bluuebunny/crossref_metadata_2025_split huggingface dataset:
Shear wave elastography evaluation of liver, pancreas, spleen and kidneys in patients with familial mediterranean fever and amyloidosis
Authors: Bayramoglu Zuhal , Akyol Sari Zeynep Nur , Koker Oya , Adaletli Ibrahim , Eker Omeroglu Rukiye 
Published: September 2021

Objectives: Amyloid deposits in a visceral organ can contribute to tissue stiffness that could be measured with shear wave elastography (SWE). We aimed to investigate changes in organ stiffness in conjunction with laboratory parameters in patients with Familial Mediterranean Fever (FMF) and amyloidosis. Methods: This prospective study included 27 FMF patients, 11 patients with amyloidosis, and 38 healthy controls. Median shear wave elasticity values of the liver, spleen, both kidneys, and pancreas on SWE were compared among study and control groups. The mean values of CRP (C-reactive protein) and ESR (erythrocyte sedimentation rate) were compared by the t–test and the median of SAA (serum amyloid A protein) was compared with the Mann–Whitney U test between FMF groups with and without amyloidosis. Spearman’s correlation analysis was performed to reveal the association between stiffness values and laboratory parameters. Results: The median liver, spleen, kidney, and pancreas elasticity values were significantly higher in the FMF group with amyloidosis compared to control subjects. The median kidney stiffness values in the FMF group with or without amyloidosis were significantly higher compared to control subjects. Median liver stiffness values in FMF patients with amyloidosis were significantly higher than FMF patients without amyloidosis. There were statistically significant positive correlations between the CRP (p = 0.001, r = 0.56), ESR (p = 0.001, r = 0.61), and SAA (p = 0.002, r = 0.53) levels with spleen stiffness, and CRP (p = 0.006, r = 0.48) and ESR (p = 0.001,r = 0.61) levels with pancreas stiffness, and ESR (p = 0.004, r = 0.51) levels with the left kidney stiffness. Conclusion: SWE could be a potential tool for noninvasive follow-up of FMF patients and also amyloid deposition. Advances in knowledge: Both acute inflammation and amyloidosis in the FMF patients could increase organ stiffness.
Mammography-based radiomics for predicting the risk of breast cancer recurrence: a multicenter study
Authors: Mao Ning , Yin Ping , Zhang Haicheng , Zhang Kun , Song Xicheng , Xing Dong , Chu Tongpeng 
Published: September 2021

Objective: This study aimed to establish a mammography-based radiomics model for predicting the risk of estrogen receptor (ER)-positive, lymph node (LN)-negative invasive breast cancer recurrence based on Oncotype DX and validated it by using multicenter data. Methods: A total of 304 potentially eligible patients with pre-operative mammography images and available Oncotype DX score were retrospectively enrolled from two hospitals. The patients were grouped as training set (168 patients), internal test set (72 patients), and external test set (64 patients). Radiomics features were extracted from the mammography images of each patient. Spearman correlation analysis, analysis of variance, and least absolute shrinkage and selection operator regression were performed to reduce the redundant features in the training set, and the least absolute shrinkage and selection operator algorithm was used to construct the radiomics signature based on selected features. Multivariate logistic regression was utilized to construct classification models that included radiomics signature and clinical risk factors to predict low vs intermediate and high recurrence risk of ER-positive, LN-negative invasive breast cancer in the training set. The models were evaluated with the receiver operating characteristic curve in the training set. The internal and external test sets were used to confirm the discriminatory power of the models. The clinical usefulness was evaluated by using decision curve analysis. Results: The radiomics signature consisting of three radiomics features achieved favorable prediction performance. The multivariate logistic regression model including radiomics signature and clinical risk factors (tumor grade and HER 2) showed good performance with areas under the curve of 0.92 (95% confidence interval [CI] 0.86 to 0.97), 0.88 (95% CI 0.75 to 1.00), and 0.84 (95% CI 0.69 to 0.99) in the training, internal and external test sets, respectively. The DCA indicated that when the threshold probability is ranges from 0.1 to 1.0, the radiomics model adds more net benefit than the “treat all” or “treat none” scheme in internal and external test sets. Conclusion: As a non-invasive pre-operative prediction tool, the mammography-based radiomics model incorporating radiomics and clinical factors show favorable predictive performance for predicting the risk of ER-positive, LN-negative invasive breast cancer recurrence based on Oncotype DX. Advances in knowledge: The mammography-based radiomics model incorporating radiomics and clinical factors shows favorable predictive performance for predicting the risk of ER-positive, LN-negative invasive breast cancer recurrence.
Association between pericoronary adipose tissue attenuation and outcome after second-generation cryoballoon ablation for atrial fibrillation
Authors: Nogami Kai , Sugiyama Tomoyo , Kanaji Yoshihisa , Hoshino Masahiro , Hara Satoshi , Yamaguchi Masao , Hada Masahiro , Sumino Yohei , Misawa Toru , Hirano Hidenori , Ueno Hiroki , Miwa Naoyuki , Yamao Kazuya , Kusa Shigeki , Hachiya Hitoshi , Kakuta Tsunekazu 
Published: September 2021

Objectives: Previous studies reported the association between inflammation and atrial fibrillation (AF). Pericoronary adipose tissue (PCAT) attenuation, PCATA, on cardiac CT angiography (CTA) reflects pericoronary inflammation. We hypothesized that the PCATA predicts AF recurrence after cryoballoon ablation (CBA) for paroxysmal and persistent AF. Methods: We studied 364 patients (median age, 65 years) with persistent (n = 41) and paroxysmal (n = 323) AF undergoing successful first-session second-generation CBA with pre-ablation cardiac CTA. Three-vessel (3V)-PCATA was defined as the mean CT attenuation value of PCAT of all three major coronary arteries. Predictors of AF recurrence during follow-up were evaluated. Results: AF recurrence after the 3-month blanking period was detected in 90 patients (24.7%) during the median follow-up of 26 (interquartile range, 19–42) months. AF recurrence was associated with prior stroke and statin use, NT-proBNP and high-sensitivity cardiac troponin-I levels, left ventricular dimension, left atrial volume index (LAVI), 3V-PCATA, and early AF recurrence during the blanking period. On multivariable Cox proportional hazard analysis, prior stroke (hazard ratio [HR], 2.208, 95% confidence interval [CI], 1.166–4.180, p = 0.015), LAVI (HR, 1.030, 95% CI, 1.010–1.051, p = 0.003), 3V-PCATA (HR, 1.034, 95% CI, 1.001–1.069, p = 0.046), and early AF recurrence (HR, 2.858, 95% CI, 1.855–4.405, p < 0.001) remained statistically significant. Conclusion: Pre-ablation CTA-derived 3V-PCATA, representing pericoronary inflammation, was an independent predictor of recurrence after first-session AF ablation using a second-generation cryoballoon. Advances in knowledge: Assessment of 3V-PCATA may identify patients at high risk of AF recurrence after CBA for AF.
Streamlining the image-guided radiotherapy process for proton beam therapy
Authors: Davies Lucy Siew Chen , McHugh Louise , Aznar Marianne , Lindsay Josh , Eccles Cynthia 
Published: September 2021

Objectives:This work evaluated the on-treatment imaging workflow in the UK’s first proton beam therapy (PBT) centre, with a view to reducing times and unnecessary imaging doses to patients.Methods:Imaging dose and timing data from the first 20 patients (70% paediatrics, 30% TYA/adult) treated with PBT using the initial image-guided PBT (IGPBT) workflow of a 2-dimensional kilo-voltage (2DkV), followed by cone-beam computed-tomography (CBCT) and repeat 2DkV was included. Pearson correlations and Bland-Altman analysis were used to describe correlations between 2DkV and CBCT images to determine if any images were superfluous.Results:229 treatment sessions were evaluated. Patient repositioning following the initial 2DkV (i2DkV) was required on 19 (8.3%) fractions. This three-step process resulted in an additional mean imaging dose of 3.4 mGy per patient, and 5.1 minutes on the treatment bed for the patient, over a whole course of PBT, compared to a two-step workflow (removing the i2DkV image). Correspondence between the mean displacements from i2DkV and CBCT was high, with R = 0.94, 0.94 and 0.80 in the anteroposterior, superiorinferior and right-left directions, respectively. Bland-Altman analysis showed very little bias and narrow limits of agreement.Conclusions:Removing the i2DkV, streamlining to a two-step workflow, would reduce treatment times and imaging dose, and has been implemented as standard verification protocol. For challenging cases (e.g. paediatric patients under GA), further investigations are required before the three-step workflow can be modified.Advances in knowledge:This is the first report assessing a preliminary imaging protocol in PBT in the UK and determining a way to reduce dose and time, which ultimately benefits the patient.
SARS-CoV-2 genome datasets analytics for informed infectious disease surveillance
Authors: Ekpenyong Moses Effiong , Udo Ifiok James , Edoho Mercy Ernest , Anwana EnoAbasi Deborah , Osang Francis Bukie , Geoffery Joseph Ikim , Dan Emmanuel Ambrose , Momodu Aliu Bolanle , Umoh Nnamso Michael , Udonyah Kingsley Christopher 
Published: September 2021

Background: The COVID-19 pandemic has ravaged economies, health systems, and lives globally. Concerns surrounding near total economic collapse, loss of livelihood and emotional complications ensuing from lockdowns and commercial inactivity, resulted in governments loosening economic restrictions. These concerns were further exacerbated by the absence of vaccines and drugs to combat the disease, with the fear that the next wave of the pandemic would be more fatal. Consequently, integrating disease surveillance mechanism into public healthcare systems is gaining traction, to reduce the spread of community and cross-border infections and offer informed medical decisions. Methods: Publicly available datasets of coronavirus cases around the globe deposited between December, 2019 and March 15, 2021 were retrieved from GISAID EpiFluTM and processed. Also retrieved from GISAID were data on the different SARS-CoV-2 variant types since inception of the pandemic. Results: Epidemiological analysis offered interesting statistics for understanding the demography of SARS-CoV-2 and helped the elucidation of local and foreign transmission through a history of contact travels. Results of genome pattern visualization and cognitive knowledge mining revealed the emergence of high intra-country viral sub-strains with localized transmission routes traceable to immediate countries, for enhanced contact tracing protocol. Variant surveillance analysis indicates increased need for continuous monitoring of SARS-CoV-2 variants. A collaborative Internet of Health Things (IoHT) framework was finally proposed to impact the public health system, for robust and intelligent support for modelling, characterizing, diagnosing and real-time contact tracing of infectious diseases. Conclusions: Localizing healthcare disease surveillance is crucial in emerging disease situations and will support real-time/updated disease case definitions for suspected and probable cases. The IoHT framework proposed in this paper will assist early syndromic assessments of emerging infectious diseases and support healthcare/medical countermeasures as well as useful strategies for making informed policy decisions to drive a cost effective, smart healthcare system.
A qualitative analysis of stakeholder experiences with Registered Reports Funding Partnerships
Authors: Drax Katie , Clark Robbie , Chambers Christopher D. , Munafò Marcus , Thompson Jacqueline 
Published: September 2021

Background: Registered Reports (RRs) could be a way to increase the quality of scientific research and literature, such as by reducing publication bias and increasing the rigour of study designs. These potential benefits have led to Registered Report funding partnerships (RRFPs or partnerships for short) between research funders and academic journals who collaborate to encourage researchers to publish RRs. In this study we investigated the research question: “What are the experiences of the stakeholders (authors, reviewers, journal editors, funders) in the various partnership models?”. Our companion paper addresses a related, but separate, research question. Methods: We conducted a thematic analysis of 32 semi-structured interviews with stakeholders (funders, editors, authors, reviewers, matchmakers) from six partnerships. Results: Interviewees had highly variable perceptions and experiences, reflecting the complex and nuanced impacts of partnerships. We identified 6 themes: “Importance of communication with authors and reviewers”, “Influence on study design”, “Appropriateness of partners”, “Potential to reduce publication bias”, “Impact on reviewer workload”, and “Insufficient evidence”. Conclusions: This was the first investigation into these novel initiatives. We hope that our findings can benefit and shape current and future partnerships.
The influence of shoulder arthrodesis on the function of the upper limb in adult patients after a brachial plexus injury: a systematic literature review with elements of meta-analysis
Authors: Górecki Michał , Czarnecki Piotr 
Published: September 2021

Based on the literature, 294 shoulder arthrodeses after brachial plexus injury in adults were assessed, mostly male; the mean age of the patients was 33 years, and the mean follow-up time was 5.5 years. The most common cause of injury was a traffic accident, especially on a motorcycle. Arthrodesis position ranged from 15 to 40 degrees of flexion, 15 to 60 degrees of abduction, and 0 to 50 degrees of internal rotation with the predominance of position by the 30-30-30 rule. Plates, screws, and external fixation were used for stabilization. The complication rate was at the level of 28%, the most common complication being delayed union or nonunion. Active movements of flexion and abduction averaged 61 and 56 degrees, respectively, while reaching the hand to the mouth, front pocket, and buttock was feasible for 69%, 71%, and 38%, respectively, after surgery. Shoulder pain was present in 77% of patients, and 28% experienced no relevant pain reduction after surgery. The subjective satisfaction rate was 82% based on significant improvement and satisfaction reported by patients after arthrodesis. Arthrodesis of the shoulder, in adult patients after brachial plexus palsy, can reduce shoulder pain, increase stability, and result in a range of motion that increases the possibility of carrying out everyday activities. This affects the high level of subjective patient satisfaction after surgery.Cite this article: EFORT Open Rev 2021;6:797-807. DOI: 10.1302/2058-5241.6.200114
Management strategies for prosthetic joint infection: long-term infection control rates, overall survival rates, functional and quality of life outcomes
Authors: Karachalios Theofilos , Komnos George A. 
Published: September 2021

DAIR (debridement, antibiotics, and implant retention), one-stage and two-stage revision surgery are the most common management strategies for prosthetic joint infection (PJI) management. Our knowledge concerning their efficacy is based on short to medium-term low-quality studies. Most studies report infection recurrence rates or infection-free time intervals. However, long-term survival rates of the infection-free joints, functional and quality of life outcome data are of paramount importance. DAIR, one-stage and two-stage revision strategies are not unique surgical techniques, presenting several variables. Infection control rates for the above strategies vary from 75% to 90%, but comparisons are difficult because different indications and patient selection criteria are used in each strategy. Recent outcome data show that DAIR and one-stage revision in selected patients (based on host, bacteriological, soft tissue and type of infection criteria) may present improved functional and quality of life outcomes and reduced costs for health systems as compared to those of two-stage revision. It is expected that health system administrators and providers will apply pressure on surgeons and departments towards the wider use of DAIR and one-stage revision strategies. It is the orthopaedic surgeon’s responsibility to conduct quality studies in order to fully clarify the indications and outcomes of the different revision strategies. Cite this article: EFORT Open Rev 2021;6:727-734. DOI: 10.1302/2058-5241.6.210008
Simons Observatory HoloSim-ML: machine learning applied to the
efficient analysis of radio holography measurements of complex optical
systems
Authors: Chesmore Grace E. , Adler Alexandre E. , Cothard Nicholas F. , Dachlythra Nadia , Gallardo Patricio A. , Gudmundsson Jon , Johnson Bradley R. , Limon Michele , McMahon Jeff , Nati Federico , Niemack Michael D. , Puglisi Giuseppe , Simon Sara M. , Wollack Edward J. , Wolz Kevin , Xu Zhilei , Zhu Ningfeng 
Published: September 2021

Near-field radio holography is a common method for measuring and
aligning mirror surfaces for millimeter and sub-millimeter telescopes.
In instruments with more than a single mirror, degeneracies arise in
the holography measurement, requiring multiple measurements and new
fitting methods. We present HoloSim-ML, a Python code for beam
simulation and analysis of radio holography data from complex optical
systems. This code uses machine learning to efficiently determine the
position of hundreds of mirror adjusters on multiple mirrors with few
micrometer accuracy. We apply this approach to the example of the
Simons Observatory 6 m telescope.
Performance characterization of a self-made terahertz photoconductive antenna
Authors: Ding Jing , Li Qingjun , Shen Yan , Wu Rui , Liu Xin , Ding Chenxin , Cui Hailin , Su Bo , Zhang Cunlin 
Published: September 2021

A terahertz (THz) photoconductive antenna is prepared using, to the best of our knowledge, a novel method, which has high yield and strong stability. It eliminates the stripping process of a thin-film THz antenna and effectively prevents the toxicity of the corrosion solution, the easy damage in the transfer process, and the weak bonding with the substrate. First, a 200 µm copper wire is bundled on a low-temperature GaAs epitaxial wafer, and then the electrode of the photoconductive antenna is fabricated using the vacuum evaporation method. Finally, the THz time-domain signal with a high signal-to-noise ratio and good repeatability is obtained using an 800 nm laser. Additionally, the influence of pump light and detection light power on THz signal intensity is studied when the total optical power is unchanged. Results show that when the total power of the laser is greater than a certain value, there is an optimal ratio between the pump power and the detection power, which can maximize the signal-to-noise ratio of the THz wave. This provides a basis for the effective application of a THz antenna and lays a foundation for improving the detection sensitivity of samples.
Mode-locked Cr:LiSAF laser far off the gain peak: tunable sub-200-fs pulses near 1  µm
Authors: Demirbas Umit , Thesinga Jelto , Kellert Martin , Reuter Simon , Sumpf Bernd , Pergament Mikhail , Kärtner Franz X. 
Published: September 2021

We report, to the best of our knowledge, the first mode-locking results of a Cr:LiSAF laser near the 1 µm region. The system is pumped only by a single 1.1 W high-brightness tapered diode laser at 675 nm. A semiconductor saturable absorber mirror (SESAM) with a modulation depth of 1.5% and non-saturable losses below 0.5% was used for mode-locking. Once mode-locked, the Cr:LiSAF laser produced almost-transform-limited sub-200-fs pulses with up to 12.5 mW of average power at a repetition rate of 150 MHz. Using an intracavity birefringent filter, the central wavelength of the pulses could be smoothly tuned in the 1000–1020 nm range. Via careful dispersion optimization, pulse widths could be reduced down to the 110-fs level. The performance in this initial study was limited by the design parameters of the SESAM used, especially its passive losses and could be improved with an optimized SESAM design.
Temporally stable fiber amplifier pumped random distributed feedback Raman fiber laser with record output power
Authors: Song Jiaxin , Ren Shuai , Liu Wei , Li Wei , Wu Hanshuo , Ma Pengfei , Zhang Hanwei , Zhou Pu 
Published: September 2021

In this Letter, we propose a scheme to use a temporally stable pump source in a high-power random distributed feedback Raman fiber laser (RRFL) with a half-open cavity. Different from conventional pump manners, the pump source is based on an Yb-doped fiber amplifier, seeded by a temporally stable phase-modulated single-frequency fiber laser for suppressing the spectral broadening and second-order Raman Stokes generation in the output laser. Using a piece of 50-m-long 20/400 µm passive fiber, the maximum output power of 1570 W was obtained with a pump power of 2025 W. The conversion efficiency with respect to the pump power was 77.5%. To the best of our knowledge, this is the highest output power ever reported in a RRFL to date. This work could provide a novel method for power scaling of RRFLs.
Monolithic high-index contrast grating mirror for a GaN-based vertical-cavity surface-emitting laser
Authors: Hong Kuo-Bin , Chang Tsu-Chi , Hjort Filip , Lindvall Niclas , Hsieh Wen-Hsuan , Huang Wei-Hao , Tsai Po-Hsun , Czyszanowski Tomasz , Haglund Åsa , Lu Tien-Chang 
Published: September 2021

In this paper, a pulsed electrically pumped GaN-based vertical-cavity surface-emitting laser (VCSEL) with one dielectric distributed Bragg reflector and one n-GaN monolithic high-index contrast grating (MHCG) mirror was demonstrated at room temperature. The reflectance of the n-GaN MHCG and cavity mode behaviors of the VCSEL with MHCG for varying n-GaN thickness, MHCG pattern diameter, and current aperture size were numerically investigated. Measured characteristics of the fabricated device showed that the lasing action started at an injection current of 10.2 mA, corresponding to a current density of about

15.1

kA/
cm

2

. Above threshold, the measured slope efficiency was

6.2
×

10

−
3

W
/
A

, and the output power was 0.13 mW at 30 mA. Moreover, the measured lasing peak occurring at 403.4 nm and the longitudinal mode spacing of 5.6 nm were in good agreement with simulations. The incorporation of an n-GaN MHCG mirror not only greatly simplified the fabrication but also substantially improved the lasing characteristics in comparison to the previous work applying

TiO

2

HCG mirrors.
Definitheit im Selkupischen
Authors: Budzisch Josefina 
Published: September 2021

The dissertation at hand deals with definiteness in Selkup. It is investigated how in Selkup – taking the three dialect groups North, Central and South Selkup into account – semantic-pragmatic definiteness is expressed, since the language lacks an explicit grammatical marker (like a definite article) for the expression of definiteness. The analysis is carried out on the basis of existing research literature, elicit data and a corpus, which is composed of 248 texts with 12,828 sentences and 77,443 tokens.In its entirety, Selkup thus shows that demonstratives, possessive associations and the non-possessive use of the possessive suffix of the third person singular are the most important strategies for marking definiteness. All types of references, however, contain large numbers of unmarked noun phrases, showing that context is often the decisive factor in deciding whether a noun phrase is to be interpreted as definite or indefinite.