bluuebunny/crossref_metadata_2025_split huggingface dataset:
Plastome phylogenomics, biogeography, and clade diversification of Paris (Melanthiaceae)
Authors: Ji Yunheng , Yang Lifang , Chase Mark W. , Liu Changkun , Yang Zhenyan , Yang Jin , Yang Jun-Bo , Yi Ting-Shuang 
Published: October 2019

Abstract
Background: Paris (Melanthiaceae) is an economically important but taxonomically difficult genus, which is unique in angiosperms because some species have extremely large nuclear genomes. Phylogenetic relationships within Paris have long been controversial. Based on complete plastomes and nuclear ribosomal DNA (nrDNA) sequences, this study aims to reconstruct a robust phylogenetic tree and explore historical biogeography and clade diversification in the genus.Results: All 29 species currently recognized in Paris were sampled. Whole plastomes and nrDNA sequences were generated by the genome skimming approach. Phylogenetic relationships were reconstructed using the maximum likelihood and Bayesian inference methods. Based on the phylogenetic framework and molecular dating, biogeographic scenarios and historical diversification of Paris were explored. Significant conflicts between plastid and nuclear datasets were identified, and the plastome tree is highly congruent with past interpretations of the morphology. Ancestral area reconstruction indicated that Paris may have originated in northeastern Asia and northern China, and has experienced multiple dispersal and vicariance events during its diversification. The rate of clade diversification has sharply accelerated since the Miocene/Pliocene boundary.Conclusions: Our results provide important insights for clarifying some of the long-standing taxonomic debates in Paris. Cytonuclear discordance may have been caused by ancient and recent hybridizations in the genus. The climatic and geological changes since the late Miocene, such as the intensification of Asian monsoon and the rapid uplift of Qinghai-Tibet Plateau, as well as the climatic fluctuations during the Pleistocene, played essential roles in driving range expansion and radiative diversification in Paris. Our findings challenge the theoretical prediction that large genome sizes may limit speciation.
Differential expression of IDA (INFLORESCENCE DEFICIENT IN ABSCISSION)-like genes in Nicotiana benthamiana during corolla abscission, stem growth and water stress
Authors: Ventimilla Daniel , Domingo Concha , Gonzalez-Ibeas Daniel , Talon Manuel , Tadeo Francisco R. 
Published: October 2019

Abstract
Background
IDA (INFLORESCENCE DEFICIENT IN ABSCISSION)-like signaling peptides and the associated HAE (HAESA)-like family of receptor kinases were originally reported in the model plant Arabidopsis thaliana (Arabidopsis) to be deeply involved in the regulation of abscission. Actually, IDA peptides, as cell-to-cell communication elements, appear to be implicated in many developmental processes that rely on cell separation events, and even in the responses to abiotic stresses. However, the knowledge related to the molecular machinery regulating abscission in economically important crops is scarce. In this work, we determined the conservation and phylogeny of the IDA -like and HAE -like gene families in relevant species of the Solanaceae family and analyzed the expression of these genes in the allopolyploid Nicotiana benthamiana, in order to identify members involved in abscission, stem growth and in the response to drought conditions.
Results
The phylogenetic relationships among the IDA -like members of the Solanaceae studied, grouped the two pairs of NbenIDA1 and NbenIDA2 protein homeologs with the Arabidopsis prepropeptides related to abscission. Analysis of promoter regions searching for regulatory elements showed that these two pairs of homeologs contained both hormonal and drought response elements, although NbenIDA2A lacked the hormonal regulatory elements. Expression analyses showed that the pair of NbenIDA1 homeologs were upregulated during corolla abscission. NbenIDA1 and NbenIDA2 pairs showed tissue differential expression under water stress conditions, since NbenIDA1 homeologs were highly expressed in stressed leaves while NbenIDA2 homeologs, especially NbenIDA2B , were highly expressed in stressed roots. In non-stressed active growing plants, nodes and internodes were the tissues with the highest expression levels of all members of the IDA -like family and their putative HAE -like receptors.
Conclusion
Our results suggest that the pair of NbenIDA1 homeologs are involved in the natural process of corolla abscission while both pairs of NbenIDA1 and NbenIDA2 homeologs are implicated in the response to water stress. The data also suggest that IDA peptides may be important during stem growth and development. These results provide additional evidence that the functional module formed by IDA peptides and its receptor kinases, as defined in Arabidopsis, may also be conserved in Solanaceae.
Elevated expression of AGGF1 predicts poor prognosis and promotes the metastasis of colorectal cancer
Authors: Zhang Xin , Sun Huimin , Chen Wanyuan , He Xianglei 
Published: October 2019

Abstract
Abstract
Background: Angiogenic factor with G-patch and FHA domains 1 (AGGF1) can promote angiogenesis and increasing evidence has highlighted the important roles of AGGF1 in tumorigenesis. However, the expression patterns as well as the biological functions of AGGF1 in colorectal cancer (CRC) remain to be established. The purpose of the present study is therefore to identify the effect of AGGF1 on prognosis and metastasis in CRC patients.
Methods: The expression level of AGGF1 in CRC was examined by qPCR, western blot and immunohistochemistry in a tissue microarray containing 101 CRC specimens. And the effect of AGGF1 on CRC cell malignance was investigated in our established stable AGGF1 upregulated and knockdown CRC cell lines.
Results: The expression level of AGGF1 in CRC tissue was not significantly different to that in adjacent normal mucosa at the mRNA level. However, at the protein level, AGGF1 expression in CRC tissues was significantly higher than in paired normal mucosa, which showed a clear association with TNM stage, AJCC stage, vascular invasion, and differentiation. Further, we revealed an apparent correlation between AGGF1 expression and poorer disease-free survival and overall survival of CRC patients. In addition, we discovered that AGGF1 significantly promoted CRC cell wound healing, migration, and invasion in vitro and distant metastasis in vivo .
Conclusions: Our study demonstrates the aberrant expression of AGGF1 in CRC and provides a basis on which to explore the application of AGGF1 as a novel prognostic biomarker for CRC patients, especially for CRC patients with distant metastasis.
Association of uncoordinated sucking pattern with developmental outcome in premature infants: a retrospective analysis
Authors: Yi You Gyoung , Oh Byung-Mo , Shin Seung Han , Shin Jin Yong , Kim Ee-Kyung , Shin Hyung-Ik 
Published: October 2019

Abstract
Background
Stress signals during sucking activity such as nasal flaring, head turning, and extraneous movements of the body have been attributed to incoordination of sucking, swallowing, and respiration (SSR) in premature infants. However, the association of uncoordinated sucking pattern with developmental outcomes has not yet been investigated. The aim of this study was to investigate whether uncoordinated sucking pattern during bottle-feeding in premature infants is associated with the developmental outcomes at 8-12 and 18-24 months of age (corrected for prematurity).
Methods
We retrospectively reviewed the medical records and video recordings for the Neonatal Oral-Motor Assessment Scale (NOMAS) of premature infants and divided them into two groups based on the presence or absence of incoordination. The Bayley-III cognition composite scores of the incoordination-positive and incoordination-negative group were compared at 8-12 and 18-24 months of age.
Results
Seventy premature infants exhibited a disorganized sucking pattern according to the NOMAS. The average Bayley-III cognition composite scores at 8-12 months of age were 92.5±15.6 and 103.0±11.3 for the incoordination-positive (n=22) and incoordination-negative groups (n=48), respectively (p=0.002). The average Bayley-III cognition composite scores at 18-24 months were 90.0±17.9 and 100.7±11.5 for the incoordination-positive (n=21) and incoordination-negative groups (n=46), respectively (p=0.005). A multiple linear regression analysis indicated that the presence of uncoordinated sucking pattern, grade 3 or 4 germinal matrix hemorrhage–intraventricular hemorrhage, and moderate to severe bronchopulmonary dysplasia were independently associated with cognitive development at 18-24 months of age.
Conclusions
Uncoordinated sucking pattern in premature infants was independently associated with a higher risk of abnormal developmental outcome in the cognitive domain of the Bayley-III at both 8-12 and 18-24 months. There may be a need for periodic follow-up and early intervention for developmental delay when incoordination of SSR that results in stress signals on the NOMAS is observed before 40 weeks postmenstrual age.
Creatine kinase elevation after robotic surgery for rectal cancer due to a prolonged lithotomy position
Authors: Tsuchiya Yuki , Munakata Shinya , Tsukamoto Ryoichi , Okazawa Yu , Mizukoshi Kosuke , Sugimoto Kiichi , Takahashi Makoto , Kojima Yutaka , Tomiki Yuichi , Sakamoto Kazuhiro 
Published: October 2019

Abstract
Background Robotic surgery for rectal cancer, which is now performed worldwide, can be associated with elevated creatine kina se levels postoperatively. In this study, we compared postoperative complications between patient undergoing robotic surgery and laparoscopic surgery. Methods We identified 66 consecutive patients who underwent curative resection for rectal cancer at Juntendo University Hospital between January 2016 and February 2019. Patients were divided into a conventional laparoscopic surgery (CLS) group (n = 38) and a robotic-assisted laparoscopic surgery (RALS) group (n = 28) before comparing various clinicodemographic factors between the groups. Results Patient age and gender, surgical approach (CLS/RALS), pathological T factor, pathological stage, duration of postoperative hospital stay, and postoperative complications were not significantly different between the RALS and CLS groups. However, the operation time was significantly longer in the RALS group (407 min) than in the CLS group ( 295 min; p < 0.001 ). Notably, the serum level of creatine kinase on postoperative day 1 was significantly higher in the CLS group (154 IU/L) than in the RALS group (525 IU/L; p < 0.001), despite there being no significant differences in the incidence of rhabdomyolysis. Conclusions Clinically relevant positioning injuries and rhabdomyolysis may occur in patients who are subjected to a prolonged and extreme Trendelenburg position or who have extra force applied to the abdominal wall because of remote center displacement. The creatine kinase value should therefore be measured after RALS to monitor for the sequelae of these potential positioning injuries.
Binding modes of potential anti-prion phytochemicals to PrPC structures in silico
Authors: Neupane Sandesh , Khadka Jenisha , Rayamajhi Sandesh , Pandey Arti S. 
Published: October 2019

Abstract
Background: Prion diseases involve the conversion of a normal, cell-surface glycoprotein (PrPC ) into a misfolded pathogenic form (PrPSC ). Cellular assays and in vivo experiments have identified various compounds with anti-prion activity which work through various mechanisms. Structures of PrPC have revealed the protein to occur in a swapped or non-swapped, monomeric or dimeric forms. Binding modes of known anti-prions is either not known, or has been determined with only the non-swapped structures of PrPC . In the current study medicinal phytochemicals from various databases have been docked with PrPC in silico to identify potential anti-prions in comparison with known anti-prion compounds to determine their binding modes and speculate possible mechanisms of inhibition of PrPC to PrPSC . Results: Eleven new phytochemicals were identified based on their binding energies and pharmacokinetic properties. The binding sites and interactions of the known and new anti-prion compounds are similar, and differences in binding modes occur in structures with very subtle differences in side chain conformations. Binding of these compounds poses steric hindrance to neighbouring molecules. Residues shown to be associated with inhibition of PrPC to PrPSC conversion form interactions with most of the compounds. Conclusions: The new compounds are mostly highly hydrophobic and are derivatives of terpenes, sterols and quinones. They might act as potent inhibitors of the PrPC to PrPSC conversion through a combination of steric hindrance and stabilization of structure through ionic/hydrophobic interactions. Their high binding energies coupled with identical binding sites as those of the known compounds, and their ability to cross the blood brain barrier makes these phytochemicals a promising group of compounds for further studies on prevention of PrPC to PrPSC .
Effect Of Maternal Growth Monitoring Knowledge On Stunting, Wasting And Underweight Among Children 0-18 Months In Tamale Metropolis Of Ghana
Authors: Bukari Mohammed , Abubakari Muzamil Mohammed , Majeed Mohammed , Abizari Abdul-Razak , Wemakor Anthony , Atosona Ambrose 
Published: October 2019

Abstract
Objective: This study sought to assess maternal growth monitoring knowledge and its effect on stunting, wasting and underweight among children 0-18 months in the Tamale Metropolis.An analytical cross-sectional study design, involving 340 mother-child pairs randomly selected from 4 health facilities in the Tamale Metropolis, was used. A structured questionnaire was used to collect information on socio-demographic characteristics and maternal growth monitoring knowledge. Weight and length of children were taken to assess nutritional status (stunting, underweight and wasting). Logistic regression analysis was used to determine the association between maternal growth monitoring knowledge level and child nutritional status. Results: The study revealed that 87.6% of mothers had good knowledge on growth monitoring. The prevalence of stunting, underweight and wasting were 9.4%, 25.9% and 17.9% respectively. A binary logistic regression analysis revealed that there is no association between maternal growth monitoring knowledge and stunting [Adjusted Odds Ratio (AOR) = 0.593; 95% Confidence Interval (CI): 0.170-2.067], underweight (AOR= 1.56; 95% CI: 0.697-3.612) and wasting (OR= 0.881; 95% CI: 0.414-1.876) among children 0-18 months in the Tamale Metropolis.
Predictors of 1-year mortality in patients on prolonged mechanical ventilation after surgery in intensive care unit: a multicenter, retrospective cohort study
Authors: Sun Yue-ming , Li Shuangling , Wang Shu-Peng , Li Chen , Li Gang , Xu Jia-Xuan , Wang Hong-Zhi , Liu Fei , Yao Gai-Qi , Chang Zhi-Gang , Liu Ya-Lin , Shang Mei-Xia , Wang Dong-xin 
Published: October 2019

Abstract
Objectives: The requirement of prolonged mechanical ventilation (PMV) is associated with increased medical care demand and expenses, high early and long-term mortality, and worse life quality. However, no study has assessed the prognostic factors associated with 1-year mortality among PMV patients, not less than 21 days after surgery. This study analyzed the predictors of 1-year mortality in patients requiring PMV in intensive care units (ICUs) after surgery. Design: Multicenter, retrospective cohort study Setting: ICUs at 5 tertiary hospitals in Beijing Participants: Patients who required PMV after surgery between January 2007 and June 2016 were enrolled. Interventions: None Measurements and Main Results: Of the 124 patients enrolled, the cumulative 1-year mortality was 74.2% (92/124). From the multivariable Cox proportional hazard analysis, cancer diagnosis (hazard ratio [HR] 2.14, 95% confidence interval [CI] 1.37-3.35; P<0.01), no tracheostomy (HR 2.01, 95% CI 1.22-3.30; P<0.01), enteral nutrition intolerance (HR 1.88, 95% CI 1.19-2.97; P=0.01), blood platelet count ≤150´10 9 /L (HR 1.77, 95% CI 1.14-2.75; P=0.01), requirement of vasopressors (HR 1.78, 95% CI 1.13-2.80; P=0.02), and renal replacement therapy (HR 1.71, 95% CI 1.01-2.91; P=0.047) on the 21 st day of mechanical ventilation were associated with shortened 1-year survival. Conclusions: For patients who required PMV after surgery, cancer diagnosis, no tracheostomy, enteral nutrition intolerance, blood platelet count ≤150´10 9 /L, vasopressor requirement, and renal replacement therapy on the 21 st day of mechanical ventilation were associated with shortened 1-year survival. The prognosis in PMV patients in ICUs can facilitate the decision-making process of physicians and patients’ family members on treatment schedule.
Effects of Low Versus Standard Pressure Pneumoperitoneum on Renal Syndecan-1 Shedding and VEGF Receptor-2 Expression in Living-donor Nephrectomy: A Randomized Controlled Study
Authors: Aditianingsih Dita , Mochtar Chaidir Arif , Lydia Aida , Siregar Nuryati Chairani , Margyaningsih Nur Ita , Madjid Amir Sjarifuddin , Suwarto Suhendro 
Published: October 2019

Abstract
Background
Laparoscopic nephrectomy is a preferred technique for living kidney donation. However, positive-pressure pneumoperitoneum may have an unfavorable effect on the remaining kidney and other distant organs due to inflamed vascular endothelium and renal tubular cell injury in response to increased systemic inflammation. Early detection of vascular endothelial and renal tubular response is needed to prevent further kidney injury due to increased intraabdominal pressure induced by pneumoperitoneum. Transperitoneal laparoscopic living donor nephrectomy represented a human model of mild increasing intraabdominal pressure. This study aimed to assess the effect of increased intraabdominal pressure on vascular endothelium and renal tubular cells by comparing the effects of low and standard pressure pneumoperitoneum on vascular endothelial growth factor receptor-2 (VEGFR-2) expression and the shedding of syndecan-1 as the early markers to a systemic inflammation.
Methods
We conducted a prospective randomized study on 44 patients undergoing laparoscopic donor nephrectomy. Subjects were assigned to standard (12 mmHg) or low pressure (8 mmHg) groups. Baseline, intraoperative, and postoperative plasma interleukin-6, syndecan-1, and sVEGFR-2 were quantified by ELISA. Syndecan-1 and VEGFR-2 expression were assessed immunohistochemically in renal cortex tissue. Renal tubule and peritubular capillary ultrastructures were examined using electron microscopy. Perioperative hemodynamic changes, end-tidal CO2, serum creatinine, blood urea nitrogen, and urinary KIM-1 were recorded.
Results
The low pressure group showed lower intra- and postoperative heart rate, intraoperative plasma IL-6, sVEGFR-2 levels and plasma syndecan-1 than standard pressure group. Proximal tubule syndecan-1 expression was higher in the low pressure group. Proximal-distal tubules and peritubular capillary endothelium VEGFR-2 expression were lower in low pressure group. The low pressure group showed renal tubule and peritubular capillary ultrastructure with intact cell membranes, clear cell boundaries, and intact brush borders, while standard pressure group showed swollen nuclei, tenuous cell membrane, distant boundaries, vacuolizations, and detached brush borders.
Conclusion
The low pressure pneumoperitoneum attenuated the inflammatory response and resulted in reduction of syndecan-1 shedding and VEGFR-2 expression as the renal tubular and vascular endothelial proinflammatory markers to injury due to a systemic inflammation in laparoscopic nephrectomy.
Trial registration
ClinicalTrial.gov NCT:03219398, July 17th 2017.
Keywords: pneumoperitoneum, renal resistive index, interleukin-6, syndecan-1, sVEGFR-2, laparoscopic nephrectomy
Prediction of sediment transport rates in gravel-bed rivers using Gaussian process regression
Authors: Roushangar Kiyoumars , Shahnazi Saman 
Published: October 2019

AbstractEstimating sediment transport rate in rivers has high importance due to the difficulties and costs associated with its measurement, which has drawn the attention of experts in water engineering. In this study, Gaussian process regression (GPR) is applied to predict the sediment transport rate for 19 gravel-bed rivers in the United States. To compare the performance of GPR, the support vector machine (SVM) as a common type of kernel-based models was developed. Model inputs of sediment transport were prepared based on two scenarios: the first scenario considers only hydraulic characteristics and the second scenario was formed using hydraulic and sediment properties. Obtained results revealed that the GPR models present better performance compared to the SVM models and other empirical sediment transport formulas. Also, it was found that incorporating the second scenario as input led to better predictions. In addition, performing sensitivity analysis showed that the ratio of average velocity to shear flow velocity is the most effective parameter in predicting the sediment transport rate of gravel-bed rivers.
The role of agent-based modeling and multi-agent systems in flood-based hydrological problems: a brief review
Authors: Simmonds Jose , Gómez Juan A. , Ledezma Agapito 
Published: October 2019

AbstractFlood problems are complex phenomena with a direct relationship with the hydrological cycle; these are natural processes occurring in water systems, that interact at different spatial and temporal scales. In modeling the hydrological phenomena, traditional approaches, like physics-based mathematical equations and data-driven modeling (DDM) are used. Advances in hydroinformatics are helping to understand these physical processes, with improvements in the collection and analysis of hydrological data, information and communication technologies (ICT), and geographic information systems (GIS), offering opportunities for innovations in model implementation, to improve decision support for the response to societally important floods impacting our societies. This paper offers a brief review of agent-based models (ABMs) and multi-agent systems (MASs) methodologies' applications for solutions to flood problems, their management, assessment, and efforts for forecasting stream flow and flood events. Significant observations from this review include: (i) contributions of agent technologies, as a growing methodology in hydrology; (ii) limitations; (iii) capabilities of dealing with distributed and complex domains; and (iv), the capabilities of MAS as an increasingly accepted point of view applied to flood modeling, with examples presented to show the variety of system combinations that are practical on a specialized architectural level for developing and deploying sophisticated flood forecasting systems.