bluuebunny/crossref_metadata_2025_split huggingface dataset:
Motion in Magnetic Resonance
Authors: Runge Val M. , Richter Johannes K. , Heverhagen Johannes T. 
Published: April 2019

Abstract
Recent innovations in magnetic resonance, involving both hardware and software, that effectively deal with motion—whether inadvertent on the part of the patient or due to respiration and cardiac contraction—are reviewed, emphasizing major current advances. New technology involving motion sensing (kinetic, respiratory, and beat) is enabling simpler, faster, and more robust monitoring of the sources of motion. This information is being integrated, with new innovative imaging approaches, to effectively manage motion and its impact on image quality. Additional impact has been made by the use of compressed sensing and simultaneous multislice imaging, with these techniques maturing and being adopted to decrease scan time and thus the effect of motion. Guidance in terms of clinical use for techniques that effectively combat motion is provided, focusing on enabling faster and improved clinical scans. Magnetic resonance imaging is on the cusp of a major new leap forward in terms of image quality and clinical utility enabled by these technological advances.
Postoperative Complications of Plastic and Reconstructive Surgery in Solid Organ Transplant Recipients
Authors: Ka Soon Il , Kim Sung-Eun 
Published: April 2019

Introduction:
As the number of organ transplants and the survival rate increase, solid organ transplant patients will need more plastic and reconstructive surgery. However, such patients take immunosuppressants, including prednisone, which makes wound healing slower and plastic surgeons more hesitate to operate. In this study, we examined postoperative complications of organ transplant patients who have undergone plastic and reconstructive surgery.

Materials & Methods:
Between 2002 and 2018, the total number of patients who visited our clinic after receiving organ transplants was 77. Retrospective reviews were performed on 35 patients, excluding those who received conservative treatment. Demographics, underlying diseases, causes of organ transplantation, immunosuppressive regimen, types of procedures, and postoperative complications were analyzed.

Results:
A total of 35 patients received 42 procedures. Eleven patients had undergone kidney transplantation, and 24 had undergone liver transplantation. The type of procedures were local flap (23.8%), primary closure (23.8%), skin graft (11.9%), and free flap (2.4%). There were 2 cases of aesthetic surgery. Among all the cases, complications occurred in 8 procedures (19%). Hematoma was the most common complication, followed by skin necrosis. All except 3 patients were completely healed within 6 weeks.

Discussion:
This study showed that hematoma was the most frequently occurring complication. In a few cases, wound healing was delayed. So, bleeding control was very important to prevent the development of hematoma. And organ transplants may not be a problem for plastic and reconstructive surgery.
Outcome of 1000 Patients With Gastrointestinal Stromal Tumor (GIST) Treated by Surgery in the Pre- and Post-imatinib Eras
Authors: Cavnar Michael J. , Seier Kenneth , Curtin Christina , Balachandran Vinod P. , Coit Daniel G. , Yoon Sam S. , Crago Aimee M. , Strong Vivian E. , Tap William D. , Gönen Mithat , Antonescu Cristina R. , Brennan Murray F. , Singer Sam , DeMatteo Ronald P. 
Published: April 2019

Objective:
To characterize the results of surgery for gastrointestinal stromal tumor (GIST) in the pre and post-imatinib eras at a single institution and to identify current prognostic clinicopathologic factors.

Background:
Imatinib has radically changed the management of GIST, yet the magnitude of impact on outcome across the spectrum of GIST presentation and relevance of historical prognostic factors are not well defined.

Methods:
We retrospectively analyzed 1000 patients who underwent surgery for GIST at our institution from 1982 to 2016. Patients were stratified by presentation status as primary tumor only (PRIM), primary with synchronous metastasis (PRIM + MET), or metachronous recurrence/metastases (MET), and also imatinib era (before and after it became available). Cox proportional-hazard models and Kaplan-Meier methods were used to model and estimate overall survival (OS) and recurrence-free survival (RFS).

Results:
OS was longer in the imatinib era compared with the pre-imatinib era in each presentation group, including in Miettinen high-risk primary tumors. Among PRIM patients from the pre-imatinib era, tumor site, size, and mitotic rate were independently associated with OS and RFS on multivariate analysis. PRIM patients in the imatinib era who received imatinib (neoadjuvant and/or adjuvant) had higher risk tumors, but after adjusting for treatment, only size >10 cm remained independently prognostic of RFS [hazard ratio (HR) 3.85, 95% confidence interval (CI) 2.00–7.40, P < 0.0001) and OS (HR 3.37, 95% CI 1.60–7.13, P = 0.001)].

Conclusions:
Patients treated in the imatinib era had prolonged OS across all presentations. In the imatinib era, among site, size, and mitotic rate, high-risk features were associated with treatment with the drug, but only size >10 cm correlated with outcome. Imatinib should still be prescribed for patients with high-risk features.
Impact of Oral Immunonutrition on Postoperative Morbidity in Digestive Oncologic Surgery
Authors: Challine Alexandre , Rives-Lange Claire , Danoussou Divya , Katsahian Sandrine , Ait Boudaoud Amel , Gaujoux Sébastien , Dousset Bertrand , Carette Claire , Lazzati Andrea , Czernichow Sébastien 
Published: April 2019

Objective:
The objective of the present study was to assess the effect of preoperative immunonutrition on a nationwide scale.

Background:
According to international guidelines, immunonutrition should be prescribed before major oncologic digestive surgery to decrease postoperative morbidity. Nevertheless, this practice remains controversial.

Methods:
We used a prospective national health database named “Echantillon généraliste des Bénéficiaires.” Patients were selected with ICD10 codes of cancer and digestive surgery procedures from 2012 to 2016. Two groups were identified: with reimbursement of immunonutrition 45 days before surgery (IN-group) or not (no-IN-group). Primary outcome was 90-day severe morbidity. Secondary outcomes were postoperative length of stay (LOS) and overall survival. Logistic regression and survival analysis adjusted with IPW method were performed.

Results:
One thousand seven hundred seventy-one patients were included. The proportion of different cancers was as follows: 72% patients were included in the colorectal group, 14% in the hepato-pancreato-biliary group, and 12% in the upper gastrointestinal group. Patients from the IN-group (n = 606, 34%) were younger (67.1 ± 11.8 vs 69.2 ± 12.2 years, P < 0.001), with increased use of other oral nutritional supplements (49.5% vs 31.8%, P < 0.001) and had more digestive anastomoses (89.4% vs 83.0%, P < 0.001). There was no significant difference between the 2 groups for 90-day severe morbidity [odds ratio (OR): 0.91, 95% confidence interval (95% CI): 0.73–1.14] or in survival (hazard ratio: 0.89, 95% CI: 0.73–1.08). LOS were shorter in the IN-group [−1.26 days, 95% CI: −2.40 to −0.10)].

Conclusion:
The preoperative use of immunonutrition before major oncologic digestive surgery was not associated with any significant difference in morbidity or mortality. However, the LOS was significantly shorter in the IN-group.
A Study on Radial Margin Status in Resected Perihilar Cholangiocarcinoma
Authors: Shinohara Kentaro , Ebata Tomoki , Shimoyama Yoshie , Mizuno Takashi , Yokoyama Yukihiro , Yamaguchi Junpei , Onoe Shunsuke , Watanabe Nobuyuki , Nagino Masato 
Published: April 2019

Objective:
To investigate radial margin (RM) status in resected perihilar cholangiocarcinoma (PHCC) and to evaluate the incidence of positive RM and its effect on survival.

Background:
Although numerous studies have reported on ductal margin (DM) status in resected PHCC, no studies have addressed RM status.

Methods:
Patients who underwent hepatectomy for PHCC between 2001 and 2014 were retrospectively reviewed. After formalin fixation, resected specimens were serially sectioned at 5-mm intervals. All serial sections were color-copied, and RMs and DMs were identified and indicated on the color copies.

Results:
Among 478 patients, 85 (17.8%) had positive surgical margins (R1 resection); of the 85 patients, 37 had positive RM alone, 33 had positive DM alone, and the remaining 15 had both positive RM and positive DM. Overall, 52 (61.2%) patients had positive RM. The sites of positive RM included the liver transection plane (n = 20) and the dissection plane in the hepatoduodenal ligament (n = 32). RM positivity on the liver transection plane was higher in left hepatectomy than in other hepatectomies (9.2% vs 1.9%, P < 0.001). RM positivity in the hepatoduodenal ligament was higher in left-sided hepatectomy than in right-sided hepatectomy (8.7% vs 3.6%, P = 0.031). The survival of the patients with positive RM was poorer than that of R0 patients (MST 2.1 vs 4.9 yrs, P < 0.001) and was similar to that of patients with positive DM. Multivariate analysis identified positive RM as one of the independent prognostic factors.

Conclusions:
Positive RM was the most common cause of R1 resection of PHCC and had similarly negative effects on survival as positive DM. Meticulous handling of the resected specimen is important to accurately evaluate RM status together with DM status.
Yoga for Women With Urgency Urinary Incontinence: A Pilot Study
Authors: Tenfelde Sandi , Tell Dina , Garfield Lindsey , Mathews Herbert , Janusek Linda 
Published: April 2019

Objectives
The objective of this study was to evaluate the feasibility of a gentle yoga program for women with urgency urinary incontinence (UUI). Also, these preliminary data can evaluate if yoga improves symptom burden, quality of life, and inflammatory biomarkers for women with UUI.

Methods
This prospective nonrandomized single-arm pilot study evaluated the effectiveness of a twice-weekly, 8-week gentle yoga intervention to reduce UUI symptom burden. Changes in symptom burden were measured using the Pelvic Floor Distress Inventory 20. Secondary measures included quality of life, depressive symptoms, sleep, stress, anxiety, and inflammatory biomarkers. Outcomes were evaluated with paired t testing.

Results
Twelve women completed the yoga intervention with no adverse outcomes noted. Urgency symptom burden was significantly improved after the intervention (P = 0.01), and women reported an increase in quality of life (P = 0.04) after the yoga intervention. Following the yoga intervention, the majority of women reported symptoms as “much better” (n = 4 [33%]) and “a little better” (n = 5 [42%]), with 3 women (25%) reporting “no change.” Women also reported significant reduction in depressive symptoms (P = 0.03) and better quality of sleep (P = 0.03). No significant changes were found in anxiety or stress perception. Plasma levels of the inflammatory biomarker tumor necrosis factor α were reduced after yoga intervention (P = 0.009); however, no significant postyoga changes were found for interleukin 6 or C-reactive protein.

Conclusions
This study provides preliminary evidence that yoga is a feasible complementary therapy that reduces incontinence symptom burden, along with improving quality of life, depressive symptoms, and sleep quality. Additionally, yoga may lower inflammatory biomarkers associated with incontinence.
Normothermic Machine Perfusion Enhances Intraoperative Hepatocellular Synthetic Capacity: A Propensity Score-matched Analysis
Authors: Ionescu Mihnea-Ioan , Tillakaratne Suchintha , Hodson James , Gunson Bridget , Nasralla David , Pinter Carvalheiro da Silva Boteon Amanda , Sermon Kate , Mergental Hynek , Isaac John R. , Roberts John K. , Muiesan Paolo , Friend Peter , Mirza Darius F. , Bennett Davinia , Perera M. Thamara P.R. 
Published: April 2019

Background.
Normothermic machine perfusion (NMP) of liver grafts is increasingly being incorporated in clinical practice. Current evidence has shown NMP plays a role in reconditioning the synthetic and energy capabilities of grafts. Intraoperative coagulation profile is a surrogate of graft quality and preservation status; however, to date this aspect has not been documented.

Methods.
The liver transplantation recipients who received NMP liver grafts in the QEHB between 2013 and 2016 were compared in terms of intraoperative thromboelastography characteristics (R time, K time, α-angle, maximum amplitude, G value, and LY30) to a propensity score-matched control group, where the grafts were preserved by traditional static cold storage (SCS).

Results.
After propensity matching, none of the thromboelastography characteristics were found to differ significantly between the 72 pairs of SCS and NMP organs when measured preimplantation. However, postimplantation, NMP organs had significantly shorter K time (median: 2.8 vs 3.6 min, P = 0.010) and R + K time (11.4 vs 13.7 min, P = 0.016), as well as significantly larger α-angle (55.9° vs 44.8°, P = 0.002), maximum amplitude (53.5 vs 49.6 mm, P = 0.044), and G values (5.8 vs 4.9k dynes/cm2, P = 0.043) than SCS organs. Hyperfibrinolysis after implantation was also mitigated by NMP, with fewer patients requiring aggressive factor correction during surgery (LY30 = 0, NMP vs SCS: 83% vs 60%, P = 0.004). Consequently, NMP organs required significantly fewer platelet units to be transfused during the transplant procedure (median: 0 vs 5, P = 0.001).

Conclusions.
In this study, we have shown that NMP liver grafts return better coagulation profiles intraoperatively, which could be attributed to the preservation of liver grafts under physiological conditions.
NRF2 drug repurposing using a question-answer artificial intelligence system
Authors: Mickael Michel-Edwar , Pajares Marta , Enache Ioana , Manda Gina , Cuadrado Antonio 
Published: April 2019

AbstractDrug repurposing represents an innovative approach to reduce the drug development timeline. Text mining using artificial intelligence methods offers great potential in the context of drug repurposing. Here, we present a question-answer artificial intelligence (QAAI) system that is capable of repurposing drug compounds. Our system employs a Google semantic AI universal encoder to compute the sentence embedding of an imposed text question in relation to publications stored in our RedBrain JSON database. Sentences similarity is calculated using a sorting function to identify drug compounds. We demonstrate our system’s ability to predict new indications for already existing drugs. Activation of the NRF2 pathway seems critical for enhancing several diseases prognosis. We experimentally validated the prediction for the lipoxygenase inhibitor drug zileuton as a modulator of the NRF2 pathway in vitro, with potential applications to reduce macrophage M1 phenotype and ROS production. This novel computational method provides a new approach to reposition of known drugs in order to treat neurodegenerative diseases. Github for the database and the code can be downloaded fromhttps://gist.github.com/micheledw/5a165b44345d45105d715340b88c756b
Trichoplein controls endothelial cell function by regulating autophagy
Authors: Martello Andrea , Lauriola Angela , Mellis David , Parish Elisa , Dawson John C , Imrie Lisa , Vidmar Martina , Gammoh Noor , Mitic Tijana , Brittan Mairi , Mills Nicholas , Carragher Neil O , D’Arca Domenico , Caporali Andrea 
Published: April 2019

AbstractAutophagy is an essential cellular quality control process that emerged critical for vascular homeostasis. Here we describe, the role for Trichoplein (TCHP) protein in linking autophagy with endothelial cells (ECs) function. The depletion of TCHP in ECs impairs migration and sprouting. TCHP directly binds PCM1, to regulate degradation of GABARAP, thus leading to a defective autophagy. Mechanistically, TCHP is indispensable for autophagosome maturation and its depletion resulted in the accumulation of SQSTM1/p62 (p62) and unfolded protein aggregates in ECs. The latter process is coupled to TCHP-mediated NF-kB activation. Of note, low levels of TCHP and high p62 levels were detected in primary ECs from patients with coronary artery disease. In addition, Tchp knock-out mice showed accumulation of p62 in the heart and cardiac vessels and reduced cardiac vascularization. Here, we reveal an autophagy-mediated mechanism for TCHP down-regulation, which poses a plausible target for regulation of endothelial function.
Genomic analysis reveals selection signatures of Yucatan miniature pig on its X chromosome during domestication
Authors: Zhang Wei , Wang Yuanlang , Yang Min , Wu Xudong , Zhang Xiaodong , Ding Yueyun , Yin Zongjun 
Published: April 2019

AbstractYucatan miniature pig (YMP), a naturally small breed, has been domesticated in the hot and arid Yucatan Peninsula for a long time. However, its selection signatures on the X chromosome remain poorly understood. In this study, we focused on elucidating the selection signatures of YMP on the X chromosome during its domestication and breeding, using the whole-genome sequencing data. We performed population admixture analyses to determine its genetic relationships with other domesticated breeds and wild boars. Subsequently, we used two approaches, the fixation index (Fst) and π ratios, to identify the selection signatures with 100 kb windows sliding in 10 kb steps. As a result, we found that the ectodysplasin A (EDA) gene was related with hypoplasia or absence of hair and sweat glands. This could uncover the relative lack of odor in YMP and the presence of hypoplasia or absence of hair in pigs. Furthermore, we found several genes under selection in other animals. A bioinformatics analysis of the genes in selection regions showed that they were associated with growth, lipid metabolism, reproduction, and immune system. Our findings will lead to a better understanding of the unique genetic and phenotypic characteristics of YMP and offer a plausible method for their utilization as an animal model for hair and odor disease research.
Clinical long-read sequencing of the human mitochondrial genome for mitochondrial disease diagnostics
Authors: Wood Elizabeth , Parker Matthew D , Dunning Mark J , Hesketh Sirisha , Wang Dennis , Pink Ryan , Fratter Carl 
Published: April 2019

AbstractPurposeLong-read, third generation, sequencing technologies have the potential to improve current state of the art diagnostic strategies. In order to determine if long-read sequencing technologies are suitable for the diagnosis of mitochondrial disorders due to mitochondrial DNA (mtDNA) variants, particularly large deletions, we compared the performance of Oxford Nanopore Technologies (ONT) MinION to current diagnostic methods.MethodsWe sequenced mtDNA from nine patients with mtDNA deletion disorders and three normal controls with both ONT MinION and Illumina MiSeq. We applied a computational pipeline to estimate the positions of mtDNA deletions in patients, and subsequently validated the breakpoints using Sanger sequencing.ResultsWe were able to detect mtDNA deletions with a MinION workflow, successfully calling the disease causing event in all cases. Sequencing coverage was in most cases significantly more (p=0.03, Wilcoxon test) uniform with MinION than with MiSeq and subsequent correction of MinION reads improved breakpoint accuracy and reduced false positives. Although heteroplasmic single nucleotide variants are detectable, the high number of false positives and false negatives precludes their use in diagnostics at this time.ConclusionThe MinION is becoming an increasingly attractive diagnostic tool due to the reducing cost, increasing accuracy, and the speed at which data can be obtained.
Altered dynamics may drift pathological fibrillization in membraneless organelles
Authors: Tüű-Szabó B. , Hoffka G. , Duro N. , Koczy L. , Fuxreiter M. 
Published: April 2019

AbstractProtein phase transition can generate non-membrane bound cellular compartments, which can convert from liquid-like to solid-like states. While the molecular driving forces of phase separation have been largely understood, much less is known about the mechanisms of material-state conversion. We apply a recently developed algorithm to describe the weak interaction network of multivalent motifs, and simulate the effect of pathological mutations. We demonstrate that linker dynamics is critical to the material-state of biomolecular condensates. We show that linker flexibility/mobility is a major regulator of the weak, heterogeneous meshwork of multivalent motifs, which promotes phase transition and maintains a liquid-like state. Decreasing linker dynamics increases the propensity of amyloid-like fragments via hampering the motif-exchange and reorganization of the weak interaction network. In contrast, increasing linker mobility may compensate rigidifying mutations, suggesting that the meshwork of weak, variable interactions may provide a rescue mechanism from aggregation. Motif affinity, on the other hand, has a moderate impact on fibrillization. Here we demonstrate that the fuzzy framework provides an efficient approach to handle the intricate organization of membraneless organelles, and could also be applicable to screen for pathological effects of mutations.
Joint RElaxation-Diffusion Imaging Moments (REDIM) to probe neurite microstructure
Authors: Ning Lipeng , Gagoski Borjan , Szczepankiewicz Filip , Westin Carl-Fredrik , Rathi Yogesh 
Published: April 2019

AbstractJoint relaxation-diffusion measurements can provide new insight about the tissue microstructural properties. Most recent methods have focused on inverting the Laplace transform to recover the joint distribution of relaxation-diffusion. However, as is well-known, this problem is notoriously ill-posed and numerically unstable. In this work, we address this issue by directly computing the joint moments of transverse relaxation rate and diffusivity, which can be robustly estimated. To zoom into different parts of the joint distribution, we further enhance our method by applying multiplicative filters to the joint probability density function of relaxation and diffusion and compute the corresponding moments. We propose an approach to use these moments to compute several novel scalar indices to characterize specific properties of the underlying tissue microstructure. Furthermore, for the first time, we propose an algorithm to estimate diffusion signals that are independent of echo time based on the moments of the marginal probability density function of diffusion. We demonstrate its utility in extracting tissue information not contaminated with multiple intra-voxel relaxation rates. We compare the performance of four types of filters that zoom into tissue components with different relaxation and diffusion properties and demonstrate it on an in-vivo human dataset. Experimental results show that these filters are able to characterize heterogeneous tissue microstructure. Moreover, the filtered diffusion signals are also able to distinguish fiber bundles with similar orientations but different relaxation rates. The proposed method thus allows to characterize the neural microstructure information in a robust and unique manner not possible using existing techniques.