bluuebunny/crossref_metadata_2025 huggingface dataset:
From physical to social interactions: The relative entropy model
Authors: Neuman Yair , Vilenchik Dan , Cohen Yochai
Published: January 2020

Complex social systems at various scales of analysis (e.g. dyads, families, tribes, etc.) are formed and maintained through verbal interactions. Therefore, the ability to (1) model these interactions and (2) to use models of interaction for identifying significant relations may be of interest to the social sciences. Adopting the perspective of social physics, we present a general approach for modeling interactions through relative entropy. For illustrating the benefits of the approach, we derive measures of “perspective-taking” and use them for identifying significant-romantic relations in a data set composed of the verbal interactions taken place at the famous TV series “Sex and the City”. Using these measures, we show that significant-romantic relations can be identified with success. These results provide preliminary support for the benefits of using the proposed approach.
Effectiveness of intraoperative intraocular lens use on improving surgical safety for dense cataract phacoemulsification: a randomized controlled trial
Authors: Zeng Mingbing , Wang Rong , Cheng Bing , Yang Chengwu , Chen Yunxin , Liu Xialin
Published: January 2020

We designed this study to assess if surgical safety can be improved by intraoperative use of intraocular lens (IOL) for cataract phacoemulsification. We performed phacoemulsification cataract removal on 401 patients. We randomly assigned these patients into three groups: the standard setting (Group I, n = 134), with reduced vacuum and flow rate (Group II, n = 137), and with IOL insertion before the last quadrant was emulsified with standard setting (Group III, n = 130). The primary outcomes included the risk of posterior capsular rupture (PCR), ultrasound time, energy, and complications. The secondary outcomes included central corneal thickness (CCT), CCT changes, endothelial cells (ETC) counting, ETC loss, and the best corrected distance visual acuity (BCVA) measured on day 1, day 7 and day 30. If PCR occurred, we emulsified the residual lens materials after insertion of IOL and clean of the prolapsed vitreous. We found that the risk of PCR in Group III (0/130) was lower than Group I (9/134, corrected relative risk (RR) = 18.44, 95% CI: 1.08–313.56) and Group II (3/137, corrected RR = 6.64, 95% CI: 0.35–27.41). Group III showed better BCVA on day 1 and 7, less ECC loss on day 7 and 30, and less CCT increase on day 1 and 7. No cases converted to extracapsular cataract extraction. No residual lens materials misdirected into vitreous cavity. Intraoperative use of IOL can improve surgical safety for dense cataract phacoemulsification.
Plasma-activated medium promotes autophagic cell death along with alteration of the mTOR pathway
Authors: Yoshikawa Nobuhisa , Liu Wenting , Nakamura Kae , Yoshida Kosuke , Ikeda Yoshiki , Tanaka Hiromasa , Mizuno Masaaki , Toyokuni Shinya , Hori Masaru , Kikkawa Fumitaka , Kajiyama Hiroaki
Published: January 2020

The biological function of non-thermal atmospheric pressure plasma has been widely accepted in several types of cancer. We previously developed plasma-activated medium (PAM) for clinical use, and demonstrated that PAM exhibits a metastasis-inhibitory effect on ovarian cancer through reduced MMP-9 secretion. However, the anti-tumor effects of PAM on endometrial cancer remain unknown. In this study, we investigated the inhibitory effect of PAM on endometrial cancer cell viability in vitro. Our results demonstrated that AMEC and HEC50 cell viabilities were reduced by PAM at a certain PAM ratio, and PAM treatment effectively increased autophagic cell death in a concentration dependent manner. In addition, we evaluated the molecular mechanism of PAM activity and found that the mTOR pathway was inactivated by PAM. Moreover, our results demonstrated that the autophagy inhibitor MHY1485 partially inhibited the autophagic cell death induced by PAM treatment. These findings indicate that PAM decreases the viability of endometrial cancer cells along with alteration of the mTOR pathway, which is critical for cancer cell viability. Collectively, our data suggest that PAM inhibits cell viability while inducing autophagic cell death in endometrial cancer cells, representing a potential novel treatment for endometrial cancer.
Author Correction: Mice adaptively generate choice variability in a deterministic task
Authors: Belkaid Marwen , Bousseyrol Elise , Durand-de Cuttoli Romain , Dongelmans Malou , Duranté Etienne K. , Yahia Tarek Ahmed , Didienne Steve , Hanesse Bernadette , Come Maxime , Mourot Alexandre , Naudé Jérémie , Sigaud Olivier , Faure Philippe
Published: January 2020

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Recent advances in fluorescence resonance energy transfer-based probes in nucleic acid diagnosis
Authors: Chen Jiaxin , Shi Cheng , Kang Xin yue , Shen Xu tong , Lao Xingzhen , Zheng Heng
Published: January 2020

Nucleic acid diagnosis is a method that diagnoses human conditions and diseases by directly exploring the existing states or defects of nucleic acids using theoretical and technical approaches from molecular biology.
Evidence and evolution of Criegee intermediates, hydroperoxides and secondary organic aerosols formedviaozonolysis of α-pinene
Authors: Bagchi Arnab , Yu Youqing , Huang Jhih-Hong , Tsai Cheng-Cheng , Hu Wei-Ping , Wang Chia C.
Published: January 2020

The first experimental evidence of Criegee intermediates formedviaα-pinene ozonolysis and the formation of secondary organic aerosols is reported using a rapid scan time-resolved FTIR spectrometer coupled with a long-path aerosol cooling chamber.
Vibrations of the guanine–cytosine pair in chloroform: an anharmonic computational study
Authors: Green James A. , Improta Roberto
Published: January 2020

Anharmonic calculations provide new insights on the vibrations of strongly hydrogen bonded systems such as the Gua–Cyt pair.
Oxidative C–N bond cleavage of (2-pyridylmethyl)amine-based tetradentate supporting ligands in ternary cobalt(ii)–carboxylate complexes
Authors: Chakraborty Biswarup , Ghosh Ivy , Jana Rahul Dev , Paine Tapan Kanti
Published: January 2020

Co(ii)–carboxylate complexes of N4 ligands containing (2-pyridylmethyl)amine backbone activate O2 and exhibit oxidative C–N bond cleavage of the ligands. The coordination of carboxylate co-ligand plays important role to affect the ligand oxidation.
Understanding the sodium storage mechanisms of organic electrodes in sodium ion batteries: issues and solutions
Authors: Rajagopalan Ranjusha , Tang Yougen , Jia Chuankun , Ji Xiaobo , Wang Haiyan
Published: January 2020

Organic materials offer a new opportunity to develop high-performance, low-cost, environmentally benign sodium ion batteries. This review provides insights into the different sodium storage mechanisms in various categories of organic materials.
β-Sitosterol regulated microRNAs in endothelial cells against an oxidized low-density lipoprotein
Authors: Jiang Yue-Hua , Li Xiao , Niu Weipin , Wang DongLi , Wu Bo , Yang Chuan-Hua
Published: January 2020

β-sitosterol is shown to demonstrate endothelial protective effects, which inhibited apoptosis, increased cell migration, and improved mitochondrial function of human aortic endothelial cells.
A jaboticaba extract prevents prostatic damage associated with aging and high-fat diet intake
Authors: Lamas C. A. , Kido L. A. , Montico F. , Collares-Buzato C. B. , Maróstica M. R. , Cagnon V. H. A.
Published: January 2020

Jaboticaba extract prevented the prostatic lesion development in aging and/or overweight mice, mainly interfering in cell proliferation, hormonal and angiogenesis pathways.
Two-dimensional square-grid iron(ii) coordination polymers showing anion-dependent spin crossover behavior
Authors: Shin Jong Won , Jeong Ah Rim , Jeong Jong Hwa , Zenno Hikaru , Hayami Shinya , Min Kil Sik
Published: January 2020

Two-dimensional Fe-based coordination polymers with square-grid shapes were prepared by self-assembly and exhibited an interesting spin crossover behavior depending on the coordinated counter ions.
The effects of the crosslinking position and degree of conjugation in perylene tetraanhydride bisimide microporous polymers on fluorescence sensing performance
Authors: Hu Chen , Gao Ying-Chun , Zhang Can , Liu Min , Geng Tong-Mou
Published: January 2020

In this study, two fluorescence conjugated microporous polymers based on perylene tetraanhydride bisimide (DP4A0 and DP4A2) were prepared via Sonogashira–Hagihara cross-coupling polymerization for the efficient detection of o-nitrophenol (o-NP).
Tailoring the AlCl3/iPr2O/Et2O initiation system for highly reactive polyisobutylene synthesis in pure n-hexane
Authors: Xie Dan , Zhu Shan , Lu Yangcheng
Published: January 2020

Effective HRPIB synthesis in n-hexane was achieved by tailoring the AlCl3/iPr2O/Et2O initiation system using a novel preparation method.
Dimerization of terminal alkynes promoted by a heterobimetallic Zr/Co complex
Authors: Beattie Jeffrey W. , Wang Canning , Zhang Hongtu , Krogman Jeremy P. , Foxman Bruce M. , Thomas Christine M.
Published: January 2020

A reduced ZrIV/Co−I heterobimetallic complex facilitates the formation of 1,3-enynes from terminal alkynes through a cooperative bimetallic C–H activation process.
Gold nanoparticle assembly on porous silicon by pulsed laser induced dewetting
Authors: Fulton Alison Joy , Ozhukil Kollath Vinayaraj , Karan Kunal , Shi Yujun
Published: January 2020

This work reports the influence of the substrate in the pulsed laser-induced dewetting (PLiD) of Au thin films for the fabrication of nanoparticle (NP) arrays.
Regioselective convergent synthesis of 2-arylidene thiazolo[3,2-a]pyrimidines as potential anti-chikungunya agents
Authors: Fares Mohamed , McCosker Patrick M. , Alsherbiny Muhammad A. , Willis Anthony C. , Clark Timothy , Neyts Johan , Jochmans Dirk , Keller Paul A.
Published: January 2020

Convergent and convenient regioselective synthesis of novel thiazolo[2,3-a]pyrimidines was accomplished using the one-pot reaction of 6-ethylthiouracil, bromoacetic acid, anhydrous sodium acetate, acetic anhydride, acetic acid and suitable aldehyde.
A student's introduction to academic publishing
Authors: Hare Roseanna
Published: January 2020

Publication really is the brick in the wall of scientific advancement. It facilitates the important communication of research from scientists around the world, driving forward key discoveries, whilst enhancing the careers of those that have toiled over the lab bench. However, especially early in your career, it is easy to focus on what to publish rather than how to publish. With the changing landscape of scholarly publishing and the move to a more open research culture, there has never been a better time to get clued up on the ins and outs of the publishing process. This guide aims to answer all your essential publishing questions, so that when it comes to preparing your research paper you are well informed about the publishing practicalities.
Effect of puerarin on action potential and sodium channel activation in human hypertrophic cardiomyocytes
Authors: Lin Yu-hui , Ni Xiao-Bin , Zhang Jian-wu , Ou Cai-wen , He Xiao-qing , Dai Wen-jun , Chen Xi-ming , Chen Min-sheng
Published: January 2020

Objective: To study the effect of puerarin on electrophysiology using a hypertrophic cardiomyocyte (HC) model.

Materials and methods: Human urine epithelial cells were used to generate the HC model (hiPSC-CM). Cardiomyocyte hypertrophy was induced by applying 10 nM endothelin-1 (ET-1). Effects of puerarin pre-treatment (PPr) and post-treatment (PPo) on action potential, sodium current (INa) activation and inactivation, and recovery following INa inactivation were tested using patch clamp electrophysiology.

Results: Depolarization to repolarization 50% time (APD50) and repolarization 30% time (APD30) were significantly prolonged in the PPo and PPr groups compared with the controls. However, there were no significant differences in the action potential depolarization amplitude (APA) or the maximum depolarization velocity (Vmax) in phase 0. The PPr group had a slightly shortened APD90, and an extended APD50 and APD30, but did not exhibit any significant changes in stage A of APA and Vmax. The PPo group did not exhibit any significant changes in INa, while 12 h of PPr improved INa. However, puerarin did not significantly affect the activation, inactivation, or recovery of the sodium channel.

Conclusions: Cardiomyocyte hypertrophy significantly decreased the Vmax of the action potential and the peak density of INa. PPr inhibited the decrease in Vmax and increased the peak density of INa. Thus, puerarin could be used to stabilize the electrophysiological properties of hypertrophic cardiomyocytes and reduce arrhythmias.
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

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.
A precise analytical approximation for the deprojection of the Sérsic profile
Authors: Vitral Eduardo , Mamon Gary A.
Published: January 2020

The Sérsic model shows a close fit to the surface brightness (or surface density) profiles of elliptical galaxies and galaxy bulges, and possibly also those of dwarf spheroidal galaxies and globular clusters. The deprojected density and mass profiles are important for many astrophysical applications, in particular for mass-orbit modeling of these systems. However, the exact deprojection formula for the Sérsic model employs special functions that are not available in most computer languages. We show that all previous analytical approximations to the 3D density profile are imprecise at low Sérsic index (n ≲ 1.5). We derived a more precise analytical approximation to the deprojected Sérsic density and mass profiles by fitting two-dimensional tenth-order polynomials to the residuals of the analytical approximations by Lima Neto et al. (1999, MNRAS, 309, 481; LGM) for these profiles, relative to the numerical estimates. Our LGM-based polynomial fits have typical relative precision better than 0.2% for both density and mass profiles, for Sérsic indices 0.5 ≤ n ≤ 10 and radii 0.001 <  r/Re <  1000. Our approximation is much more precise than previously published approximations (except, in some models, for a few discrete values of the index). An appendix compares the deprojected Sérsic profiles with those of other popular simple models.
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.
Radiation hardness studies and detector characterisation at the JSI TRIGA reactor
Authors: Snoj L. , Ambrožič K. , Čufar A. , Goričanec T. , Jazbec A. , Lengar I. , Pungerčič A. , Radulović V. , Rupnik S. , Štancar Ž. , Žerovnik G. , Žohar A. , Cindro V. , Kramberger G. , Mandić I. , Mikuž M. , Barbot L. , Carcreff H. , Destouches C. , Fourmentel D. , Gruel A. , Villard J.F.
Published: January 2020

The JSI TRIGA reactor features several in-core and ex-core irradiation facilities, each having different properties, such as neutron/gamma flux intensity, spectra and irradiation volume. A series of experiments and calculations was performed in order to characterise radiation fields in irradiation channel thus allowing users to perform irradiations in a well characterised environment. Since 2001 the reactor has been heavily used for radiation hardness studies for components used at accelerators such as the Large Hadron Collider (LHC) at CERN. Since 2010 it has been extensively used for testing of new detectors and innovative data acquisition systems and methods developed and used by the CEA. Recently, several campaigns were initiated to characterise the gamma field in the reactor and use the experimental data for improvement of the treatment of delayed gammas in Monte Carlo particle transport codes. In the future it is planned to extend the testing options by employing pulse mode operation, installation of a high energy gamma ray irradiation facility and allow irradiation of larger samples at elevated temperature.
A model for suspension of clusters of particle pairs
Authors: Mecherbet Amina
Published: January 2020

In this paper, we considerNclusters of pairs of particles sedimenting in a viscous fluid. The particles are assumed to be rigid spheres and inertia of both particles and fluid are neglected. The distance between each two particles forming the cluster is comparable to their radii 1/Nwhile the minimal distance between the pairs is of orderN−1/2. We show that, at the mesoscopic level, the dynamics are modelled using a transport-Stokes equation describing the time evolution of the positionxand orientationξof the clusters. Under the additional assumption that the minimal distance is of orderN−1/3, we investigate the case where the orientation of each cluster is initially correlated to its position. In this case, a local existence and uniqueness result for the limit model is provided.
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

Das 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

Academic 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.
Effect of duration of restricted-feeding on nutrient excretion, animal performance, and carcass characteristics of Holstein × Zebu finishing steers
Authors: Silva F. A. S. , Valadares Filho S. C. , Godoi L. A. , Silva B. C. , Pacheco M. V. C. , Zanetti D. , Benedeti P. D. B. , Silva F. F. , Felix T. L.
Published: January 2020

Restricted-feeding may be a useful management tool available to reduce environmental impact in feedlots. Therefore, the objectives of the present study were to determine the effects of the duration of restricted-feeding on nitrogen (N) and phosphorus (P) excretion, growth performance and carcass characteristics of finishing steers. Twenty-five Holstein × Zebu steers (average initial bodyweight (BW) = 319 ± 16.2 kg; age = 19 ± 1 months) were used. Five steers were slaughtered to provide baseline empty BW (EBW) and empty body composition at Day 0. The remaining steers were randomly allotted to four groups of five steers, which were restricted to 85% ad libitum feed intake for either 0 (R0), 28 (R28), 42 (R42) or 84 (R84) days of an 84-day finishing period. All steers were fed a diet of 40% corn silage and 60% concentrate (DM basis) for 84 days. Total excretion of faeces and urine were collected during two periods: Days 25 to 27 (period 1) and Days 73 to 75 (period 2). The DM intake, average daily gain (ADG) and gain-to-feed ratio (G:F) were evaluated in three blocks, Days 0 to 28, Days 28 to 42 and Days 42 to 84. As expected, DM, N and P intakes were greater (P < 0.05) for R0 steers than R28, R42 and R84 steers when steers in R28, R42 and R84 treatments were restricted. When transitioned to ad libitum feeding, R28 and R42 steers had similar (P > 0.05) DM, N and P intakes compared with R0 steers. Faecal N and urinary P excretions did not differ (P ≥ 0.40) among restricted and ad libitum-fed steers in either period evaluated. However, greater (P < 0.05) faecal P excretions were observed in steers fed ad libitum intake in period 2 (R0). Phosphorus retention in period 2, and whole-body N retention were greatest (P < 0.05) in steers fed R28 and least (P < 0.05) in steers fed R84, steers fed R0 and steers fed R42 were intermediate and not different (P > 0.05). Final BW, overall ADG, G:F and carcass characteristics were not affected (P ≥ 0.11) by treatments. Restricted-feeding Holstein × Zebu steers to 85% of ad libitum intake for 84 days in the feedlot reduced DM intake and P excretion, without impairing steer growth performance or carcass characteristics. Nevertheless, it is important to highlight that the small sample size was one limitation of this present experiment.
Matthiessen on Halliday
Authors: Matthiessen Christian M. I. M. , Wang Bo , Ma Yuanyi
Published: January 2020

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

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

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).
Connecting through culture
Authors: Bowler Sue
Published: January 2020

Sue Bowler explores the power of the arts to shine a light on science in western Ireland.
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

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

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 < .001 for each virus). In the OP setting, rates of AGE due to norovirus were higher than rate for the other 3 viruses. Children <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

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 < .05) and cervical Mycoplasma genitalium was reduced (4% vs 14%, P < .05). Pelvic tenderness was also less common among women receiving metronidazole (9% vs 20%, P < .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.
Duration of Exposure Among Close Contacts of Patients With Infectious Tuberculosis and Risk of Latent Tuberculosis Infection
Authors: Reichler Mary R , Khan Awal , Yuan Yan , Chen Bin , McAuley James , Mangura Bonita , Sterling Timothy R ,   Tuberculosis Epidemiologic Studies Consortium Task Order 2 Team, Bakhtawar I , LeDoux C , McAuley J , Beison J , Fitzgerald M , Naus M , Nakajima M , Schluger N , Hirsch-Moverman Y , Moran J , Blumberg H , Tapia J , Singha L , Hershfeld E , Roche B , Mangura B , Sevilla A , Sterling T , Chavez-Lindell T , Maruri F , Dorman S , Cronin W , Munk E , Khan A , Yuan Y , Chen B , Yan F , Shen Y , Zhao H , Zhang H , Bessler P , Fagley M , Reichler M , Reichler M , Sterling T , Tapia J , Hirsch C , Luo C , Bakhtawar I , LeDoux C , McAuley J , Beison J , Fitzgerald M , Naus M , Nakajima M , Schluger N , Hirsch-Moverman Y , Moran J , Blumberg H , Tapia J , Singha L , Hershfeld E , Roche B , Mangura B , Sevilla A , Sterling T , Chavez-Lindell T , Maruri F , Dorman S , Cronin W , Munk E , Khan A , Yuan Y , Chen B , Yan F , Shen Y , Zhao H , Zhang H , Bessler P , Fagley M , Reichler M , Reichler M , Sterling T , Tapia J , Hirsch C , Luo C
Published: January 2020

Background

Predictors of latent tuberculosis infection (LTBI) among close contacts of persons with infectious tuberculosis (TB) are incompletely understood, particularly the number of exposure hours.

Methods

We prospectively enrolled adult patients with culture-confirmed pulmonary TB and their close contacts at 9 health departments in the United States and Canada. Patients with TB were interviewed and close contacts were interviewed and screened for TB and LTBI during contact investigations.

Results

LTBI was diagnosed in 1390 (46%) of 3040 contacts, including 624 (31%) of 2027 US/Canadian-born and 766 (76%) of 1013 non-US/Canadian-born contacts. In multivariable analysis, age ≥5 years, male sex, non-US/Canadian birth, smear-positive index patient, and shared bedroom with an index patient (P < .001 for each), as well as exposure to >1 index patient (P < .05), were associated with LTBI diagnosis. LTBI prevalence increased with increasing exposure duration, with an incremental prevalence increase of 8.2% per 250 exposure hours (P < .0001). For contacts with <250 exposure hours, no difference in prevalence was observed per 50 exposure hours (P = .63).

Conclusions

Hours of exposure to a patient with infectious TB is an important LTBI predictor, with a possible risk threshold of 250 hours. More exposures, closer exposure proximity, and more extensive index patient disease were additional LTBI predictors.
Into the wild: new yeast genomes from natural environments and new tools for their analysis
Authors: Libkind D , Peris D , Cubillos F A , Steenwyk J L , Opulente D A , Langdon Q K , Rokas A , Hittinger C T
Published: January 2020

Genomic studies of yeasts from the wild have increased considerably in the past few years. This revolution has been fueled by advances in high-throughput sequencing technologies and a better understanding of yeast ecology and phylogeography, especially for biotechnologically important species. The present review aims to first introduce new bioinformatic tools available for the generation and analysis of yeast genomes. We also assess the accumulated genomic data of wild isolates of industrially relevant species, such as Saccharomyces spp., which provide unique opportunities to further investigate the domestication processes associated with the fermentation industry and opportunistic pathogenesis. The availability of genome sequences of other less conventional yeasts obtained from the wild has also increased substantially, including representatives of the phyla Ascomycota (e.g. Hanseniaspora) and Basidiomycota (e.g. Phaffia). Here, we review salient examples of both fundamental and applied research that demonstrate the importance of continuing to sequence and analyze genomes of wild yeasts.
Extensive Genomic Rearrangements along with Distinct Mobilome and TALome are Associated with Extreme Pathotypes of a Rice Pathogen
Authors: Kaur Amandeep , Bansal Kanika , Patil Prabhu B
Published: January 2020

Xanthomonas oryzae pv. oryzae (Xoo) is a serious pathogen of rice which displays tremendous interstrain variation. The emergence of highly-virulent strains of Xoo is a major threat to rice cultivation. Evolutionary insights into genome dynamics of highly virulent strains as compared with the less-virulent ones are crucial for understanding the molecular basis of exceptional success of Xoo as a highly evolved plant pathogen. In the present study, we report complete genome sequence of Xoo strains with extreme-virulent pathotypes (XVPs) characterized based on their reaction toward ten resistance (Xa) genes. One strain, IXO1088, can overcome resistance mediated by all the ten resistance genes while the other strain IXO704 cannot overcome any of them. Interestingly, our investigation revealed that XVPs display dramatic variation in the genome structure with numerous rearrangements/inversions. Moreover, XVPs also possess distinct transposon content and prophage elements that may provide genomic flux required for the acquisition of novel gene cassettes and structural changes in the genome. Interestingly, analysis of transcription activator-like effector proteins, which are major virulence determinants of Xanthomonas pathogen show marked variation in the transcription activator-like effector content and DNA binding domain of tal genes. Overall, the present study indicates the possible role of mobilomes and repetitive elements in major structural and sequence alterations, which may be leading to the emergence of novel and extreme pathotypes. The knowledge and resource of XVPs will be invaluable in the further systematic understanding of evolution and management of variant pathotypes of Xoo.
Vedolizumab Induced Clinical, Endoscopic, and Histological Improvement in Common Variable Immunodeficiency Disease–associated Intestinal Enteropathy
Authors: Akhtar Hisham Javed , Markandey Bharat , Ma Christopher , Ramsewak Darryl , Walsh Joanna C , Jairath Vipul
Published: January 2020

After treatment with vedolizumab, a patient with diarrhea and malnutrition secondary to common variable immune deficiency (CVID)–related enteropathy was able to achieve clinical, endoscopic, and histological improvement. Vedolizumab may be a treatment option for patients with CVID-associated enteropathy.