bluuebunny/crossref_metadata_2025_split huggingface dataset:
Eliminating biasing signals in lung cancer images for prognosis predictions with deep learning
Authors: van Amsterdam W. A. C. , Verhoeff J. J. C. , de Jong P. A. , Leiner T. , Eijkemans M. J. C. 
Published: December 2019

AbstractDeep learning has shown remarkable results for image analysis and is expected to aid individual treatment decisions in health care. Treatment recommendations are predictions with an inherently causal interpretation. To use deep learning for these applications in the setting of observational data, deep learning methods must be made compatible with the required causal assumptions. We present a scenario with real-world medical images (CT-scans of lung cancer) and simulated outcome data. Through the data simulation scheme, the images contain two distinct factors of variation that are associated with survival, but represent a collider (tumor size) and a prognostic factor (tumor heterogeneity), respectively. When a deep network would use all the information available in the image to predict survival, it would condition on the collider and thereby introduce bias in the estimation of the treatment effect. We show that when this collider can be quantified, unbiased individual prognosis predictions are attainable with deep learning. This is achieved by (1) setting a dual task for the network to predict both the outcome and the collider and (2) enforcing a form of linear independence of the activation distributions of the last layer. Our method provides an example of combining deep learning and structural causal models to achieve unbiased individual prognosis predictions. Extensions of machine learning methods for applications to causal questions are required to attain the long-standing goal of personalized medicine supported by artificial intelligence.
Zn2+ and mPTP mediate resveratrol-induced myocardial protection from endoplasmic reticulum stress
Authors: He Yifei , Fu Yu , Xi Mengyao , Zheng Huan , Zhang Yidong , Liu Yulin , Zhao Yang , Xi Jinkun , He Yonggui 
Published: December 2019

AbstractResveratrol displays cardioprotective activity; however, its mechanism of action remains unclear. In the current study, resveratrol-induced myocardial protection from endoplasmic reticulum stress (ERS) was investigated, focusing on the roles of Zn2+ and the mitochondrial permeability transition pore (mPTP). We found, using the MTT/LDH kit, that 2-DG-induced ERS significantly decreased H9c2 cell viability. Resveratrol markedly inhibited the expression of endoplasmic reticulum chaperone GRP 78/94 and ERS-related apoptosis proteins CHOP, Caspase12, and JNK induced by 2-DG. The zinc ion chelator TPEN, and ERK/GSK-3β inhibitors PD98059 and SB216763 and their siRNAs blocked resveratrol function. The AKT inhibitor LY294002 and siRNA did not alter the action of resveratrol. In addition, resveratrol significantly increased the phosphorylation of ERK and GSK-3β. Resveratrol prevented 2-DG-induced mPTP opening and increased intracellular Zn2+ concentration indicated by TMRE and Newport Green DCF fluorescence intensity, which were further abrogated by ERK/GSK-3β inhibitors and siRNAs. Our data suggested that resveratrol protected cardiac cells from ERS by mobilizing intracellular Zn2+ and preventing mPTP opening through the ERK/GSK-3β but not PI3K/AKT signaling pathway.
Intra and Inter-Rater Reliability for Deep Neck Flexor and Neck Extensor Muscle Endurance Tests in Subjects with and without Subclinical Neck Pain
Authors: Alahmari Khalid A. , Reddy Ravi S. , Silvian Paul , Ahmad Irshad , Kakarparthi Venkata Nagaraj , Rengaramanujam Kanagaraj 
Published: December 2019

Abstract
Purpose Deep neck flexor (DNF) and neck extensor (NE) muscle endurance tests are a part of standard assessment procedure in routine physical therapy practice and these tests needs to be reliable.
Materials and Methods Intra-rater (between-day) and inter-rater (within-day) reliability was assessed for 2 neck muscle endurance tests in 26 subclinical neck pain and 31 normal subjects by 2 blinded assessors. The tests conducted included 1) DNF endurance test performed in supine and 2) NE muscle endurance test performed in prone position.
Results and discussion The Intra-rater and inter-rater reliability was determined by means of Intra Class Correlation (ICC), with 95% confidence intervals. The intra rater reliability testing showed good agreement for both DNF (ICC=0.76 and 0.78) and NE muscle endurance (ICC=0.75 and 0.76) tests. Meanwhile, the inter-rater reliability showed moderate to good agreement for both DNF (ICC – 0.58 and 0.61) and NE muscle endurance tests (ICC – 0.57 and 0.74) in subjects with subclinical neck pain. Subclinical neck pain subjects had a significantly lower endurance holding times compared to normal (p<0.001).
Conclusion The intra and inter rater reliability ranged from moderate to good agreement. Neck flexor and extensor muscle endurance can be measured reliably in a clinical setup in subjects with subclinical neck pain.
Definitive therapy of colonic angioectasia by submucosal coagulation
Authors: Sriram Nagaraj , Bar-Yishay Iddo , Kumarasinghe Priyanthi , Yusoff Ian , Segarajasingam Dev , Bourke Michael J. , Raftopoulos Spiro 
Published: December 2019

Abstract
Background and study aims Colonic angioectasia are the most common vascular lesions in the gastrointestinal tract and are among the most common causes for chronic or recurrent lower gastrointestinal bleeding. Endoscopic treatment involves a variety of techniques, all of which focus on destruction of the mucosal abnormality. However, recurrent bleeding after endoscopic treatment is common, with more than one treatment frequently necessary. We report a technique for definitive treatment of colonic angioectasia by targeting the feeding submucosal vessel.
Patients and methods Analogous to endoscopic mucosal resection, a submucosal injection is made beneath the target lesion which is then removed by electrocautery snare resection of the mucosal lesion. The exposed feeding vessel is then destroyed by application of coagulation current. The resection defect is closed by clips.
Results Six patients with a total of 14 colonic angioectasia were treated over the study period. All lesions were destroyed without adverse events.
Conclusion Elevation, hot snare resection and coagulation (ESC) of the visible vessel for treating colonic angioectasia appears safe and effective. Larger prospective comparative studies are required to assess its specific role.
Secure Linking of Data from Population-Based Cancer Registries with Healthcare Data to Evaluate Screening Programs
Authors: Bartholomäus Sebastian , Siegert Yannik , Hense Hans Werner , Heidinger Oliver 
Published: December 2019

Abstract
Background The evaluation of population-based screening programs, like the German Mammography Screening Program (MSP), requires collection and linking data from population-based cancer registries and other sources of the healthcare system on a case- specific level. To link such sensitive data, we developed a method that is compliant with German data protection regulations and does not require written individual consent.
Methods Our method combines a probabilistic record linkage on encrypted identifying data with ‘blinded anonymisation’. It ensures that all data either are encrypted or have a defined and measurable degree of anonymity. The data sources use a software to transform plain-text identifying data into a set of irreversibly encrypted person cryptograms, while the evaluation attributes are aggregated in multiple stages and are reversibly encrypted. A pseudonymisation service encrypts the person cryptograms into record assignment numbers and a downstream data-collecting centre uses them to perform the probabilistic record linkage. The blinded anonymisation solves the problem of quasi-identifiers within the evaluation data. It allows selecting a specific set of the encrypted aggregations to produce data export with ensured k-anonymity, without any plain-text information. These data are finally transferred to an evaluation centre where they are decrypted and analysed. Our approach allows creating several such generalisations, with different resulting suppression rates allowing dynamic balance information depth with privacy protection and also highlights how this affects data analysability.
Results German data protection authorities approved our concept for the evaluation of the impact of the German MSP on breast cancer mortality. We implemented a prototype and tested it with 1.5 million simulated records, containing realistically distributed identifying data, calculated different generalisations and the respective suppression rates. Here, we also discuss limitations for large data sets in the cancer registry domain, as well as approaches for further improvements like l-diversity and how to reduce the amount of manual post-processing.
Conclusion Our approach enables secure linking of data from population-based cancer registries and other sources of the healthcare system. Despite some limitations, it enables evaluation of the German MSP program and can be generalised to be applicable to other projects.
Genetic analysis of postoperative recurrence of pancreatic cancer potentially owing to needle tract seeding during EUS-FNB
Authors: Kawabata Hidemasa , Miyazawa Yuki , Sato Hiroki , Okada Tetsuhiro , Hayashi Akihiro , Iwama Takuya , Fujibayashi Shugo , Goto Takuma , Sasajima Junpei , Takauji Shuhei , Fujiya Mikihiro , Torimoto Yoshihiro , Tanino Mishie , Omori Yuko , Ono Yusuke , Karasaki Hidenori , Mizukami Yusuke , Okumura Toshikatsu 
Published: December 2019

Abstract
Background and study aims Needle tract seeding during endoscopic ultrasound fine-needle biopsy (EUS-FNB) remains a concern. We investigated whether such seeding occurred in a patient with pancreatic ductal adenocarcinoma (PDA).
Patient and methods Surgically resected and EUS-FNB-derived specimens were genotyped to determine if a gastric wall tumor that emerged 3 years after curative resection of an early-stage PDA was clonally related to the original tumor.
Results The gastric tumor histologically resembled the primary PDA; the lesions also shared KRAS, SMAD4, and RNF43 mutations. Genotyping of the preoperative EUS-FNB specimen, in which cancer was not detected, nevertheless revealed mutations that were identical to those in the resected primary and recurrent tumors. While the primary PDA had a low frequency of mutant SMAD4, such mutations were highly prevalent in both the EUS-FNB and recurrent tumor specimens.
Conclusions The genetic lineages of sampled tissues from our patient revealed that needle tract seeding may have incidentally occurred when a subset of neoplastic cells within a heterogeneous tumor (i. e., an aggressive clone) was targeted during EUS-FNB.
Predictive Validity of Each Item of the
8-Item Short-Form Health Survey for All-Cause
Mortality in Japanese patients with type 2
diabetes: A prospective Cohort Study (Diabetes
Distress and Care Registry at Tenri [DDCRT
19])
Authors: Hayashino Yasuaki , Okamura Shintaro , Tsujii Satoru , Ishii Hitoshi ,   for the Diabetes Distress and
                                                  Care Registry at Tenri Study Group*
Published: December 2019

Abstract
Aims While health-related quality of life
(HRQOL) is reported to be associated with
mortality, this assessment was made using surveys
with a large number of questions, not specifically
focused on populations with diabetes, or in
western countries alone. We thus evaluated the
predictive validity of summary scores, and each
item score of the 8-Item Short-Form Health Survey
in Japanese individuals with type-2 diabetes.
Materials and Methods Longitudinal data
from 3269 individuals with diabetes were obtained
from a large Japanese diabetes registry. To assess
the independent correlation between the 10-point
scores of the SF-8 physical component summary
(PCS) and mental component summary (MCS), each
item score, and all-cause mortality, the Cox
proportional hazards model was used with
adjustment for potential confounders.
Results Mean cohort parameters included age
(64.9 years [SD 11.2]), body mass index
(24.6 kg/m2 [SD, 3.9]), and HbA1c level
(7.5% [SD, 1.2]; or 58.6 mmol/mol [SD, 12.7]). We
recorded 248 deaths during the median follow-up of
7.2 years (incidence ratio, 12.2 per 1000
person-years). Multivariable-adjusted HRs for
all-cause mortality were 0.780 (95%CI,
0.674–0.902; p=0.001) and 0.776 (95%CI,
0.656–0.917; p=0.003), respectively, for 10-point
increment of PCS and MCS scores. Higher score of
any single item of SF-8 was associated with lower
risk of all-cause mortality even after adjusting
for possible confounders.
Conclusions As assessed by the SF-8, higher
PCS, MCS, and any single 1-item scores were
associated with lower risk of all-cause mortality
in Japanese individuals with type 2 diabetes.
Pharmakologisches Neuroenhancement in Deutschland
Authors: Schäfer Markus 
Published: December 2019

ZusammenfassungHintergrund Die Angaben zur Verbreitung des pharmakologischen Neuroenhancements (pNE) in Deutschland variieren stark. Der Beitrag diskutiert, inwieweit dieser Umstand methodischen Aspekten der Prävalenzstudien geschuldet sein könnte.Methode Der Beitrag gibt einen Überblick zum aktuellen Forschungsstand und beleuchtet methodische Probleme der Prävalenzforschung in Deutschland.Ergebnisse Die Prävalenzangaben variieren je nach Erhebungsmethode, abgefragtem Zeitpunkt der Einnahme und untersuchten Zielgruppen und Stoffen bei verschreibungspflichtigen und illegalen Substanzen zwischen einem und 39%. Für frei erhältliche Mittel werden z. T. höhere Prävalenzen berichtet. Es lassen sich 4 große methodische Probleme der Forschung identifizieren: 1.) Die Heterogenität der Definitionen, 2.) die Heterogenität der Befragungsmethoden und die Qualität der Stichproben(ziehungen), 3.) Defizite bei der Frageformulierung, 4.) das Fehlen wichtiger Angaben in den zugehörigen Veröffentlichungen.Schlussfolgerung Verlässliche Aussagen zur Verbreitung von pNE in Deutschland sind schwierig. Zwischen den Untersuchungen bestehen inhaltlich und methodisch große Unterschiede, die Ergebnisse lassen sich nur bedingt vergleichen. Notwendig sind regelmäßige bevölkerungsrepräsentative Erhebungen auf Basis einheitlicher Definitionen.
Does Heart Valve Team Risk Assessment Predict Outcomes after Transcatheter Aortic Valve Replacement?
Authors: Catalano Michael A. , Rutkin Bruce , Kohn Nina , Hartman Alan , Yu Pey-Jen 
Published: December 2019

AbstractConsideration for transcatheter aortic valve replacement (TAVR) necessitates an integrated risk assessment by members of the Heart Valve Team. The utility of the integrated risk assessment for predicting TAVR outcomes is not established. This article aims to compare the utility of the integrated risk assessment to that of the Society of Thoracic Surgeons Predicted Risk of Mortality (STS-PROM) score for predicting patient outcomes after TAVR. A total of 274 patients who underwent TAVR from January 2016 to August 2017 were included in this study. Patients were deemed intermediate or high risk by two surgeons on the Heart Valve Team based on an integrated risk assessment that incorporates the STS-PROM score, fragility measures, end-organ dysfunction, and surgeon evaluation. Patients were also deemed low, intermediate, or high risk based solely on their STS-PROM scores of <3%, ≥3% to <8%, and ≥8%, respectively. Differences in postoperative outcomes between intermediate- and high-risk groups as categorized by the integrated risk assessment versus STS-PROM were compared. There were no statistically significant differences in postoperative outcomes between patients who were deemed high and intermediate risk by the Heart Valve Team risk assessment. In contrast, postoperative complication rates were significantly higher in patients deemed high risk as compared with intermediate risk by STS-PROM. Integrated risk assessment by the Heart Valve Team is not superior to STS-PROM in predicting postoperative outcomes in patients undergoing TAVR.
Bots fired: examining social bot evidence in online mass shooting conversations
Authors: Schuchard Ross , Crooks Andrew , Stefanidis Anthony , Croitoru Arie 
Published: December 2019

AbstractMass shootings, like other extreme events, have long garnered public curiosity and, in turn, significant media coverage. The media framing, or topic focus, of mass shooting events typically evolves over time from details of the actual shooting to discussions of potential policy changes (e.g., gun control, mental health). Such media coverage has been historically provided through traditional media sources such as print, television, and radio, but the advent of online social networks (OSNs) has introduced a new platform for accessing, producing, and distributing information about such extreme events. The ease and convenience of OSN usage for information within society’s larger growing reliance upon digital technologies introduces potential unforeseen risks. Social bots, or automated software agents, are one such risk, as they can serve to amplify or distort potential narratives associated with extreme events such as mass shootings. In this paper, we seek to determine the prevalence and relative importance of social bots participating in OSN conversations following mass shooting events using an ensemble of quantitative techniques. Specifically, we examine a corpus of more than 46 million tweets produced by 11.7 million unique Twitter accounts within OSN conversations discussing four major mass shooting events: the 2017 Las Vegas concert shooting, the 2017 Sutherland Springs church chooting, the 2018 Parkland School Shooting and the 2018 Santa Fe school shooting. This study’s results show that social bots participate in and contribute to online mass shooting conversations in a manner that is distinguishable from human contributions. Furthermore, while social bots accounted for fewer than 1% of total corpus user contributors, social network analysis centrality measures identified many bots with significant prominence in the conversation networks, densely occupying many of the highest eigenvector and out-degree centrality measure rankings, to include 82% of the top-100 eigenvector values of the Las Vegas retweet network.
Detailed characterisation of the LEIR intensity limitations for a Pb ion beam
Authors: Saa Hernandez A , Bartosik H , Biancacci N , Hirlander S , Moreno D , Zampetakis M 
Published: December 2019

Abstract
The equilibrium emittance of the Pb beam in the CERN Low Energy Ion Ring (LEIR) results from the interplay of electron cooling and heating processes, as intra-beam scattering and space charge. In this paper we present the measurements of the emittance evolution as a function of intensity, working point and resonance excitation, and compare them with the simulations of the heating processes. Optimum settings for normal and skew sextupoles have been found for the compensation of resonances excited by the lattice.
Space Charge Driven Resonances in the CERN PS
Authors: Asvesta F , Bartosik H , Huschauer A , Papaphilippou Y 
Published: December 2019

Abstract
In the CERN Proton Synchrotron space charge driven resonances are excited around the operational working point due to the periodicity of the optics functions. In this paper, the resonances are studied using analytical methods, i.e. the evaluation of the resonance driving terms connected to the space charge potential of Gaussian distributions. Furthermore, the resonances are characterized in measurements and simulations for various beams. The beams considered are different in terms of brightness, in order to study the dependence of the resonance strength on the space charge force.
Effect of beam-beam kick on electron beam quality in first bunched electron cooler
Authors: Seletskiy S. , Blaskiewicz M. , Fedotov A. , Kayran D. , Kewisch J. 
Published: December 2019

Abstract
The low energy RHIC electron cooler (LEReC) currently under commissioning at BNL is going to be the first non-magnetized bunched electron cooler (EC). For successful cooling LEReC requires that the electrons in the cooling section (CS) have small angles with respect to co-propagating ions. Since there is no strong magnetic field in the CS, the effects of ions on both the trajectory and focusing of the e-bunches is critical. In this paper we consider the ion beam kick on the electron bunches and derive requirements to the respective alignment of electron and ion beams in non-magnetized coolers.
Development of a beam window protection system for the J-PARC linac
Authors: Takahashi H , Hatakeyama S , Sawabe Y , Miyao T , Ishiyama T , Suzuki T 
Published: December 2019

Abstract
In J-PARC Linac, some beam dumps are used for beam conditioning and study. A beam window is installed in the beam line of the beam dump. In 2018, a beam study using a 0- degree beam dump in the Linac resulted in damage to the beam window when the beam intensity has exceeded the tolerance. So as not to repeat this experience, it was decided to immediately advance the development of a beam window protection system. The present paper describes the protection system built as an emergency measure and the tests of its performance.
Time Varying RF Phase Noise for Longitudinal Emittance Blow-up
Authors: Albright S , Quartullo D 
Published: December 2019

Abstract
RF phase noise was shown to be effective for controlled longitudinal emittance blow-up in the Proton Synchrotron Booster (PSB) at CERN during beam tests in 2017, with further developments in 2018. At CERN, RF phase noise is used operationally in the Super Proton Synchrotron (SPS) and Large Hadron Collider (LHC). In this paper we show that it is suitable for operation with a variety of beam types in the PSB. In the PSB the synchrotron frequency changes by approximately a factor 4 during the 500 ms acceleration ramp, requiring large changes in the frequency band of the noise. During 2018, a new method of calculating the noise parameters has been demonstrated, which gives upper and lower bounds to the noise frequency band that are smoothly varying through the ramp. The new calculation method has been applied to operational beams accelerated in both single and double RF harmonics, the final results are presented here.
Evaluation of 2-D Transverse Beam Profile Monitor Using Gas Sheet at J-PARC LINAC
Authors: Kamiya J , Okabe K. , Kinsho M. , Moriya K. , Yamada I. , Ogiwara N. , Hikichi Y. , Wada K. 
Published: December 2019

Abstract
A transverse beam profile monitor, which detects ions or luminescence generated by the interaction between the beam and the gas molecules distributed in a sheet shape, has been developed in the J-PARC LINAC. To know about the gas density distribution of the sheet-shaped gas, which affects the intensity distribution of the detected signal, the calculation by the Monte Carlo simulation code was performed. The calculation results showed that the gas with a narrow width along beam direction distributes enough uniformly within a realistic beam cross-sectional size. In addition, the unsaturated region against the MCP voltage and the injected gas pressure are evaluated based on the measurement with a beam. The results showed that the measurement in the low injected gas pressure with the appropriate applied voltage range is important to measure the beam profile in the unsaturated region.
Lasers for Novel Accelerators
Authors: Gizzi L.A. , Koester P. , Labate L. , Mathieu F. , Mazzotta Z. , Toci G. , Vannini M. 
Published: December 2019

Abstract
Novel accelerator schemes are rapidly emerging in the wake of laser-plasma acceleration research and involve advanced high-power laser drivers for their operation. Significant progress has been made in laser performance during the past decade, including repetition rate, average and peak power, and footprint, making these systems attractive for many applications, including novel accelerators. Here we discuss laser driver requirements for the proposed novel accelerator schemes, examine emerging technologies and introduce a viable laser driver concept for a first generation of plasma accelerators.