bluuebunny/crossref_metadata_2025_split huggingface dataset:
A computational method for prioritizing targeted therapies in precision oncology: performance analysis in the SHIVA01 trial
Authors: Petak Istvan , Kamal Maud , Dirner Anna , Bieche Ivan , Doczi Robert , Mariani Odette , Filotas Peter , Salomon Anne , Vodicska Barbara , Servois Vincent , Varkondi Edit , Gentien David , Tihanyi Dora , Tresca Patricia , Lakatos Dora , Servant Nicolas , Deri Julia , du Rusquec Pauline , Hegedus Csilla , Bello Roufai Diana , Schwab Richard , Dupain Celia , Valyi-Nagy Istvan T. , Le Tourneau Christophe 
Published: June 2021

AbstractPrecision oncology is currently based on pairing molecularly targeted agents (MTA) to predefined single driver genes or biomarkers. Each tumor harbors a combination of a large number of potential genetic alterations of multiple driver genes in a complex system that limits the potential of this approach. We have developed an artificial intelligence (AI)-assisted computational method, the digital drug-assignment (DDA) system, to prioritize potential MTAs for each cancer patient based on the complex individual molecular profile of their tumor. We analyzed the clinical benefit of the DDA system on the molecular and clinical outcome data of patients treated in the SHIVA01 precision oncology clinical trial with MTAs matched to individual genetic alterations or biomarkers of their tumor. We found that the DDA score assigned to MTAs was significantly higher in patients experiencing disease control than in patients with progressive disease (1523 versus 580, P = 0.037). The median PFS was also significantly longer in patients receiving MTAs with high (1000+ <) than with low (<0) DDA scores (3.95 versus 1.95 months, P = 0.044). Our results indicate that AI-based systems, like DDA, are promising new tools for oncologists to improve the clinical benefit of precision oncology.
Cyanocobalamin prevents cardiomyopathy in type 1 diabetes by modulating oxidative stress and DNMT-SOCS1/3-IGF-1 signaling
Authors: Kakoki Masao , Ramanathan Purushotham V. , Hagaman John R. , Grant Ruriko , Wilder Jennifer C. , Taylor Joan M. , Charles Jennette J. , Smithies Oliver , Maeda-Smithies Nobuyo 
Published: June 2021

AbstractPatients with long-standing diabetes have a high risk for cardiac complications that is exacerbated by increased reactive oxygen species (ROS) production. We found that feeding cyanocobalamin (B12), a scavenger of superoxide, not only prevented but reversed signs of cardiomyopathy in type 1 diabetic Elmo1H/HIns2Akita/+ mice. ROS reductions in plasma and hearts were comparable to those in mice treated with other antioxidants, N-acetyl-L-cysteine or tempol, but B12 produced better cardioprotective effects. Diabetes markedly decreased plasma insulin-like growth factor (IGF)-1 levels, while B12, but not N-acetyl-L-cysteine nor tempol, restored them. B12 activated hepatic IGF-1 production via normalization of S-adenosylmethionine levels, DNA methyltransferase (DNMT)-1/3a/3b mRNA, and DNA methylation of promoters for suppressor of cytokine signaling (SOCS)-1/3. Reductions of cardiac IGF-1 mRNA and phosphorylated IGF-1 receptors were also restored. Thus, B12 is a promising option for preventing diabetic cardiomyopathy via ROS reduction and IGF-1 retrieval through DNMT-SOCS1/3 signaling.
A neural crest cell isotropic-to-nematic phase transition in the developing mammalian gut
Authors: Chevalier Nicolas R. , Ammouche Yanis , Gomis Anthony , Langlois Lucas , Guilbert Thomas , Bourdoncle Pierre , Dufour Sylvie 
Published: June 2021

AbstractWhile the colonization of the embryonic gut by neural crest cells has been the subject of intense scrutiny over the past decades, we are only starting to grasp the morphogenetic transformations of the enteric nervous system happening in the fetal stage. Here, we show that enteric neural crest cell transit during fetal development from an isotropic cell network to a square grid comprised of circumferentially-oriented cell bodies and longitudinally-extending interganglionic fibers. We present ex-vivo dynamic time-lapse imaging of this isotropic-to-nematic phase transition and show that it occurs concomitantly with circular smooth muscle differentiation in all regions of the gastrointestinal tract. Using conditional mutant embryos with enteric neural crest cells depleted of β1-integrins, we show that cell-extracellular matrix anchorage is necessary for ganglia to properly reorient. We demonstrate by whole mount second harmonic generation imaging that fibrous, circularly-spun collagen I fibers are in direct contact with neural crest cells during the orientation transition, providing an ideal orientation template. We conclude that smooth-muscle associated extracellular matrix drives a critical reorientation transition of the enteric nervous system in the mammalian fetus.
The Relevance of the Availability of Visual Speech Cues During Adaptation to Noise-Vocoded Speech
Authors: Trotter Antony S. , Banks Briony , Adank Patti 
Published: June 2021

Purpose
This study first aimed to establish whether viewing specific parts of the speaker's face (eyes or mouth), compared to viewing the whole face, affected adaptation to distorted noise-vocoded sentences. Second, this study also aimed to replicate results on processing of distorted speech from lab-based experiments in an online setup.

Method
We monitored recognition accuracy online while participants were listening to noise-vocoded sentences. We first established if participants were able to perceive and adapt to audiovisual four-band noise-vocoded sentences when the entire moving face was visible (AV Full). Four further groups were then tested: a group in which participants viewed the moving lower part of the speaker's face (AV Mouth), a group in which participants only see the moving upper part of the face (AV Eyes), a group in which participants could not see the moving lower or upper face (AV Blocked), and a group in which participants saw an image of a still face (AV Still).

Results
Participants repeated around 40% of the key words correctly and adapted during the experiment, but only when the moving mouth was visible. In contrast, performance was at floor level, and no adaptation took place, in conditions when the moving mouth was occluded.

Conclusions
The results show the importance of being able to observe relevant visual speech information from the speaker's mouth region, but not the eyes/upper face region, when listening and adapting to distorted sentences online. Second, the results also demonstrated that it is feasible to run speech perception and adaptation studies online, but that not all findings reported for lab studies replicate.

Supplemental Material

https://doi.org/10.23641/asha.14810523
Tracking down the origin of superbubbles and supergiant shells in the Magellanic Clouds with Minkowski tensor analysis
Authors: Collischon Caroline , Sasaki Manami , Mecke Klaus , Points Sean D. , Klatt Michael A. 
Published: June 2021

Aims.We develop an automatic bubble-recognition routine based on Minkowski functionals (MF) and tensors (MT) to detect bubble-like interstellar structures in optical emission line images.Methods.Minkowski functionals and MT are powerful mathematical tools for parameterizing the shapes of bodies. Using the papaya2-library, we created maps of the desired MF or MT of structures at a given window size. We used maps of the irreducible MTψ2, which is sensitive to elongation, to find filamentary regions in Hα, [S II], and [O III] images of the Magellanic Cloud Emission Line Survey. Using the phase ofψ2, we were able to draw lines perpendicular to each filament and thus obtain line-density maps. This allowed us to find the center of a bubble-like structure and to detect structures at different window sizes.Results.The detected bubbles in all bands are spatially correlated to the distribution of massive stars, showing that we indeed detect interstellar bubbles without large spatial bias. Eighteen out of 59 supernova remnants in the Large Magellanic Cloud (LMC) and 13 out of 20 superbubbles are detected in at least one wavelength. The lack of detection is mostly due to surrounding emission that disturbs the detection, a too small size, or the lack of a (circular) counterpart in our emission line images. In line-density maps at larger scales, maxima can be found in regions with high star formation in the past, often inside supergiant shells (SGS). In SGS LMC 2, there is a maximum west of the shell where a collision of large gas clouds is thought to have occurred. In the Small Magellanic Cloud (SMC), bubble detection is impaired by the more complex projected structure of the galaxy. Line maps at large scales show large filaments in the SMC in a north-south direction, especially in the [S II] image. The origin of these filaments is unknown.
Stability of polycyclic aromatic hydrocarbon clusters in protoplanetary discs
Authors: Lange K. , Dominik C. , Tielens A. G. G. M. 
Published: June 2021

Context. The infrared signature of polycyclic aromatic hydrocarbons (PAHs) is present in many protostellar discs, and these species are thought to play an important role in the heating of the gas in the photosphere.
Aims. We consider PAH cluster formation as one possible cause for non-detections of PAH features in protoplanetary discs. We test the necessary conditions for cluster formation and cluster dissociation by stellar optical and far-UV photons in protoplanetary discs using a Herbig Ae/Be and a T Tauri star disc model.
Methods. We perform Monte Carlo and statistical calculations to determine dissociation rates for coronene, circumcoronene, and circumcoronene clusters with sizes of between 2 and 200 cluster members. By applying general disc models to our Herbig Ae/Be and T Tauri star model, we estimate the formation rate of PAH dimers and compare these with the dissociation rates.
Results. We show that the formation of PAH dimers can take place in the inner 100 AU of protoplanetary discs in sub-photospheric layers. Dimer formation takes seconds to years, allowing them to grow beyond dimer size in a short time. We further demonstrate that PAH clusters increase their stability while they grow when they are located beyond a critical distance that depends on stellar properties and PAH species. The comparison with the local vertical mixing timescale allows a determination of the minimum cluster size necessary for the survival of PAH clusters.
Conclusions. Considering the PAH cluster formation sites, cluster survival in the photosphere of the inner disc of Herbig stars is unlikely because of the high UV radiation. For the T Tauri stars, survival of coronene, circumcoronene, and circumcircumcoronene clusters is possible, and cluster formation should be considered as one possible explanation for low PAH detection rates in T Tauri star discs.
Drei Dekaden Darmresektionen bei Patienten mit M. Crohn
Authors: Iesalnieks Igors , Agha Ayman , Dederichs Frank , Schlitt Hans Jürgen 
Published: June 2021

Zusammenfassung
Einleitung Die Behandlung des M. Crohn – vor allem die medikamentöse – erlebte in den letzten 20–30 Jahren einen starken Wandel. Die vorliegende Beobachtungsstudie fasst alle Darmresektionen wegen M. Crohn zusammen, die in den letzten 3 Dekaden an 2 großen spezialisierten Zentren durchgeführt wurden. Die perioperativen Trends und Entwicklungen sollten identifiziert werden.
Methoden Eingeschlossen wurden alle Darmresektionen bei M. Crohn. Ausschlusskriterien waren: Resektionen bei Malignität, abdominoperineale Rektumexstirpationen wegen Crohn-Analfisteln, ausschließliche Stomaanlagen und -rückverlagerungen und Resektionen, die einen anderen Grund als M. Crohn hatten. Die Daten wurden von 1992 bis 2004 retrospektiv und danach prospektiv gesammelt. Ausgewertet wurden 6 Zeiträume: 1992–1995, 1996–2000, 2001–2005, 2006–2010, 2011–2015 und 2016–2020.
Ergebnisse Es wurden 811 Darmresektionen ausgewertet. Zwischen 2000 und 2015 konnten gleich mehrere sehr starke Trends beobachtet werden: erhöhte präoperative Einnahme von Immunmodulatoren und Biologika, sinkende präoperative Steroideinnahme, Verzicht auf präoperative Darmvorbereitung, erhöhter Anteil an voroperierten Patienten und Patienten, die sich mit penetrierendem Befallsmuster vorstellten, Einführung neuer Operationstechniken (Laparoskopie, Stapleranastomosen) und signifikante Erhöhung der postoperativen Morbidität und Stomachirurgie. In den letzten 5 Jahren seit 2016 zeigten sich folgenden Entwicklungen: signifikant weniger Operationen unter Steroideinnahme oder Immunmodulatoren, signifikant mehr Operationen unter Biologika, Wiedereinführung der präoperativer Darmvorbereitung, starke Reduktion der Morbidität und Stomaanlage, höheres Alter der Patienten, weniger aktive Raucher, weniger Operationen wegen penetrierenden Befallsmusters, sehr starker Anstieg laparoskopischer Operationen.
Schlussfolgerung Vor allem in den letzten 5 Jahren scheint die Crohn-Chirurgie wesentlich sicherer und weniger invasiv zu werden. Die Daten können jedoch nicht auf größere Populationen übertragen werden.
COVID-19 and the Ophthalmology Residency Match: Data from Applicants' Perspectives
Authors: Steren Benjamin , Parikh Ankur , Ahmed Bilal , Young Benjamin , Sridhar Jayanth , Kombo Ninani 
Published: June 2021

Abstract
Background The coronavirus disease 2019 (COVID-19) pandemic has had a profound impact on medical education, particularly for those applying to residency programs in 2020 to 2021. This study describes the challenges for potential ophthalmology residency applicants so that residency leadership can make informed decisions about changes to the process.
Methods A survey was distributed electronically via social media and medical school ophthalmology interest groups from June 18, 2020 to July 2, 2020 to individuals interested in applying to ophthalmology residency in the United States. Survey questions included demographics and perceived impacts of COVID-19 on ability, confidence, intention to apply, and perceptions toward changes in the application process for the 2020 to 2021 ophthalmology residency application cycle.
Results One-hundred sixteen total responses were received. Eighty-six responses (74%) were from individuals intending to apply in the 2020 to 2021 application cycle. Most respondents (86%) felt that their application would be affected by COVID-19 with 51% feeling less confident. Only four (5%) felt that they could adequately compile a rank list following a video interview, and over half (51%) anticipated applying to more programs than they originally intended. Academic plans of seven (8%) respondents were significantly altered via deferral of application or cancellation of a research year. Thirty-nine (45%) students reported delayed ophthalmology electives, with less than half (41%) feeling that they had adequate clinical exposure to be prepared for residency.
Conclusion The COVID-19 pandemic has had a substantial impact on the 2020 to 2021 ophthalmology residency application cycle. As stakeholders begin to approach this cycle, these findings will help them make effective and informed decisions to create the best overall experience for all involved.
Profound Hypotonia and Respiratory Failure due to Suspected Nemaline Myopathy in a Preterm Infant
Authors: Akuamoah-Boateng Gloria , Stetson Raymond C. , Kaemingk Bethany D. , Bieber David A. , Brumbaugh Jane E. 
Published: June 2021

AbstractCongenital myopathies, such as nemaline myopathy, may present with hypotonia and respiratory failure in the neonatal period. Respiratory function can be further compromised in affected infants by the development of chylous effusions. We present the case of a preterm male infant born at 326/7 weeks' gestation, who was profoundly hypotonic and required intubation at birth. His clinical course progressed from acute to chronic respiratory failure with mechanical ventilation dependence. He developed bilateral chylous pleural effusions during the newborn period. Whole exome sequencing identified an ACTA1 gene mutation leading to the presumed diagnosis of nemaline myopathy. This case highlights the need to include congenital myopathies in the differential for a preterm newborn with hypotonia and respiratory failure.
Immunological Testing in Assisted Reproductive Technology
Authors: Odendaal Joshua , Quenby Siobhan 
Published: June 2021

AbstractFetal implantation requires carefully orchestrated involvement of the maternal immune system. Aberrant function within implantation has been suggested as a cause of implantation failure. The emergence of immunological theories of miscarriage has led to immunological testing as an adjuvant treatment in assisted reproductive technology; however, it remains controversial, with mixed evidence both for immunological cause and the benefits of immunological testing. Literature on common methods of immunological testing within assisted reproductive technology is reviewed including those of peripheral and uterine natural killer cells, chronic endometritis, and T-helper cells cytokine ratio. There is little consensus in the evidence on immunological testing in the context of recurrent implantation failure. The field is limited by a lack of uniformity in approach to testing and heterogeneity of the pathophysiological cause. Nevertheless, the maternal immune system is heavily involved in implantation and the new era of personalized medicine ensures that a more defined approach to immunological testing will be achieved.
Polycaprolactone Mesh for Asian Rhinoplasty: Outcomes and Complications of Composite Septal Extension Graft Compared to Mesh-Only Graft
Authors: Hyun Seung , Cho Seung Woo , Baek Rong-Min 
Published: June 2021

AbstractDespite the great demand of aesthetic rhinoplasty in Asian population, it is difficult to obtain the lasting ideal tip projection along with lengthening of the nose due to the small and weak nasal septum. The shortage of available septal cartilage to work with is another major obstacle. A retrospective study was conducted between January 2017 and December 2019 in Seoul, Korea. A total of 774 patients underwent septorhinoplasty using polycaprolactone (PCL) mesh for the cosmetic enhancement of the nasal tip and the projection. Comparisons of aesthetic outcomes, patients' satisfaction surveys, and complications were performed between PCL mesh-only group and composite PCL group. Of all the patients, 97.5% of the patients in composite PCL group were rated more than 3 scores in aesthetic outcomes, whereas 90.4% in mesh-only group (p-value = 0.0002). About 96.7% of the patients with composite PCL rated their satisfaction level as more than satisfied, whereas 94.3% in mesh-only group (p-value = 0.0365). Overall, there were 17 patients in composite PCL group who exhibited complications including decreased tip projection, deviated nasal tip, mesh infection, and mesh exposure. However, there were two patients who had mesh injection in mesh-only group. Septorhinoplasty with septal extension graft using composite PCL graft provides robust support to the aesthetically modified projection and the lengthened nose without obvious complications on the nasal tip. Such technique allows surgeons to overcome the nature of Asian nose that is weak and small, and also provides satisfaction to patients who desire ideal tip projections and dramatic changes.
Monte Carlo analyses of the fusion neutron and gamma signals from the chromium self-powered detector
Authors: Raj Prasoon , Angelone Maurizio , Fischer Ulrich , Klix Axel 
Published: June 2021

To test the applicability of self-powered detectors (SPDs) for radiation monitoring in fusion reactor blankets, several irradiation tests have been undertaken with the ad hoc designed Cr-SPD, which presents the novelty of using chromium as the emitter material. This detector was exposed to an intense 60Co gamma-ray source, and to the 14 MeV neutrons produced by the D–T fusion reaction. Detailed analyses of the measured signals have been done here using a Monte Carlo modeling technique. We describe the simulations of the fusion neutron and gamma tests of the Cr-SPD, and compare their results with the experimental ones. Keeping in view the difficulty in computational reproduction of the sophisticated nuclear-electrical phenomena behind low-level SPD signals, our model is found to perform well, giving correct electrical polarities and orders of magnitude of the signals, as well as valuable insights into their different components. Our experience has highlighted the deficits and the needed improvements for the traditional SPD simulation techniques for prompt signal analyses.
Monitoring the COVID-19 epidemic with nationwide telecommunication data
Authors: Persson Joel , Parie Jurriaan F. , Feuerriegel Stefan 
Published: June 2021

SignificanceTo manage the current epidemic, policymakers need tools that help them in evidence-based decision making. In particular, decision support is needed to assess policy measures by their ability to enforce social distancing. A solution is offered by our work: We use mobility data derived from telecommunication metadata as a proxy for social distancing, and, based on this, we demonstrate how the effect of policy measures can be monitored in a nationwide setting. Compared to the status quo, this provides a clear benefit: Monitoring policy measures through case counts has a substantial time lag, whereas our approach allows for monitoring in near real time.
How Saudi migrants’ metapragmatic judgments of Arabic L1 nonverbal greetings change after intense and prolonged exposure to English
Authors: Alshahrani Hessa , Dewaele Jean-Marc 
Published: June 2021

Abstract
This study investigates the impact of spending more than three years in an English environment on Saudi migrants’ metapragmatic judgments of Arabic L1 nonverbal greetings and their personality traits. Participants are 437 adults comprising three groups: Saudi L2 speakers of English in the UK, Saudis in Saudi Arabia, and British L1 speakers of English in the UK. They observed and rated an audiovisual stimulus illustrating Saudi L1 nonverbal greeting behaviours of handshake and cheek-to-cheek kiss. Statistical analyses revealed that appropriateness ratings by Saudi migrants in the UK diverged from those by Saudis in Saudi Arabia and approximated those of English L1 users in the UK. Moreover, appropriateness ratings by Saudi migrants were differently associated with personality profiles, which differed for three traits between the two Saudi groups. These findings suggest change in L1 metapragmatic judgements as well as personality as a result of prolonged and intense exposure to an L2. The results are interpreted in the light of Cook’s (2012) concept of multicompetence.
Tanaka–Ito α-continued fractions and matching
Authors: Carminati Carlo , Langeveld Niels , Steiner Wolfgang 
Published: June 2021

Abstract
Two closely related families of α-continued fractions were introduced in 1981: by Nakada on the one hand, by Tanaka and Ito on the other hand. The behavior of the entropy as a function of the parameter α has been studied extensively for Nakada’s family, and several of the results have been obtained exploiting an algebraic feature called matching. In this article we show that matching occurs also for Tanaka–Ito α-continued fractions, and that the parameter space is almost completely covered by matching intervals. Indeed, the set of parameters for which the matching condition does not hold, called the bifurcation set, is a zero measure set (even if it has full Hausdorff dimension). This property is also shared by Nakada’s α-continued fractions, and yet there also are some substantial differences: not only does the bifurcation set for Tanaka–Ito continued fractions contain infinitely many rational values, it also contains numbers with unbounded partial quotients.