bluuebunny/crossref_metadata_2025_split huggingface dataset:
HDAC3 Is Required for XPC Recruitment and Nucleotide Excision Repair of DNA Damage Induced by UV Irradiation
Authors: Nishimoto Koji , Niida Hiroyuki , Uchida Chiharu , Ohhata Tatsuya , Kitagawa Kyoko , Motegi Akira , Suda Takafumi , Kitagawa Masatoshi 
Published: June 2020

Abstract

Recent studies have demonstrated that lysine acetylation of histones is crucial for nucleotide excision repair (NER) by relaxing the chromatin structure, which facilitates the recruitment of repair factors. However, few studies have focused on the contribution of histone deacetylases (HDAC) to NER. Here, we found that histone H3 Lys14 (H3K14) was deacetylated by HDAC3 after UV irradiation. Depletion of HDAC3 caused defects in cyclobutene pyrimidine dimer excision and sensitized cells to UV irradiation. HDAC3-depleted cells had impaired unscheduled DNA synthesis, but not recovery of RNA synthesis, which indicates that HDAC3 was required for global genome NER. Moreover, xeroderma pigmentosum, complementation group C (XPC) accumulation at the local UV-irradiated area was attenuated in HDAC3-depleted cells. In addition to the delay of XPC accumulation at DNA damage sites, XPC ubiquitylation was inhibited in HDAC3-depleted cells. These results suggest that the deacetylation of histone H3K14 by HDAC3 after UV irradiation contributes to XPC recruitment to DNA lesions to promote global genome NER.

Implications:
Involvement of histone deacetylation for XPC accumulation after UV irradiation indicates conversion of chromatin structure is essential for nucleotide excision repair in human cancer cells.
Beyond Atoms and Accidents
Authors: Ibrahim Bilal 
Published: June 2020

Abstract
This article explores a novel approach to the analysis of the external world in postclassical Ashʿarite kalām. While discussions of physical reality and its fundamental constituents in the classical period of Islamic thought turned chiefly on the opposing views of kalām atomism and Aristotelian hylomorphism, in the postclassical period kalām thinkers in the Ashʿarite tradition forge a new frame of inquiry. Beginning most earnestly with the philosophical works of Fakhr al-Dīn al-Rāzī, a critical approach is developed addressing received views in ontology, including the relation of substance to accident, the status of Aristotelian form and matter, and part-to-whole relations. Drawing on Rāzī’s al-Mulakhkhaṣ and al-Mabāḥith, kalām thinkers develop several concepts to distinguish arbitrary or mind-dependent (iʿtibārī) composites (‘man-plus-stone’) from non-arbitrary composites (e.g., tree, paste, and house). Most notably, they adopt a substance-plus-accident ontology in opposition to the Aristotelian hylomorphism of falsafa. The mutakallimūn will conceive of composites as possessing ‘real unity’ (ḥaqīqa muttaḥida) while dispensing with the explanatory and causal role of Aristotelian substantial forms.
Ṣadrā’s Use of Fakhr al-Dīn al-Rāzī’s al-Mabāḥith al-mashriqiyya in the Asfār
Authors: Bonmariage Cécile 
Published: June 2020

Abstract
The aim of this paper is to show that, in several chapters of the Asfār, Ṣadrā’s use of Fakhr al-Dīn al-Rāzī’s al-Mabāhith al-mashriqiyya is far more extensive than what a superficial reading, focusing only on explicit quotations, might indicate, and to explore what knowing this can bring to our reading of Ṣadrā’s text. It analyzes what Ṣadrā does with his source and examines a few examples to illustrate why it matters to know.
The effect of 10-min dispatch-assisted cardiopulmonary resuscitation training: a randomized simulation pilot study
Authors: Fukushima Hidetada , Asai Hideki , Seki Tadahiko , Takano Keisuke , Bolstad Francesco 
Published: June 2020

Abstract
Background
Immediate bystander cardiopulmonary resuscitation (CPR) is essential for survival from sudden cardiac arrest (CA). Current CPR guidelines recommend that dispatchers assist lay rescuers performing CPR (dispatch-assisted CPR (DACPR)), which can double the frequency of bystander CPR. Laypersons, however, are not familiar with receiving CPR instructions from dispatchers. DACPR training can be beneficial for lay rescuers, but this has not yet been validated. The aim of this study was to determine the effectiveness of simple DACPR training for lay rescuers.

Methods
We conducted a DACPR simulation pilot study. Participants who were non-health care professionals with no CPR training within 1 year prior to this study were recruited from Nara Medical University Hospital. The participants were randomly assigned to one of the two 90-min adult basic life support (BLS) training course groups: DACPR group (standard adult BLS training plus an additional 10-min DACPR training) or Standard group (standard adult BLS training only). In the DACPR group, participants practiced DACPR through role-playing of a dispatcher and an emergency caller. Six months after the training, all subjects were asked to perform a 2-min CPR simulation under instructions given by off-duty dispatchers.

Results
Out of the 66 participants, 59 completed the simulation (30 from the DACPR group and 29 from the Standard group). The CPR quality was similar between the two groups. However, the median time interval between call receipt and the first dispatch-assisted compression was faster in the DACPR group (108 s vs 129 s, p = 0.042).

Conclusions
This brief DACPR training in addition to standard CPR training can result in a modest improvement in the time to initiate CPR. Future studies are now required to examine the effect of DACPR training on survival of sudden CA.
A flexible network-based imputing-and-fusing approach towards the identification of cell types from single-cell RNA-seq data
Authors: Qi Yang , Guo Yang , Jiao Huixin , Shang Xuequn 
Published: June 2020

AbstractBackgroundSingle-cell RNA sequencing (scRNA-seq) provides an effective tool to investigate the transcriptomic characteristics at the single-cell resolution. Due to the low amounts of transcripts in single cells and the technical biases in experiments, the raw scRNA-seq data usually includes large noise and makes the downstream analyses complicated. Although many methods have been proposed to impute the noisy scRNA-seq data in recent years, few of them take into account the prior associations across genes in imputation and integrate multiple types of imputation data to identify cell types.ResultsWe present a new framework, NetImpute, towards the identification of cell types from scRNA-seq data by integrating multiple types of biological networks. We employ a statistic method to detect the noise data items in scRNA-seq data and develop a new imputation model to estimate the real values of data noise by integrating the PPI network and gene pathways. Meanwhile, based on the data imputed by multiple types of biological networks, we propose an integrated approach to identify cell types from scRNA-seq data. Comprehensive experiments demonstrate that the proposed network-based imputation model can estimate the real values of noise data items accurately and integrating the imputation data based on multiple types of biological networks can improve the identification of cell types from scRNA-seq data.ConclusionsIncorporating the prior gene associations in biological networks can potentially help to improve the imputation of noisy scRNA-seq data and integrating multiple types of network-based imputation data can enhance the identification of cell types. The proposed NetImpute provides an open framework for incorporating multiple types of biological network data to identify cell types from scRNA-seq data.
Exact solving and sensitivity analysis of stochastic continuous time Boolean models
Authors: Koltai Mihály , Noel Vincent , Zinovyev Andrei , Calzone Laurence , Barillot Emmanuel 
Published: June 2020

Abstract
Background
Solutions to stochastic Boolean models are usually estimated by Monte Carlo simulations, but as the state space of these models can be enormous, there is an inherent uncertainty about the accuracy of Monte Carlo estimates and whether simulations have reached all attractors. Moreover, these models have timescale parameters (transition rates) that the probability values of stationary solutions depend on in complex ways, raising the necessity of parameter sensitivity analysis. We address these two issues by an exact calculation method for this class of models.

Results
We show that the stationary probability values of the attractors of stochastic (asynchronous) continuous time Boolean models can be exactly calculated. The calculation does not require Monte Carlo simulations, instead it uses graph theoretical and matrix calculation methods previously applied in the context of chemical kinetics. In this version of the asynchronous updating framework the states of a logical model define a continuous time Markov chain and for a given initial condition the stationary solution is fully defined by the right and left nullspace of the master equation’s kinetic matrix. We use topological sorting of the state transition graph and the dependencies between the nullspaces and the kinetic matrix to derive the stationary solution without simulations. We apply this calculation to several published Boolean models to analyze the under-explored question of the effect of transition rates on the stationary solutions and show they can be sensitive to parameter changes. The analysis distinguishes processes robust or, alternatively, sensitive to parameter values, providing both methodological and biological insights.

Conclusion
Up to an intermediate size (the biggest model analyzed is 23 nodes) stochastic Boolean models can be efficiently solved by an exact matrix method, without using Monte Carlo simulations. Sensitivity analysis with respect to the model’s timescale parameters often reveals a small subset of all parameters that primarily determine the stationary probability of attractor states.
Incremental prognostic value of aortic stiffness in addition to myocardial ischemia by cardiac magnetic resonance imaging
Authors: Kaolawanich Yodying , Boonyasirinant Thananya 
Published: June 2020

Abstract
Background
Aortic stiffness is an independent predictor of cardiovascular (CV) events and mortality. However, no data exists for the prognosis of combined aortic stiffness and myocardial ischemia. Using cardiac magnetic resonance (CMR) imaging, we assessed the association of aortic stiffness by pulse wave velocity (PWV), myocardial ischemia, and CV events in patients with known or suspected coronary artery disease (CAD).

Methods
Velocity-encoded CMR was performed in 520 patients who had undergone adenosine stress CMR. The PWV was determined between the mid-ascending and mid-descending thoracic aorta. Patients were divided into 4 groups by PWV (higher or lower PWV) and myocardial ischemia (positive or negative ischemia). Combined CV events including mortality, acute coronary syndrome, heart failure, coronary revascularization, and stroke were analyzed among the 4 groups.

Results
The median follow-up period was 46.5 months, and the median PWV was 10.54 m/sec. Myocardial ischemia was positive in 199 patients (38.3%). The group with a higher PWV and positive ischemia had the most CV events (hazard ratio 8.94, p <  0.001). The group with a higher PWV and negative ischemia also was significantly associated with CV events (HR 2.19, p = 0.02). Groups with a lower PWV-positive ischemia and a higher PWV-negative ischemia showed no difference in terms of CV events (HR 0.60, p = 0.08). Patients with myocardial ischemia who had higher PWV demonstrated significantly higher event rates than those who had lower PWV (HR 2.41, p <  0.001). Multivariate analysis demonstrated that myocardial ischemia and PWV were independent predictors for combined CV events (HR 2.71, p <  0.001 and HR 2.42, p <  0.001, respectively).

Conclusions
Stress perfusion CMR provided prognostic utility in patients with known or suspected CAD. Adding aortic stiffness to stress perfusion CMR could improve risk assessment and prediction for future CV events.
Feasibility and behavioral effects of prolonged static and dynamic standing as compared to sitting in older adults with type 2 diabetes mellitus
Authors: Marusic Uros , Müller Martijn L. T. M. , Alexander Neil B. , Bohnen Nicolaas I. 
Published: June 2020

Abstract
Background
Physical inactivity is prevalent in older adults with type 2 diabetes mellitus (T2DM) and may exacerbate their clinical symptoms. The aim of this study was to examine the feasibility of 4-h regular versus more dynamic standing sessions while performing routine desktop activities as a non-exercise physical activity intervention in older adults with T2DM to increase non-exercise activity.

Methods
Twelve older adult patients with T2DM (3 female; age 71 ± 4 years; Body mass index 34 ± 5 kg/m2) completed three sessions (baseline sitting followed by “static” or “dynamic” desktop standing sessions). Participants stood behind a regular height-adjustable desk in the “static” standing session. An upright dynamic standing desk, which provides cues to make small weight-shifting movements, was used for the “dynamic” standing session. Oxygen consumption, cognitive performance, as well as net standing duration, total movement activity, and musculoskeletal discomfort were assessed during all three sessions.

Results
All participants were able to complete all sessions. Oxygen consumption and overall movements progressively increased from sitting to static and dynamic standing, respectively (p < 0.001). The duration of breaks during standing (p = 0.024) and rate of total musculoskeletal discomfort development (p = 0.043) were lower in the dynamic standing compared to static standing sessions. There was no evidence of executive cognitive worsening during either standing session compared to sitting.

Conclusions
Prolonged 4-h standing as a simple non-exercise physical intervention is feasible in older adults with T2DM and may have metabolic (oxygen consumption) benefits. Increasing movement during desktop standing may offer incremental benefits compared to regular standing. Prolonged desktop standing might provide an effective intervention in T2DM older participants to target sedentariness.

Trial registration
ClinicalTrials.gov (NCT04410055), retrospectively registered May 27, 2020.
Understanding the holistic experiences of living with a kidney transplant: an interpretative phenomenological study (protocol)
Authors: McKeaveney C. , Noble H. , Courtney A. E. , Gill P. , Griffin S. , Johnston W. , Maxwell A. P. , Teasdale F. , Reid J. 
Published: June 2020

AbstractBackgroundCurrently very little is known about the perceptions and experiences of kidney transplant recipients from a qualitative perspective. As highlighted by the European Kidney Health Alliance recommendations, providing holistic care to kidney patients is important however this is currently an unmet care need in renal disease. It is imperative to understand patient experiences to ensure that they are included in key strategies and future renal service planning. Ignoring these important patient views means that there is a significant risk of inappropriate renal service provision and lack of adequate support impacting on overall health.MethodA purposive sampling strategy will recruit individuals currently living with a kidney transplant, 6 months to 5 years post-transplant. A maximum of 30 patients will be recruited between two Regional Nephrology units within the United Kingdom via clinical gatekeepers. In-depth interviews will be undertaken with participants living with a kidney transplant across the two sites. Interviews will be digitally-recorded, transcribed verbatim and subjected to interpretative phenomenological analysis.DiscussionRenal healthcare professionals need to understand more than the biological impact of receiving a kidney transplant. Understanding the holistic and multi-domain experiences that these patients experience will help healthcare professionals to recognize the needs of this group and ensure more responsive care.
Prediction of generalization of ocular myasthenia gravis under immunosuppressive therapy in Northwest China
Authors: Ding Jiaqi , Zhao Sijia , Ren Kaixi , Dang Dan , Li Hongzeng , Wu Fang , Zhang Min , Li Zhuyi , Guo Jun 
Published: June 2020

Abstract
Background
It is well demonstrated that immunosuppressants can reduce, but not eliminate the risk of generalized development in ocular myasthenia gravis (OMG). In this study, we aimed to explore the predictive factors of generalized conversion of OMG patients who received immunosuppressive treatments.

Methods
OMG patients under immunosuppressive treatments in Tangdu Hospital from June 2008 to June 2012 were retrospectively reviewed. Baseline clinical characteristics were documented. Patients were followed up regularly by face-to-face interview and the main outcome measure was generalized conversion. The logistic regression analysis was performed to determine the predictive factors of generalization of OMG.

Results
Two hundred twenty-three eligible OMG patients completed the final follow-up visit and 38 (17.0%) progressed to generalized MG (GMG) at a median time to generalization of 0.9 year. Patients with adult onset and positive repetitive nerve stimulation (RNS) of facial or axillary nerve had higher conversion rate than those with juvenile onset and negative RNS (p = 0.001; p = 0.019; p = 0.015, respectively). Adult-onset patients converted earlier than juvenile-onset OMG patients (p = 0.014). Upon multivariate logistic regression analysis, age of onset (Odds ratio [OR] 1.023, 95% confidence interval [CI] 1.006–1.041, p = 0.007) and positive facial nerve RNS (OR 2.826, 95%CI 1.045–5.460, p = 0.038) were found to be positively associated with generalized development. Moreover, an obviously negative association was found for disease duration (OR 0.603, 95%CI 0.365–0.850, p = 0.019).

Conclusions
Age of onset, disease duration and facial nerve RNS test can predict generalized conversion of OMG under immunosuppressive therapy. Adult-onset, shorter disease duration and facial nerve RNS-positive OMG patients have a higher risk of generalized development.
Metrics of perineal support (MOPS) study
Authors: Kalis Vladimir , Rusavy Zdenek , Havelkova Linda , Zitka Tomas , Tolar David , Ismail Khaled M. 
Published: June 2020

Abstract
Background
Manual perineal protection (MPP) is an intrapartum intervention suggested to protect perineal integrity during childbirth. Proper execution of MPP is complex and evaluation of its true contribution is difficult in the clinical setting because of the large number of obstetric variables, some of which are hardly quantifiable. In this study we aimed to gather initial data on the forces executed by the accoucheur’s thumb, index and middle fingers during MPP at the time of fetal head expulsion, quantify the duration of the intervention and investigate the timely interaction of the different components of MPP.

Methods
Two bespoke right-handed measurement gloves (MG), with built in sensors, were designed and produced. The MG allowed the electronic real-time measurement of applied forces during MPP and transferred this data wirelessly to an integrated computer system. Sterile gloves were worn over the MG when used at the time of birth. The study was undertaken between January and December 2019. Singleton, term pregnant women having their first vaginal birth who provided a valid written consent were enrolled into this prospective pilot study. All deliveries were undertaken by one of two obstetricians experienced in MPP.

Results
Twenty women were enrolled. The mean duration of execution of MPP during the last contraction was 13.6 s. In 20% it lasted < 5 s. The overall mean values of the average and maximum forces of the thumb, index and middle fingers were 26.7 N; 25.5 N; 20.2 N and 34.3 N; 32.6 N; and 27.6 N respectively. The onset of fingers and thumb activity was simultaneous in 13 cases (65%), while in seven (35%) deliveries the middle finger’s force activity was initiated later.

Conclusions
MPP during fetal head expulsion happens over a short period of time. In the majority of cases the thumb and fingers actions started simultaneously. There were differences in the duration of application and the forces executed by the fingers and thumb between the two practitioners, however this was only significant for thumb measurements. The results obtained will aid in improving further MPP modeling studies to optimize the technique.
Innovative health care mobility services in the US
Authors: Wolfe Mary K. , McDonald Noreen C. 
Published: June 2020

Abstract
Background
Transportation barriers prevent millions of people from accessing health care each year. Health policy innovations such as shared savings payment models (commonly used in accountable care organizations) present financial incentives for providers to offer patient transportation to medical care. Meanwhile, ridesourcing companies like Uber and Lyft have entered the market to capture a significant share of spending on non-emergency health care transportation. Our research examines the current landscape of innovative health care mobility services in the US.

Methods
We conducted an environmental scan to identify case examples of utilization of ridesourcing technology to facilitate non-emergency health care transportation and developed a typology of innovative health care mobility services. The scan used a keyword-based search of news publications with inductive analysis. For each instance identified, we abstracted key information including: stakeholders, launch date, transportation provider, location/service area, payment/booking method, target population, level of service, and any documented outcomes.

Results
We discovered 53 cases of innovation and among them we identified three core types of innovation or collaboration. The first and most common type of innovation is when a health care provider leverages ridesourcing technology to book patient trips. This involves both established and nascent transportation companies tailoring the ridesourcing experience to the health care industry by adding HIPAA-compliance to the booking process. The second type of innovation involves an insurer or health plan formally partnering with a ridesourcing company to expand transportation offerings to beneficiaries or offer these services for the first time. The third type of innovation is when a paratransit provider partners with a ridesourcing company; these cases cite increased flexibility and reliability of ridesourcing services compared to traditional paratransit.

Conclusions
Ridesourcing options are becoming a part of the mode choice set for patients through formal partnerships between ridesourcing companies, health care providers, insurers, and transit agencies. The on-demand nature of rides, booking flexibility, and integration of ride requests and payment options via electronic medical records appear to be the strongest drivers of this innovation.
DNA steganography: hiding undetectable secret messages within the single nucleotide polymorphisms of a genome and detecting mutation-induced errors
Authors: Na Dokyun 
Published: June 2020

Abstract
Background
As cell engineering technology advances, more complex synthetically designed cells and metabolically engineered cells are being developed. Engineered cells are important resources in industry. Similar to image watermarking, engineered cells should be watermarked for protection against improper use.

Results
In this study, a DNA steganography methodology was developed to hide messages in variable regions (single nucleotide polymorphisms) of the genome to create hidden messages and thereby prevent from hacking. Additionally, to detect errors (mutations) within the encrypted messages, a block sum check algorithm was employed, similar to that used in network data transmission to detect noise-induced information changes.

Conclusions
This DNA steganography methodology could be used to hide secret messages in a genome and detect errors within the encrypted messages. This approach is expected to be useful for tracking cells and protecting biological assets (e.g., engineered cells).