bluuebunny/crossref_metadata_2025_split huggingface dataset:
lncRNA CRNDE promotes the proliferation and metastasis by acting as sponge miR-539-5p to regulate POU2F1 expression in HCC
Authors: Li Zhixi , Wu Gang , Li Jie , Wang Youyu , Ju Xueming , Jiang Wenjun 
Published: March 2020

Abstract
Background This article focuses on the roles and mechanism of lncRNA CRNDE on the progression of HCC. Methods We used qRT-PCR to detect the expression of lncRNA CRNDE in HCC cells, normal cells and clinical tissues. MTT assay, FCM analysis, Transwell migration and invasion assay were used to detect the effects of lncRNA CRNDE on cell viability, apoptosis, migration and invasion of HCC cells. The expression of apoptosis-related proteins Bcl-2, Bax, Cleaved Caspase 3, Cleaved Caspase 9, EMT epithelial marker E-cadherin and mesothelial marker Vimentin were analyzed by Western blot. Online prediction software was used to predict the binding sites between lncRNA CRNDE and miR-539-5p, or miR-539-5p and POU2F1 3’UTR. Dual luciferase reporter assay, qRT-PCR and RNA pulldown were used to detect target-relationship between lncRNA CRNDE and miR-539-5p. Dual luciferase reporter assay, qRT-PCR, Western blot and Immunofluorescence were used to detect target-relationship between miR-539-5p and POU2F1. qRT-PCR was used to detect the expression of miR-539-5p and POU2F1 in clinical tissues. Rescue experiments was used to evaluate the association among lncRNA CRNDE, miR-539-5p and POU2F1. Finally, we used Western blot to detect the effects of lncRNA CRNDE, miR-539-5p and POU2F1 on NF-κB and AKT pathway. Results lncRNA CRNDE was highly expressed in HCC cells and HCC tissues compared with normal cells and the corresponding adjacent normal tissues. lncRNA CRNDE promoted the cell viability, migration and invasion of HCC cells, while inhibited the apoptosis and promoted the EMT process of HCC cells. lncRNA CRNDE adsorbed miR-539-5p acts as a competitive endogenous RNA to regulate POU2F1 expression indirectly. In HCC clinical tissues, miR-539-5p expression decreased and POU2F1 increased compared with the corresponding adjacent normal tissues. lncRNA CRNDE/miR-539-5p/POU2-
F1 participated the NF-κB and AKT pathway in HCC. Conclusion lncRNA CRNDE promotes the expression of POU2F1 by adsorbing miR-539-5p, thus promoting the progression of HCC.
Keywords : HCC, lncRNA CRNDE, miR-539-5p, POU2F1, ceRNA
Putting together the pieces of the puzzle – Part II - Assessing harbour porpoise (Phocoena phocoena) carcasses potentially subjected to grey seal (Halichoerus grypus) predation
Authors: Neer Abbo van , Gross Stephanie , Kesselring Tina , Grilo Miguel L. , Ludes-Wehrmeister Eva , Roncon Giulia , Siebert Ursula 
Published: March 2020

Abstract
The authors have withdrawn this preprint from Research Square.
Anatomical Variation of the Psoas Valley: A Scoping Review
Authors: Kuroda Yuichi , Rai Ankit , Saito Masayoshi , Khanduja Vikas 
Published: March 2020

Abstract
Background: This scoping review aimed to investigate the literature on the anatomy of the psoas valley, an anterior depression on the acetabular rim, and propose a unified definition of the anatomical structure, describe its dimensions, anatomical variations and clinical implications. Methods: A systematic computer search of EMBASE, PubMed and Cochrane for literature related to the psoas valley was undertaken using Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) guidelines. Clinical outcome studies, prospective/retrospective case series, case reports and review articles that described the psoas valley and its synonyms were included. Studies on animals as well as book chapters were excluded. Results: Of the 313 articles, the filtered literature search identified 14 papers describing the psoas valley and its synonyms such as iliopsoas notch, a notch between anterior inferior iliac spine and the iliopubic eminence, Psoas-U and anterior wall depression. Most of these were cross-sectional studies that mainly analyzed normal skeletal hips. In terms of anatomical variation, 4 different configurations of the anterior acetabular rim have been identified and it was found that the curved type was the most frequent while the straight type may be nonexistent. Additionally, the psoas valley tended to be deeper in males as compared with females. Several papers established the psoas valley, or Psoas-U in a consistent location at approximately 3 o'clock on the acetabular rim which may have implications with labral pathology. Conclusion: This review highlights the importance of the anatomy of the psoas valley which is a consistent bony landmark. The anatomy and the anatomical variations of the psoas valley need to be well-appreciated by surgeons involved in the management of young adults with hip pathology and also joint replacement surgeons to ensure appropriate seating of the acetabular component.
Weakly-supervised Convolutional Neural Networks of Renal Tumor Segmentation in Abdominal CTA Images
Authors: Yang Guanyu , Wang Chuanxia , Yang Jian , Chen Yang , Tang Lijun , Shao Pengfei , Dillenseger Jean-Louis , Shu Huazhong , Luo Limin 
Published: March 2020

Abstract
Background: Renal cancer is one of the ten most common cancers in human beings. The laparoscopic partial nephrectomy (LPN) is an effective way to treat renal cancer. Localization and delineation of the renal tumor from pre-operative CT Angiography (CTA) is an important step for LPN surgery planning. Recently, with the development of the technique of deep learning, deep neural networks can be trained to provide accurate pixel-wise renal tumor segmentation in CTA images. However, constructing the training dataset with a large amount of pixel-wise annotations is a time-consuming task for the radiologists. Therefore, weakly-supervised approaches attract more interest in research. Methods: In this paper, we proposed a novel weakly-supervised convolutional neural network (CNN) for renal tumor segmentation. A three-stage framework was introduced to train the CNN with the weak annotations of renal tumors, i.e. the bounding boxes of renal tumors. The framework includes pseudo masks generation, group and weighted training phases. Clinical abdomina CT angiographic images of 200 patients were applied to perform the evaluation. Results: Extensive experimental results show that the proposed method achieves a higher dice coefficient (DSC) of 0.826 than the other two existing weakly-supervised deep neural networks. Furthermore, the segmentation performance is close to the fully supervised deep CNN. Conclusions: The proposed strategy improves not only the efficiency of network training but also the precision of the segmentation.
A comparison among PCNL, Miniperc and Ultraminiperc for lower calyceal stones between 1 and 2 cm: A multicenter experience
Authors: Bozzini Giorgio , Aydogan Tahsin B , Sighinolfi Maria Chiara , Besana Umberto , Calori Alberto , Lorenzo Berti , Govorov Alexander , Pushkar Dmitry Y , Pini Giovannalberto , Pastore Antonio Luigi , Romero-Otero Javier , Rocco Bernardo , Buizza Carlo 
Published: March 2020

Abstract
Background Conventional Percutaneous Lithotripsy (PCNL) has been an effective, successful and easy approach for lower calyceal stones however risks of complications and nephron loss are inevitable. Our aim is to compare the efficacy and safety of PCNL, MiniPerc(MP) and UltraMiniPerc(UMP) for lower calyceal stones between 1 and 2 cm with a multicenter prospective randomized study. Methods Patients with single lower calyceal stone were enrolled. Exclusion criteria were the presence of coagulation impairments, age of <18 or >75, presence of infection or serious comorbidities. Patients were randomized in three groups; A: PCNL; B: MP; C: UMP. Patients were controlled with abdomen X-ray and computerized tomography scan after 3 months. A negative X-ray or an asymptomatic patient with stone fragments < 3 mm size were the criteria to assess the stone-free status. Patient characteristics, stone free rates (SFR)s, complications and re-treatment rates were analyzed. Results Between January 2015 and June 2018, 132 consecutive patients were enrolled. 44 patients for the Group A, 47 for Group B and 41 for Group C. The mean stone size were 16.38, 17.82 and 15.23mm respectively in Group A, B and C(p=0.34). The overall SFR was significantly higher in Group A(86.3%) and B(82.9%) as compared to Group C(78%)(p<0.05).The re-treatment rate was significantly higher in Group C(12.1%) and complication rates was higher in Group A (13.6%) as compared to others(p<0.05). Conclusions PCNL and MP were more effective than UMP to obtain a better SFR. Auxiliary and re-treatment rates were higher in UMP. On the other hand for such this kind of stones PCNL had more complications. Overall evaluation favors MP as a better indication in stones 1-2 cm size.
Slope Mass Rating-based Analysis to Assess Rockfall Hazard on Yogyakarta Southern Mountain, Indonesia
Authors: Triana Karlina , Hermawan Koko 
Published: March 2020

Abstract
The main road to the Parangtritis Beach tourism site in the southern Yogyakarta Province, Indonesia, has full of local and economic activities. The road was made mainly by karst mountains cutting and resulting in almost vertical long and high slopes by its side. Rockfall is being the most potential hazards occurred in this area. The purpose of this study is to determine the rockfalls hazard assessment along the main road using Slope Mass Rating (SMR) analysis. Parameters used in rockfall hazard assessment are SMR with additional valuation from the slope height and the block size. The necessary data of each parameter obtained by direct measurement and the uniaxial compressive strength test in the laboratory. Geomechanics analysis, stereographic projection analysis, and hazard parameters weighting are needed to produce research results in form Rockfall Hazard Zonation Map in the research location. The results showed that the largest percentage of rockfalls hazard class is very low class, with 83,83% of the total hazard classes, associated with normal SMR score (51,66 – 51,75), slope height between 2,85 – 4,57 m, and block size 0,2 – 0,3 m. Followed by intermediate class with 7,16% of the total hazard classes with very bad to bad SMR score (5,82 – 38,15), slope height between 4,26 – 8,96 m, and block size 0,3 – 1,0 m. In the third position followed by a low class with 4,28% of the total hazard classes with bad to normal SMR score (31,17 – 53,03), slope height between 3,52 – 5,28 m, and block size 0,2 – 0,7 m. The last position was taken by high class with 4,19% of the total hazard classes with very bad to bad SMR score (18,31 – 36,50), slope height between 3,62 – 7,82 m, and block size 0,7 – 1,3 m. The SMR analysis also identified the influence of rock types with the rockfall occurrence. Hazard zonation map verification showed a congeniality with the results of rockfalls quantity inventory in the research area.
Construct validity of the Functional Status Score for the Intensive Care Unit: a prospective observational study using actigraphy in mechanically-ventilated patients
Authors: Camus-Molina Agustín , González-Seguel Felipe , Castro-Ávila Ana Cristina , Leppe Jaime 
Published: March 2020

Abstract
Background The Functional Status Score for the Intensive Care Unit (FSS-ICU) is a widely used instrument, designed to measure the mobility of critically ill patients that is available in English, Portuguese, Turkish and Spanish. The lack of a gold standard for measuring mobility limits the validation of outcome measures. However, actigraphy, from which measures movement intensity can be derived, is a potential alternative in the intensive care unit (ICU). Thus, this study aimed to assess the construct validity (hypotheses testing) of the FSS-ICU using continuous actigraphy from ICU admission to ICU discharge. Methods This prospective observational study included mechanically-ventilated patients selected from a 12-bed academic medical-surgical ICU. The Chilean-Spanish version of the FSS-ICU was used to evaluate its correlation with activity counts, activity time (>99 counts per minute) and inactivity time (0-99 counts per minute) measured by actigraphy ( GT9X Link ActiGraph). The FSS-ICU was assessed on awakening and at ICU discharge, while actigraphy variables were recorded from ICU admission to ICU discharge. Results Of 92 patients screened, 30 were analysed. The median FSS-ICU was 19 (IQR 10–26) points on awakening and 28.5 (IQR 22–32) at ICU discharge. There was no floor/ceiling effect of the FSS-ICU at awakening (0%/0%) and only a ceiling effect at ICU discharge that was acceptable (0%/10%). Less activity time was associated with better mobility on the FSS-ICU at both awakening (rho = -0.62, P<0.001) and ICU discharge (rho = -0.79, P<0.001). Activity counts and activity time were not correlated as expected with the FSS-ICU. Conclusions The FSS-ICU had a strong correlation with inactivity time during the ICU stay. These findings enhance the available clinimetric properties of the FSS-ICU.
A high-resolution, spatially explicit estimate of fossil-fuel CO2 emissions from the Tokyo Metropolis, Japan
Authors: Cong Richao , Saito Makoto , Oda Tomohiro , Fukui Tetsuo , Hirata Ryuichi , Ito Akihiko 
Published: March 2020

Abstract
Background: The quantification of urban greenhouse gas (GHG) emissions is an important task in combating climate change. Emission inventories that include spatially explicit emission estimates facilitate the accurate tracking of emission changes, identification of emission sources, and formulation of policies for climate-change mitigation. Many currently available gridded emission estimates are based on the disaggregation of country- or state-wide emission estimates, which may be useful in describing city-wide emissions but are of limited value in tracking changes at subnational levels. Urban GHG emissions should therefore be quantified with a true bottom-up approach. Results: Multi-resolution, spatially explicit estimates of fossil-fuel carbon dioxide (FFCO2) emissions from the Tokyo Metropolis, Japan, were derived. Spatially explicit emission data were collected for point (e.g., power plants and waste incinerators), line (mostly traffic), and area (e.g., residential and commercial areas) sources. Emissions were mapped on the basis of emission rates calculated for source locations. Activity, emissions, and spatial data were integrated, and the results were visualized using a geographic information system approach. Conclusions: The annual total FFCO2 emissions from the Tokyo Metropolis in 2014 were 44,855 Gg CO2, with the road-transportation sector (16,323 Gg CO2) accounting for 36.4% of the total. Spatial emission patterns were verified via a comparison with the East Asian Air Pollutant Emission Grid Database for Japan (EAGrid-Japan), which demonstrated the applicability of this methodology to other prefectures and therefore the entire country.
Exploring willingness to participate in future Human Infection Studies in Lusaka, Zambia: A nested qualitative exploratory study
Authors: Kunda-Ng'andu Evelyn Muleba , Chirwa Masuzyo , Mwamba Chanda , Simuyandi Michelo , Chipungu Jenala , Ngandu Esnart , Mwanyungwi Hope , Chilengi Roma , Sharma Anjali 
Published: March 2020

Abstract
Background: Human Infection Studies (HIS) involve intentional infection of volunteers with a challenge agent or pathogen in controlled conditions with the aim of developing vaccines. Though sub-Saharan Africa carries the highest burden of vaccine-preventable diseases, the region is only now being primed to conduct HIS relevant to its population. Given the imminent introduction of HIS in Zambia, we sought to understand potential participants’ willingness to volunteer for such studies. Methods : We used a qualitative exploratory approach to understand potential participants’ perceptions on HIS participation using the example of typhoid. Healthy adults, recruited using random selection from higher learning institutions in Lusaka, participated in 15 in-depth interviews (IDIs) while others were purposefully included in five focus group discussions (FGDs). Results : Participants considered typhoid a serious disease with potential for life-long consequences and death. After sharing audio visual materials introducing the concepts of HIS, some participants expressed unrestricted willingness to participate, others said that they needed to consult parents and professors, and some expressed fear of death and illness. Though willing to be quarantined for up to six months, participants expressed concerns regarding separation from family and duties, having insufficient information to decide, inadequate access to care, severe disease, life-long injury or side-effects, death, and vaccine failure. These concerns along with possibility of underlying conditions that compromise individual immunity, competing priorities, parental refusal, and distrust of study or vaccine efficacy could lead to refusal to participate. Reasons for willingness to participate included monetary compensation, altruism and being part of a team that comes up with a vaccine. Conclusions: Though afraid of deliberate typhoid infection, potential participants are willing to participate if given adequate information, time to consult trusted persons, compensation and assurance of adequate care.
Tolerance to Nitrogen ions enrichment in a Gulf of Mexico's freshwater submerged grass
Authors: Carrera Violeta Ruiz , Sánchez Alberto J , Leal Elvira Rios 
Published: March 2020

Abstract
BackgroundTolerance to the enrichment of ionic nitrogen (N) with ammonium (NH 4 ) and nitrate (NO 3 ) needs to be distinguished in a submerged grass ecotype-species of freshwater wetlands. Concentrations of total Nitrogen (TN: 500 to 2000 µgL -1 ) and three N sources (NS: NH 4 , NO 3 , 1:1 NH 4 :NO 3 ratio) in an overlaying aqueous phase, using local tap water as control (174 µgL -1 TN), were evaluated in rooted autotrophic juvenile Vallisneria americana established in vitro in two-phase culture medium. The treatments ranged from 7 to 111 µM TN. Phenotypes changes, pH and ionic strength in the aqueous phase were registered at 15 days. In addition, biomass of lyophilized leaf and root as well as N contents (gas and high-performance liquid chromatography) were analysed to estimate accumulations of N-NH 4 , N-NO 3 and N-NO 2 .ResultsAll individuals showed phenotypic similarities. Accumulation of N-NH 4 was discarded, but the accumulations of N-NO 3 and N-NO 2 in both tissues were significantly different (p<0.001 and 0.0001), revealing so much that the maximum cumulative responses coincided with a deficit of N as both showed a linear decrease in their cumulative capacity linked to an increase in micromolar TN. ConclusionsThe results provide direct evidence of the tolerance to N enrichment with three different N sources in the focal ecotype at the seedling stage, based mainly on its cumulative capacity of N-NO 3 and N-NO 2 under eutrophic conditions. The findings imply that NO 2 is a relevant ion in the tolerance to N enrichment in overlaying water with NH 4 and NO 3 ions. Future studies of N cumulative effect with an in vitro approximation will be to support stress predictions by N enrichment. Keywords : Hydrocharitaceae. Eutrophization. Stress in vitro. Ammonium. Nitrate. Nitrogen endogenous
Magnaporthe oryzae Systemic Defense Trigger 1 (MoSDT1)-Mediated Metabolites Regulate Defense Response in Rice
Authors: Duan Guihua , Li Chunqin , Liu Yanfang , Ma Xiaoqing , Luo Qiong , Yang Jing 
Published: March 2020

Abstract
Background: Some of the pathogenic effector proteins play an active role in stimulating the plant defense system to strengthen plant resistance.Results: In this study, ultra-high performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UHPLC/Q-TOF-MS) was implemented to identify altered metabolites in transgenic rice containing over-expressed M. oryzae Systemic Defense Trigger 1 (MoSDT1) that was infected at three-time points. The characterized dominating metabolites were organic acids and their derivatives, organic oxygen compounds, lipids, and lipid-like molecules. Among the identified metabolites, shikimate, galactinol, trehalose, D-mannose, linolenic acid, dopamine, tyramine, and L-glutamine are precursors for the synthesis of many secondary defense metabolites Carbohydrate, as well as amino acid metabolic, pathways were revealed to be involved in plant defense responses and resistance strengthening.Conclusion: The increasing salicylic acid (SA) and jasmonic acid (JA) content enhanced interactions between JA synthesis/signaling gene, SA synthesis/receptor gene, raffinose/fructose/sucrose synthase gene, and cell wall-related genes all contribute to defense response in rice. The symptoms of rice after M. oryzae infection were significantly alleviated when treated with six identified metabolites, i.e., galactol, tyramine, L-glutamine, L-tryptophan, α-terpinene, and dopamine for 72 h exogenously. Therefore, these metabolites could be utilized as an optimal metabolic marker for M. oryzae defense.#These authors contributed equally to this work.
Dynamic Simulation of Continuous Mixed Sugars Fermentation with Increasing Cell Retention Time for Lactic Acid Production using Enterococcus mundtii QU 25
Authors: Wang Ying , Chan Ka-Lai , Abdel-Rahman Mohamed Ali , Sonomoto Kenji , Leu Shao-Yuan 
Published: March 2020

Abstract
Background: Simultaneous and effective conversion of both pentose and hexoses in fermentation is a critical and challenging task toward the lignocellulosic economy. This study aims to investigate the feasibility of an innovative co-fermentation process featured with cell recycle unit (CF/CR) for mixed sugar utilization. A l-lactic acid producing strain Enterococcus mundtii QU 25 was applied in the continuous fermentation process to utilize the mixed sugar at different productivities over the changes of flowing conditions. Structured numerical platform were constructed with the experiments to optimize the biological process and clarify the cell metabolisms through kinetics analysis. The structured model, kinetic parameters, and achievement of the fermentation strategy shall provide new insights towards whole sugar fermentation via real-time monitoring for process control and optimization.Results: Significant carbon catabolite repression of co-fermentation using glucose/xylose mixture was overcome by replacing glucose with cellobiose, of which the consumption ratio of hexose to pentose was improved dramatically from 10.4:1 to 2.17:1. An outstanding product concentration of 65.15 g·L -1 and productivity of 13.03 g·L -1 ·h -1 were achieved with 50 g·L -1 cellobiose and 30 g·L -1 xylose, at an optimized dilution rate of 0.2 h -1 with gradually increased cell retention time. Among the total lactic acid production, xylose contributed to more than 34% of the mixed sugars, which was close to the related contents in agricultural residuals. The model successfully simulated the transition of sugar consumption, cell growth, and lactic acid production among the batch, continuous process, and CF/CR system.Conclusion: Cell retention time played a critical role in balancing pentose and hexose consumption, cell decay, and lactic acid production in the CF/CR process. With the increase of cell concentration, consumption of mixed sugars increased with the productivity of final products, hence the impacts of substrate inhibiting reduced. With the validated parameters, the model showed highest accuracy simulating the CF/CR process, of which significantly longer cell retention times over hydraulic retention time were tested.