dedicated time and space; institutional support; readings or educational material; socialization opportunities; and shared responsibility. Administrators, students, faculty members and support staff involved in the delivery of interdisciplinary doctoral programs are called upon to consider the introduction and/or strengthening of writing groups for the purpose of enhanced interdisciplinary learning.
Matthiessen on Halliday
Authors: Matthiessen Christian M. I. M. , Wang Bo , Ma Yuanyi 
Published: January 2020

Abstract
Christian M. I. M. Matthiessen was a long-time collaborator and close friend of M. A. K. Halliday, and has
co-authored various books with Halliday, some of which have not yet been published. In the second part of the interview,
Matthiessen discusses Halliday’s engagement with computational linguistics, provides details of Halliday’s experiences as a
language teacher, comments on Halliday’s contributions to language development, introduces Halliday’s collaboration with Basil
Bernstein and Halliday’s conception of language as social semiotics, and reflects on Halliday’s influence on Matthiessen
himself.
Metaphors we feel by: stratal tension
Authors: Martin J. R. 
Published: January 2020

ABSTRACT
This paper revisits the traditional concept of lexical metaphor from the perspective of SFL work on grammatical metaphor, exploring its interpretation as inter-stratal tension, and commenting on its rhetorical significance from both ideational and interpersonal points of view. Its goal has been to show how two key parameters of SFL theory, stratification and metafunction, can be deployed to provide an integrated comprehensive perspective on metaphor of all kinds. This involves drawing on SFL work on ideational and interpersonal meaning across strata, by way of clarifying what is meant by inter-stratal tension and outlining some foundations for research towards further formalisation of descriptions of the layers of meaning involved in metaphorical processes.
Synchronous Pulmonary Adenocarcinomas
Authors: Pagan Carlos A , Shu Catherine A , Crapanzano John P , Lagos Galina G , Stoopler Mark B , Rizvi Naiyer A , Heymann Jonas J , Sonett Joshua R , Fernandes Helen , Saqi Anjali 
Published: January 2020

Abstract

Objectives
To determine concordance/discordance between morphology and molecular testing (MT) among synchronous pulmonary carcinomas using targeted next generation sequencing (NGS), with and without comprehensive molecular review (CMR), vs analyses of multiple singe genes (non-NGS).

Methods
Results of morphologic and MT assessment were classified as concordant, discordant, or indeterminate. For discordant cases, comprehensive histologic assessment (CHA) was performed.

Results
Forty-seven cases with 108 synchronous tumors were identified and underwent MT (NGS, n = 23 and non-NGS, n = 24). Histology and MT were concordant, discordant, and indeterminate in 53% (25/47), 21% (10/47), and 26% (12/47) of cases, respectively. CHA of the 10 discordant cases revised results of three cases.

Conclusions
There is discordance between histology and MT in a subset of cases and MT provides an objective surrogate for staging synchronous tumors. A limited gene panel is sufficient for objectively assessing a relationship if the driver mutations are distinct. Relatedness of mutations require CMR with a larger NGS panel (eg, 50 genes).
First Report of Candidatus Mycoplasma haemohominis Infection in Australia Causing Persistent Fever in an Animal Carer
Authors: Alcorn Kylie , Gerrard John , Cochrane Tara , Graham Rikki , Jennison Amy , Irwin Peter J , Barbosa Amanda D 
Published: January 2020

Abstract

Background
Hemotropic mycoplasmas (hemoplasmas) infect animals and humans and can lead to clinical syndromes mainly characterized by hemolytic anemia. A novel pathogen, Candidatus Mycoplasma haemohominis, was recently associated with a case of human hemoplasmosis in Europe. Here we report the first detection of this pathogen in an Australian patient exhibiting persistent fever, hemolytic anemia, and pancytopenia over a 10-month period.

Methods
After exhaustive negative testing for human infectious diseases, whole genome sequencing (WGS) was performed on the patient’s bone marrow aspirate, using an Illumina NextSeq500 platform. Conventional polymerase chain reaction (PCR), followed by Sanger sequencing, was then performed on blood samples using novel Mycoplasma-specific primers targeting the 16S ribosomal RNA gene. In addition, a Mycoplasma-specific fluorescence in situ hybridization (FISH) assay was developed to differentiate Mycoplasma cells from other erythrocyte inclusions (eg, Pappenheimer and Howell-Jolly bodies) which are morphologically similar to bacterial cocci by light microscopy.

Results
WGS analysis revealed that approximately 0.04% of the total number of unmapped reads to human genome corresponded to Mycoplasma species. A 1-kb Mycoplasma 16S fragment was successfully amplified by conventional PCR, and sequence analyses revealed 100% identity with Candidatus Mycoplasma haemohominis. FISH confirmed that several (approximately 2%) epierythrocytic inclusions initially observed by light microscopy corresponded to Mycoplasma cells.

Conclusions
This represents the second report of hemolytic anemia associated with hemoplasma infection in a human, and the first report of human hemoplasmosis in Australia. This study highlights the importance of new and emerging diagnostic approaches and need for further investigations on the epidemiology of Candidatus Mycoplasma haemohominis in Australia.
The Changing Landscape of Pediatric Viral Enteropathogens in the Post–Rotavirus Vaccine Era
Authors: Halasa Natasha , Piya Bhinnata , Stewart Laura S , Rahman Herdi , Payne Daniel C , Woron Amy , Thomas Linda , Constantine-Renna Lisha , Garman Katie , McHenry Rendie , Chappell James , Spieker Andrew J , Fonnesbeck Christopher , Batarseh Einas , Hamdan Lubna , Wikswo Mary E , Parashar Umesh , Bowen Michael D , Vinjé Jan , Hall Aron J , Dunn John R 
Published: January 2020

Abstract

Background
Acute gastroenteritis (AGE) is a common reason for children to receive medical care. However, the viral etiology of AGE illness is not well described in the post–rotavirus vaccine era, particularly in the outpatient (OP) setting.

Methods
Between 2012 and 2015, children 15 days through 17 years old presenting to Vanderbilt Children’s Hospital, Nashville, Tennessee, with AGE were enrolled prospectively from the inpatient, emergency department, and OP settings, and stool specimens were collected. Healthy controls (HCs) were enrolled and frequency matched for period, age group, race, and ethnicity. Stool specimens were tested by means of reverse-transcription real-time quantitative polymerase chain reaction for norovirus, sapovirus, and astrovirus RNA and by Rotaclone enzyme immunoassay for rotavirus antigen, followed by polymerase chain reaction verification of antigen detection.

Results
A total of 3705 AGE case patients and 1563 HCs were enrolled, among whom 2885 case patients (78%) and 1110 HCs (71%) provided stool specimens that were tested. All 4 viruses were more frequently detected in AGE case patients than in HCs (norovirus, 22% vs 8%, respectively; rotavirus, 10% vs 1%; sapovirus, 10% vs 5%; and astrovirus, 5% vs 2%; P &lt; .001 for each virus). In the OP setting, rates of AGE due to norovirus were higher than rate for the other 3 viruses. Children &lt;5 years old had higher OP AGE rates than older children for all viruses.

Conclusions
Norovirus remains the most common virus detected in all settings, occurring nearly twice as frequently as the next most common pathogens, sapovirus and rotavirus. Combined, norovirus, sapovirus, rotavirus, and astrovirus were associated with almost half of all AGE visits and therefore are an important reason for children to receive medical care.
A Randomized Controlled Trial of Ceftriaxone and Doxycycline, With or Without Metronidazole, for the Treatment of Acute Pelvic Inflammatory Disease
Authors: Wiesenfeld Harold C , Meyn Leslie A , Darville Toni , Macio Ingrid S , Hillier Sharon L 
Published: January 2020

Abstract

Background
Anaerobic organisms are important pathogens in acute pelvic inflammatory disease (PID). The currently recommended PID regimen of a single dose of ceftriaxone and doxycycline for 14 days has limited anaerobic activity. The need for broader anaerobic coverage is unknown and concerns have been raised about metronidazole tolerability.

Methods
We conducted a randomized, double-blind, placebo-controlled trial comparing ceftriaxone 250 mg intramuscular single dose and doxycycline for 14 days, with or without 14 days of metronidazole in women with acute PID. The primary outcome was clinical improvement at 3 days following enrollment. Additional outcomes at 30 days following treatment were the presence of anaerobic organisms in the endometrium, clinical cure (absence of fever and reduction in tenderness), adherence, and tolerability.

Results
We enrolled 233 women (116 to metronidazole and 117 to placebo). Clinical improvement at 3 days was similar between the 2 groups. At 30 days following treatment, anaerobic organisms were less frequently recovered from the endometrium in women treated with metronidazole than placebo (8% vs 21%, P &lt; .05) and cervical Mycoplasma genitalium was reduced (4% vs 14%, P &lt; .05). Pelvic tenderness was also less common among women receiving metronidazole (9% vs 20%, P &lt; .05). Adverse events and adherence were similar in each treatment group.

Conclusions
In women treated for acute PID, the addition of metronidazole to ceftriaxone and doxycycline was well tolerated and resulted in reduced endometrial anaerobes, decreased M. genitalium, and reduced pelvic tenderness compared to ceftriaxone and doxycycline. Metronidazole should be routinely added to ceftriaxone and doxycycline for the treatment of women with acute PID.

Clinical Trials Registration
NCT01160640.