bluuebunny/crossref_metadata_2025_split huggingface dataset:
Efficient and secure computation of edit distance on genomic data
Authors: Migliore Andrea , Cimato Stelvio , Trucco Gabriella 
Published: November 2022

Abstract
Background: Genetic information are the most sensitive data for a person and must be protected from malicious attacks. In this paper we focus on the application of secure multi-party computation, a subfield of cryptography, to the computation of edit distance, one of the most used metrics among genetic similarity indicators, useful for the diagnosis and treatment of many genetically based diseases.
Results: We analyze four algorithms and compare them to the best prior results found in literature [1]:(1) the Wagner-Fischer algorithm [2], using the entire dynamic programming matrix; (2) the Wagner-Fischeralgorithm, optimized to use only the minimum needed columns for the computation; (3) the Ukkonen algorithm [3], considering a threshold of approximately 60% of the longest string; (4) the Ukkonen algorithm,using a generalized cut-off technique which reduces the number of cells to be computed. The Ukkonen algorithm with generalized cut-off is the one that performed better among the considered algorithms and it also proved to have better performances than the best prior results found in literature.
Conclusions: Securely computing the edit distance between human genomes have become very important in medical and public health domains. Improving computational performance is a key factor for real-world application scenarios.
In this work, we proposed several secure implementations of some of the most efficient edit distance algorithms, achieving better performances over existing protocols found in literature [4]. Moreover, this is the first time the Ukkonen's algorithm is proposed using all possible state-of-the-art optimizations for garbled circuits. The algorithms and protocols used in this work were also applied on both random, high-entropy, and real genomic, low-entropy strings and are provably secure with respect to the standard definition of security for Multi-Party Computation (MPC) protocols.
Does Cd possess the stimulatory effect on gas exchange and photochemistry in C3-CAM intermediate plants?
Authors: Kaczmarczyk Adriana , Nosek Michał , Kaszycki Paweł , Supel Paulina , Miszalski Zbigniew 
Published: November 2022

Abstract

The soil-grown semi-halophytic CAM (crassulacean acid metabolism) facultative model plant - Mesembryanthemum crystallinum L. (common ice plant) exhibits minute toxicity symptoms when exposed to elevated cadmium doses. In this study, photochemical activity as well as gas exchange of the soil-grown C3-CAM- performing plants to increased cadmium concentrations (0.01-10.0 mM) were investigated. An increase of net photosynthesis (PN) observed in C3- performing plants upon exposure to Cd runs in parallel with the rise of transpiration level. As the transpiration process tends to be elevated also in darkness, it gives rise to the suggestion that the first effect of Cd presence is stimulation of stomata aperture. Also, photochemical activity is well-secured in Cd-treated plants, which implies the involvement of additional mechanisms triggered to protect M. crystallinum against Cd toxicity.
A 300mV Body-biased Silicon Neuron Circuit with High Robustness against Firing Frequency Variation
Authors: Quan Jiale 
Published: November 2022

Abstract

This paper presents a body-biased silicon neuron circuit which is capable of operating at ultra-low-voltage supplies and achieves a stable firing frequency. The proposed neuron employs body-biased method to increase charging current into the membrane capacitors for compensating the extra leakage current in the subthreshold region. A second-order low-pass filter, using the property of energy storage in capacitors, is used to reset the membrane potential and implement firing frequency adaption mechanism. Body-biased transistors are as well employed as voltage-controlled resistors to control the current flowing through the membrane capacitance. The circuit is capable of obtaining precise firing frequencies by biasing the body voltages of critical PMOS transistors, which make the circuit usable for frequency coding Spiking Neural Network (SNN). The designed neuron is implemented in 55nm bulk CMOS technology with an area of 400 µm2 that consumes about 639fJ@1kHz. We present circuit post-layout simulation results and demonstrate the circuit’s ability to produce biologically plausible neural dynamics with compact designs, and compare the energy consumption and stability with published state-of-the-art neuron circuits. Finally, the proposed circuit is proved to maintain a good robustness over process variation and Monte Carlo analysis with relative error 2.43% in firing rate of approximate 145Hz.
Vitreoretinal Amyloidosis:
Clinical Features, OCT/A Insights, Gene Mutations, and Outcomes of Pars Plana Vitrectomy Surgery
Authors: Zhou Nan , Yang Li , Xu Xiaolin , Wei Wen-Bin , Liu Yueming 
Published: November 2022

Abstract
Purpose: To describe the OCT/A findings, surgical findings and outcomes of vitrectomy among 8 eyes of 4 patients with vitreoretinal amyloidosis.
Participants: Eight eyes of 4 Asian patients with a diagnosis of vitreoretinal amyloidosis from Jan 10, 2008, to Sep 10, 2021.
Methods: Detailed history-taking, ocular and systemic examinations and genetic analysis of transthyretin mutation were performed. Vitreous biopsy, followed by 23- to 25-G pars plana vitrectomy was performed in all patients, and followed up on days 1, 7, and 30 and then, every 3 months.
Results: The mean age at presentation was 45 years, with a 1:1 female-to-male distribution. The median follow-up was 85.3 (2-150) months. The OCT/A features of the vertical hyperreflective lesions appeared as punctate with moderate or high reflectivity, affecting all layers of the neuroretina in 7 eyes of 4 patients (7 of 8 eyes [87.5%]), and subtle needle-shaped patterns in 6 of 8 eyes (75%). Cotton-wool or waxy vitreous with firm vitreous adhesions beyond the major arcades and along the secondary retinal vessels was observed during vitrectomy in all eyes. The preoperative best-corrected visual acuity (BCVA) was ≤ 20/200 in 4 eyes (50%), whereas the postoperative BCVA improved to 20/100 to 20/25 in all eyes (100%). No patients subsequently were observed to develop systemic amyloidosis or dysfunction during follow-up examinations.
Conclusions: The clinical clues, OCT/A features, surgical strategy, and vitrectomy outcomes in vitreoretinal amyloidosis were highlighted. We propose the term vitreoretinal amyloidosis instead of vitreous amyloidosis mainly based on the OCT/A features in this report.
Stress deficits in reward behaviour are associated with and replicated by dysregulated amygdala-nucleus accumbens pathway function
Authors: Madur Lorraine , Ineichen Christian , Bergamini Girogio , Greter Alexandra , Poggi Giulia , Cuomo-Haymour Nagiua , Sigrist Hannes , Sych Yaroslav , Paterna Jean-Charles , Bornemann Klaus , Violett Coralie , Fernandez-Albert Francesc , Alanis-Lobato Gregorio , Hengerer Bastian , Pryce Christopher 
Published: November 2022

Abstract
Reduced reward interest/learning and reward-to-effort valuation are distinct, common symptoms in neuropsychiatric disorders for which chronic stress is a major aetiological factor. Glutamate neurons in basal amygdala (BA) project to various regions including nucleus accumbens (NAc). The BA-NAc neural pathway is activated by reward and aversion, with many neurons being monovalent. In adult male mice, chronic social stress (CSS) led to both reduced discriminative reward learning (DRL) associated with decreased BA-NAc activity, and reduced reward-to-effort valuation (REV) associated, in contrast, with increased BA-NAc activity. Chronic tetanus toxin BA-NAc inhibition replicated the CSS-DRL effect and caused a mild REV reduction, whilst chronic DREADDs BA-NAc activation replicated the CSS effect on REV without affecting DRL. This study provides novel evidence that stress disruption of reward processing involves the BA-NAc neural pathway; the bi-directional effects implicate opposite activity changes in reward (learning) neurons and aversion (effort) neurons in the BA-NAc pathway following chronic stress.
Is PICC or port better for patients with malignant bone and soft tissue tumors of the lower limbs? A retrospective study
Authors: Shan Jing , Lv Sumei , Li Haihong , Wang Donglai , Zhang Xiaoyu , Liu Wei 
Published: November 2022

Abstract
Purpose: To compare the effects of peripherally inserted central catheters (PICC) and totally implantable venous access devices (port) in terms of complications and shoulder function in patients with malignant bone and soft tissue tumors of the lower limbs.
Patients and methods: We analyzed 65 cases of port and 65 cases of PICC at the orthopedic department of the Fourth Hospital of Hebei Medical University. The two groups were compared in terms of catheter indwelling time, catheter-related complications, Constant-Murley shoulder function score, and displacement of the position of the catheter end on the catheterization side.
Results: Compared to the PICC group, at six months after catheterization the port group showed better outcomes for catheter indwelling time, catheter-related complications, and Constant-Murley score for the catheterization-side shoulder joint (p < 0.05). The port group also showed less displacement of the catheter end position after 180° abduction of the catheterization-side shoulder joint (p < 0.05).
Conclusion: Compared with PICC, port can prolong catheter indwelling time, reduce catheter-related complications, and maintain shoulder joint function, which makes it an ideal venous-access approach when providing chemotherapy to patients with malignant bone and soft tissue tumors of the lower limbs.
Push out bond strength of hydraulic cements used at different thicknesses
Authors: Celia Ruiz Durán , Lucía Gancedo- Caravia , Vicente Vera González , Cristina González - Losada 
Published: November 2022

Abstract
Background: BD is a reliable hydraulic cement for those clinical situations where thick cavities need to be filled and displacement resistance plays an important role. Clinicians need to consider choosing specific hydraulic cements according to the thickness of material that needs to be used.
Methods:
The aim of this study was to compare the pushout bond strength (POBS) of three hydraulic cements Biodentine (BD), Totalfill Root Repair paste (TF) and ProRoot MTA White (PMTA), when used at thicknesses of 3 and 5 mm.
78 root slices 3 and 5 mm thick were obtained from human extracted teeth. Cylindrical cavities of 1.4 mm diameter were drilled on them and then filled with BD, TF or PMTA. Pushout tests were performed after 21 days of setting. POBS data were analyzed with robust Welch and Brown-Forsythe and Tamhane's post hoc tests. A Weibull analysis was also performed.
Results: In the 3-mm group, TF showed significantly lower bond strength than BD and PMTA. In the 5-mm groups BD showed significantly higher bond strength than TF. For TF and BD, increasing the thickness of the sample increased the bond strength, but not for PMTA group.
Conclusions: TF and BD achieve higher pushout bond strength resistance when used at a thickness of 5mm than at 3mm while the mean resistance of PMTA is less influenced by the thickness. At 5mm, BD and PMTA exhibit similar resistance to displacement. However, the behavior of BD is more predictable than that of its predecessor.
Patients with Increased Levels of Fusobacterium Tumoral Abundance are Associated with Better Outcomes in Mucinous Colorectal Cancer.
Authors: Duggan William P , Salvucci Manuela , Kisakol Batuhan , Lindner Andreas U , Reynolds Ian S , Dussmann Heiko , Fay Joanna , O'Grady Tony , Longley Daniel B , Ginty Fiona , McDonough Elizabeth , Slade Daniel J , Burke John P , Prehn Jochen H M 
Published: November 2022

Abstract
There is currently an urgent need to identify factors predictive of immunogenicity in colorectal cancer (CRC). Mucinous CRC is a distinct histological subtype of CRC, associated with a poor response to chemotherapy. Recent evidence suggests the commensal facultative anaerobe Fusobacterium may be especially prevalent in mucinous CRC. The objectives of this study were to assess the impact of Fusobacterium prevalence on immune cell expression and prognosis in mucinous CRC. Our study included two independent colorectal cancer patient cohorts, The Cancer Genome Atlas (TCGA) cohort, and a cohort of rectal cancers from the Beaumont RCSI Cancer Centre (BRCC). Multiplexed immunofluorescence staining of a tumor microarray (TMA) from the BRCC cohort was undertaken using Cell DIVE technology. Our cohorts included 87 cases (13.3%) of mucinous and 565 cases (86.7%) of non-mucinous CRC. Mucinous CRC in the TCGA dataset was associated with increased CD8 + lymphocyte (p = 0.018), regulatory T-cell (p = 0.001) and M2 macrophage (p = 0.001) expression. Similarly in the BRCC cohort, mucinous RC was associated with enhanced CD8 + lymphocyte (p = 0.022), regulatory T-cell (p = 0.047), and B-cell (p = 0.025) counts. Elevated Fusobacterium expression was associated with increased CD4+ (p = 0.031) and M1 macrophage (p = 0.006) expression, whilst M2 macrophages (p = 0.043) were under-expressed in the TCGA cohort. Increased Fusobacterium relative abundance in mucinous CRC was associated with improved clinical outcomes in our TCGA cohort despite having no association with MSI status (DSS: likelihood ratio p = 0.04, logrank p = 0.052). Fusobacterium abundance is associated with improved outcomes in mucinous CRC, possibly due its modulatory effect on the host immune response.
The relationship between the NLR and PLR and the severity of coronary calcium scoreusing multi-slice CT angiography
Authors: Vahid Eslami , Dorsa Shirini , Ghazal Sanadgol , Shima Daghighi , Masih Mansouri Tehrani Mohammad , Taraneh Faghihi Langroudi 
Published: November 2022

Abstract
Atherosclerotic diseases are one of the most common types of cardiovascular conditions which impose a heavy burden on patients’ lives. Recent studies have proved the role of inflammation and inflammatory factors in the progression of this condition. Finding a relationship between inflammatory factors and coronary calcium score (CCS), calculated by CT-angiography, may benefit affected patients. In this study, we recruited 100 patients referred to our ward to rule out coronary artery occlusion by CT-angiography. All demographic and laboratory data were collected before the CT scan. Then the coronary arteries’ total and singular calcium scores were calculated using the Angaston method. We divided our patients based on their total coronary artery calcium score. The neutrophil/lymphocyte ratio (NLR) was pointily higher in the severe CAC group, 7.70 (± 0.60), and got lower with the decrease in the severity degree of CAC. The trend for CRP was the same and got notably raised by the severity of the CAC. Analysis revealed a significant correlation between the upward trend of NLR and total calcium score (r:0.582, P-value: <0.001) in patients. The ROC curve revealed the NLR of 2.45 with a sensitivity of 81% and a specificity of 80% could successfully predict the presence of total calcium scores above 100 in our patients. The study’s results showed a significant relationship between NLR and CRP as inflammatory factors and the severity of total CCS. Moreover, it proved that total CCS and diabetes and cigarette smoking have a significant relationship as an incidental finding.
A look at the blind Kumamoto experiment combining active and passive seismic observations to avoid Rayleigh-wave modes mis-identification
Authors: Mercerat E. Diego , Mikesell T. Dylan 
Published: November 2022

Abstract
We present our pathway through participation in the blind Kumamoto exercise, particularly the Step~1 of site characterization. As a first stage, the combination of passive and active seismic imaging techniques are used to image the velocity profile beneath the KUMA site. The estimation of a broadband Rayleigh wave dispersion curve is based on crosscorrelations of ambient seismic noise and analysis of active seismic shot gathers. We calculate correlations from the entire time series (only vertical components) of each seismic array after classical pre-processing of ambient noise data (mean and trend removal, tapering and bandpass Butterworth filter between 0.05-20 Hz, whitenning, and one-bit signal binarisation). Then a passive seismic section is constructed using all available stations pairs and stacking the crosscorrelation traces with similar interstation distances. The obtained passive seismic section is analyzed using a high-resolution Radon transform in order to obtain the dispersion image of Rayleigh waves traveling through the array. Manual picking of the dispersion curve is done for each dispersion image from KUM-LL, KUM-M and KUM-SM arrays. Then, the information is merged and interpolated to obtain a final broadband dispersion curve. Additionally, active source seismic data is used with the high-resolution Radon technique to constrain the model at shallow depths ($<$~30~m). In this way, a broadband dispersion image is constructed with significant energy from 0.9~Hz to 45~Hz. The final dispersion curve is inverted using the non-linear neighborhood algorithm. Using just the fundamental mode Rayleigh wave, a first model with normal velocity variation in depth is obtained that corresponds quite well with the preferred model provided by the organizing committee. The addition of a mHVSR curve in a joint inversion better constrains the deeper part of the model ($>$~1~km). After comparison of the submitted dispersion curve to the theoretical dispersion curves for the preferred model, the authors note that there was a clear mis-interpretation in the fundamental mode of their submitted results, especially at frequencies higher than 5 Hz. Using both fundamental (only visible in the passive dataset) and first overtones of Rayleigh waves (only visible in the active seismic dataset) a refined velocity model near the shallow subsurface could have been be inferred, but we decided to keep our first submitted results. This detailed interpretation should be further studied as dispersion images from forward and backward hammer shots are quite different, which may indicate strong variations in the geometry and/or shear-wave velocities of the first meters of the subsurface.
An Evaluation of Cervix Maturity by Machine Learning and Ultrasound Images
Authors: Liu Yan-Song , Lu Shan , Wang Hong-Bo , Hou Zheng , Zhang Chun-Yu , Chong Yi-Wen , Wang Shuai , Tang Wen-Zhong , Qu Xiao-Lei , Zhang Yan 
Published: November 2022

Abstract

Background:To evaluate the improvement of evaluation accuracy of cervix maturity by adding objective ultrasound data and machine learning models to the existing traditional Bishop method.Methods:The machine learning model was trained and tested using 101 sets of data from pregnant women who were examined and had their delivery in Peking University Third Hospital in 2019-2021. The inputs of the model included cervical length, Bishop score, angle, age, induced labor time, measurement time, measurement time to induced labor time (MTILT), method of induced labor, and primiparity/multiparity. The output of the model is the predicted time from induced labor to labor. Our experiments analyzed the effectiveness of three machine learning models: XGBoost (eXtreme Gradient Boosting), CatBoost (an implementation of Gradient Boosted Decision Trees), and Random forest (RF). We considered the mean value of each scoring group of the traditional Bishop scoring method as the predicted value and calculated the mean square error of the real value and the predicted value for each data, considering the root-mean-squared error (RMSE) as the criterion to evaluate the accuracy of the model. We made a significant t-test on RMSE between the machine learning model and the traditional Bishop score.Results:The mean absolute error (MAE) of the prediction result of Bishop scoring method was 19.45 hours, and the RMSE was 24.56 hours. The prediction error of machine learning model was lower than the Bishop score method. Among the three machine learning models, the MAE of the model with the best prediction effect was 13.49 hours and the RMSE was 16.98 hours. After selection of feature the prediction accuracy of the XGBoost and RF was slightly improved. After feature selection and artificially removing the Bishop score, the prediction accuracy of the three models decreased slightly. The best model was XGBoost (p= 0.0017). Thep-value of the other two models was <0.01.Conclusion:In the evaluation of cervix maturity, the results of machine learning method are more objective and significantly accurate compared with the traditional Bishop scoring method. The machine learning method is a better predictor of cervix maturity than the traditional Bishop method.
Usefulness of percutaneous rupture for lumbar facet cysts: A retrospective study
Authors: Kanzaki Koji , Morishita Masutaro , Ishihara Yohei 
Published: November 2022

AbstractBackground: Percutaneous rupture of lumbar facet cysts (LFC) is the only non-surgical treatment able to directly reduce cysts. However, this is not yet a common procedure, and its effectiveness, including the evaluation of complications, remains unclear. This study aimed to evaluate the clinical outcomes of percutaneous rupture for LFC and elucidate whether this minimally invasive procedure could become an alternative to surgeries for cases resistant to conservative treatments.Methods: This study investigated 51 symptomatic patients with LFC for whom conservative treatments were ineffective and who underwent percutaneous rupture of the LFC. All patients were followed-up for >2 years after the treatment. Clinical evaluations (Visual Analogue Scale [VAS], recovery rate calculated with Japanese Orthopedic Association scores) and radiographic evaluations (size of LFC based on magnetic resonance imaging [MRI]) were performed from pretreatment to final follow-up.Results: Successful LFS rupture, without hospitalization and general anesthesia, was achieved in 43 patients. No serious complications occurred during treatment through the last observation. Satisfactory clinical results were obtained (VAS: 11.1 mm, recovery rate: 83.1 %), and significant reduction of LFC was recognized in all cases based on post-treatment MRI. No successful rupture cases required subsequent surgical treatments, although there were 3 cases of LFC recurrence that required an additional percutaneous rupture treatment.Conclusions: Percutaneous rupture for LFC is not only a safe and minimally invasive procedure without any serious complications or requirements for hospitalization and general anesthesia, but also a very useful procedure that can prevent surgery for cases resistant to conservative treatments.