bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic Bayesian Confirmatory Factor Analysis and Bayesian Network To Characterize a Wide Spectrum of Rice Phenotypes
Authors: Yu Haipeng , Campbell Malachy T , Zhang Qi , Walia Harkamal , Morota Gota 
Published: April 2019

AbstractWith the advent of high-throughput phenotyping platforms, plant breeders have a means to assess many traits for large breeding populations. However, understanding the genetic interdependencies among high-dimensional traits in a statistically robust manner remains a major challenge. Since multiple phenotypes likely share mutual relationships, elucidating the interdependencies among economically important traits can better inform breeding decisions and accelerate the genetic improvement of plants. The objective of this study was to leverage confirmatory factor analysis and graphical modeling to elucidate the genetic interdependencies among a diverse agronomic traits in rice. We used a Bayesian network to depict conditional dependencies among phenotypes, which can not be obtained by standard multi-trait analysis. We utilized Bayesian confirmatory factor analysis which hypothesized that 48 observed phenotypes resulted from six latent variables including grain morphology, morphology, flowering time, physiology, yield, and morphological salt response. This was followed by studying the genetics of each latent variable, which is also known as factor, using single nucleotide polymorphisms. Bayesian network structures involving the genomic component of six latent variables were established by fitting four algorithms (i.e., Hill Climbing, Tabu, Max-Min Hill Climbing, and General 2-Phase Restricted Maximization algorithms). Physiological components influenced the flowering time and grain morphology, and morphology and grain morphology influenced yield. In summary, we show the Bayesian network coupled with factor analysis can provide an effective approach to understand the interdependence patterns among phenotypes and to predict the potential influence of external interventions or selection related to target traits in the interrelated complex traits systems.
Tissue-Specific Split sfGFP System for Streamlined Expression of GFP Tagged Proteins in theCaenorhabditis elegansGermline
Authors: Hefel Adam , Smolikove Sarit 
Published: April 2019

AbstractIdentifying protein localization is a useful tool in analyzing protein function. Using GFP-fusion tags, researchers can study the function of endogenous proteins in living tissue. However, these tags are considerably large, making them difficult to insert, and they can potentially affect the normal function of these proteins. To improve on these drawbacks, we have adopted the split sfGFP system for studying the localization of proteins in the Caenorhabditis elegans germline. This system divides the “super folder” GFP into 2 fragments, allowing researchers to use CRISPR/Cas9 to tag proteins more easily with the smaller subunit, while constitutively expressing the larger subunit from another locus. These two parts are able to stably interact, producing a functional GFP when both fragments are in the same cellular compartment. Our data demonstrate that the split sfGFP system can be adapted for use in C. elegans to tag endogenous proteins with relative ease. Strains containing the tags are homozygous viable and fertile. These small subunit tags produce fluorescent signals that matched the localization patterns of the wild-type protein in the gonad. Thus, our study shows that this approach could be used for tissue-specific GFP expression from an endogenous locus.
The Role of Tissue Inhibitors of Metalloproteinases in Organ Development and Regulation of ADAMTS Family Metalloproteinases in Caenorhabditis elegans
Authors: Kubota Yukihiko , Nishiwaki Kiyoji , Ito Masahiro , Sugimoto Asako 
Published: April 2019

Abstract
Remodeling of the extracellular matrix supports tissue and organ development, by regulating cellular morphology and tissue integrity. However, proper extracellular matrix remodeling requires spatiotemporal regulation of extracellular metalloproteinase activity. Members of the ADAMTS (a disintegrin and metalloproteinase with thrombospondin motifs) family, including MIG-17 and GON-1, are evolutionarily conserved, secreted, zinc-requiring metalloproteinases. Although these proteases are required for extracellular matrix remodeling during gonadogenesis in Caenorhabditis elegans, their in vivo regulatory mechanisms remain to be delineated. Therefore, we focused on the C. elegans tissue inhibitors of metalloproteinases (TIMPs), TIMP-1 and CRI-2. Analysis of the transcription and translation products for GFP/Venus fusions, with TIMP-1 or CRI-2, indicated that these inhibitors were secreted and localized to the basement membrane of gonads and the plasma membrane of germ cells. A timp-1 deletion mutant exhibited gonadal growth defects and sterility, and the phenotypes of this mutant were fully rescued by a TIMP-1::Venus construct, but not by a TIMP-1(C21S)::Venus mutant construct, in which the inhibitor coding sequence had been mutated. Moreover, genetic data suggested that TIMP-1 negatively regulates proteolysis of the α1 chain of type IV collagen. We also found that the loss-of-function observed for the mutants timp-1 and cri-2 involves a partial suppression of gonadal defects found for the mutants mig-17/ADAMTS and gon-1/ADAMTS, and that this suppression was canceled upon overexpression of gon-1 or mig-17, respectively. Based on these results, we propose that both TIMP-1 and CRI-2 act as inhibitors of MIG-17 and GON-1 ADAMTSs to regulate gonad development in a noncell-autonomous manner.
Effect of the Interface in Plasmon-enhanced Second Harmonic
Generation from Nonlinear Optical Thin Films
Authors: Robinson Hans D. , Chen Kai , Durak Cemil , Garg Akhilesh , Davis Richey M. , Heflin James R. 
Published: April 2019

AbstractThe second order nonlinear optical (NLO) properties of two different ionic
selfassembled multilayer (ISAM) films combined with Ag nanoparticles have
been investigated. The plasmon resonances in the Ag particles concentrate
the incident light, markedly increasing in the NLO efficiencies of the
films. We find that the efficiency enhancement is significantly larger in
conventional ISAM films compared to films made using a hybrid covalent ISAM
technique (HCISAM), even though the intrinsic bulk second order non-linear
susceptibility (χ(2)) is much larger for HCISAM films. We attribute this to the
interfaces in HCISAM films being much easier to disrupt by external
perturbations such as the metal deposition by which the nanoparticles are
fabricated. We conclude that because the plasmon decay length is very short,
the plasmonic enhancement of NLO effects primarily occurs at and near the
film-particle interface. To discern the importance of the interfaces, we
surrounded thin ISAM and HCISAM films with NLOinactive buffer layers, which
confirmed this hypothesis, particularly in the case of HCISAM films.
Italian Cohort of Nivolumab Expanded Access Program in Squamous Non-Small Cell Lung Cancer: Results from a Real-World Population
Authors: Crinò Lucio , Bidoli Paolo , Delmonte Angelo , Grossi Francesco , De Marinis Filippo , Ardizzoni Andrea , Vitiello Fabiana , Lo Russo Giuseppe , Parra Hector Soto , Cortesi Enrico , Cappuzzo Federico , Calabrò Luana , Tiseo Marcello , Turci Daniele , Gamucci Teresa , Antonelli Paola , Morabito Alessandro , Chella Antonio , Giannarelli Diana , Galetta Domenico 
Published: April 2019

Abstract

Background
Nivolumab has shown a survival benefit compared with docetaxel as second-line treatment for patients with previously treated advanced squamous non-small cell lung cancer (NSCLC) in a randomized phase III trial. The experiences of patients and physicians in routine clinical practice are often different from those in a controlled clinical trial setting. We present data from the entire Italian cohort of patients with squamous NSCLC enrolled in a worldwide nivolumab NSCLC expanded access program.

Patients and Methods
Patients with pretreated advanced squamous NSCLC received nivolumab 3 mg/kg every 2 weeks for up to 24 months. Safety was monitored throughout; efficacy data collected included objective tumor response, date of progression, and survival information.

Results
The Italian cohort comprised 371 patients who received at least one dose of nivolumab. In the overall population, the objective response rate (ORR) was 18%, the disease control rate (DCR) was 47%, and median overall survival (OS) was 7.9 months (95% confidence interval 6.2–9.6). In subgroup analyses, ORR, DCR, and median OS were, respectively, 17%, 48%, and 9.1 months in patients previously treated with two or more lines of therapy (n = 209) and 8%, 40%, and 10.0 months in patients treated beyond disease progression (n = 65). In the overall population, the rate of any-grade and grade 3–4 adverse events was 29% and 6%, respectively. Treatment-related adverse events led to treatment discontinuation in 14 patients (5%). There were no treatment-related deaths.

Conclusion
To date, this report represents the most extensive clinical experience with nivolumab in advanced squamous NSCLC in current practice outside the controlled clinical trial setting. These data suggest that the efficacy and safety profiles of nivolumab in a broad, real-world setting are consistent with those obtained in clinical trials.

Implications for Practice
Nivolumab is approved in the U.S. and Europe for the treatment of advanced non-small cell lung cancer (NSCLC) after failure of prior platinum-based chemotherapy. In this cohort of Italian patients with previously treated, advanced squamous NSCLC treated in a real-world setting as part of the nivolumab expanded access program, the efficacy and safety of nivolumab was consistent with that previously reported in nivolumab clinical trials.
Toward an Expert Level of Lung Cancer Detection and Classification Using a Deep Convolutional Neural Network
Authors: Zhang Chao , Sun Xing , Dang Kang , Li Ke , Guo Xiao-wei , Chang Jia , Yu Zong-qiao , Huang Fei-yue , Wu Yun-sheng , Liang Zhu , Liu Zai-yi , Zhang Xue-gong , Gao Xing-lin , Huang Shao-hong , Qin Jie , Feng Wei-neng , Zhou Tao , Zhang Yan-bin , Fang Wei-jun , Zhao Ming-fang , Yang Xue-ning , Zhou Qing , Wu Yi-long , Zhong Wen-zhao 
Published: April 2019

AbstractBackgroundComputed tomography (CT) is essential for pulmonary nodule detection in diagnosing lung cancer. As deep learning algorithms have recently been regarded as a promising technique in medical fields, we attempt to integrate a well-trained deep learning algorithm to detect and classify pulmonary nodules derived from clinical CT images.Materials and MethodsOpen-source data sets and multicenter data sets have been used in this study. A three-dimensional convolutional neural network (CNN) was designed to detect pulmonary nodules and classify them into malignant or benign diseases based on pathologically and laboratory proven results.ResultsThe sensitivity and specificity of this well-trained model were found to be 84.4% (95% confidence interval [CI], 80.5%–88.3%) and 83.0% (95% CI, 79.5%–86.5%), respectively. Subgroup analysis of smaller nodules (&lt;10 mm) have demonstrated remarkable sensitivity and specificity, similar to that of larger nodules (10–30 mm). Additional model validation was implemented by comparing manual assessments done by different ranks of doctors with those performed by three-dimensional CNN. The results show that the performance of the CNN model was superior to manual assessment.ConclusionUnder the companion diagnostics, the three-dimensional CNN with a deep learning algorithm may assist radiologists in the future by providing accurate and timely information for diagnosing pulmonary nodules in regular clinical practices.Implications for PracticeThe three-dimensional convolutional neural network described in this article demonstrated both high sensitivity and high specificity in classifying pulmonary nodules regardless of diameters as well as superiority compared with manual assessment. Although it still warrants further improvement and validation in larger screening cohorts, its clinical application could definitely facilitate and assist doctors in clinical practice.
Birinci Sınıf Öğretmenlerinin Birinci Sınıf Matematik Dersi Öğretim Programına İlişkin Görüşlerinin İncelenmesi
Authors: KILINÇ Mehmet Barbaros , ANILAN Hüseyin 
Published: April 2019

Bu çalışmada, birinci sınıf öğretmenlerinin ilkokul birinci sınıf
matematik dersi öğretim programına ilişkin görüşlerinin belirlenmesi ve bazı
değişkenlere göre karşılaştırılması amaçlanmıştır. Araştırmanın verileri
2016–2017 eğitim öğretim yılında Eskişehir ili merkezindeki devlet
ilkokullarında görev yapan birinci sınıf öğretmenlerinden toplanmıştır.
Öğretmenlerin görüşlerinin belirlenmesinde Sarıer (2007) tarafından hazırlanan
veri toplama aracı kullanılmıştır. Veri toplama aracının uygulanması için öğretmen
seçiminde tesadüfi küme örnekleme yöntemi kullanılmıştır. Veriler bir
istatistik paket programında çözümlenmiştir. Verilerin çözümlenmesinde t testi
ve tek yönlü varyans analizi kullanılmıştır. Elde edilen sonuçlarına göre,
araştırmaya katılan öğretmenlerin birinci sınıf matematik dersi öğretim
programını genel anlamda olumlu buldukları görülmüştür. Ancak öğretmenlerin
özellikle ölçme ve değerlendirmede bazı sorunlarla karşılaştıkları
anlaşılmaktadır
The Role of Virtual Surgical Planning in Increasing the Predictability in Orthognathic Surgery
Authors: Quereshy Faisal A , Levintov Nikolay , Nguyen Justin L , DeLeonibus Maria A , Demko Catherine , Bazina Mohamed , Valiathan Manish , Baur Dale A 
Published: April 2019

Purpose: To evaluate our surgical outcomes by comparing our surgical plan to the outcome of the surgery and evaluate our efficacy using Virtual Surgical Planning and Medical Modeling software. Our aim is to determine the quality and validity of Virtual Surgical Planning when comparing pre-surgical plans with post-surgical outcomes. Patients and Methods: A cohort study was conducted for patients who underwent orthognathic surgery at a single institution. Utilizing virtual plans and models, select points for the virtual plans were compared and superimposed with that of the actual surgical movements. The primary predictor variable were the pre-surgical virtual plans of movements; the outcome variable consisted of the actual post-surgical movements. Statistical analysis was computed via IBM SPSS Version 25 software utilizing a paired t-test assuming equal variance with alpha (p<0.05). The sample of patients included those who had pre-operative and post-operative cone beam computed tomography scans, a virtual surgical plan, CAD/CAM splints, and LeFort I osteotomy and bilateral sagittal split osteotomy.Results: The study consisted of ten patients between the ages of 18-51 years old. Pre and post surgical plans were superimposed and four points of measurement were compared along 3 dimensional planes. There were no statistical significant associations between the virtually planned and post surgical planned values.Conclusion: Our results suggest that the use of virtual surgical planning in orthognathic surgery yields favorable and accurate surgical outcomes regarding rotational movements with minor degrees of discrepancies.
REVALUATION HARMONIZATION: DIGGING THE SOLUTION OF TRADITIONAL AND MODERN MARKET CONFLICTS IN SURAKARTA
Authors: . Harun , Yuspin Wardah , . Handoyo 
Published: April 2019

Purpose of Study: The research aims to determine: 1) the policy implementation of legal protection of traditional markets in Surakarta, and 2) The causes of conflict between traditional markets and modern markets in Surakarta.Methodology: The research used the sociological juridical approach with traditional markets in Surakarta as the study population. The sampling technique was purposive sampling by classifying the market class with sub-populations based on the homogeneous typology.Results: The results of this research were: (1) the implementation of legal protection of traditional markets in Surakarta included the preventive, repressive, and functional legal protection, (2) the causes of conflict between the modern and traditional markets in Surakarta examined from juridical normative and sociology. The conflict can be solved by preventive and repressive legal protection.Implications/Applications: The efforts to prevent conflict in the traditional markets are in the form of regulatory and implementation. Therefore, the enforcement and legal protection model of traditional markets in Surakarta can be implemented properly.
RADIATE – Radial Dysplasia Assessment, Treatment and Aetiology: Protocol for the development of a core outcome set using a Delphi survey
Authors: Murphy George , Logan Malcolm , Smith Gill , Sivakumar Bran 
Published: April 2019

Abstract
Background: Radial dysplasia (RD) is a disfiguring, potentially disabling congenital upper limb anomaly. Multiple surgical techniques are in current use, with little agreement on the optimal treatment approach. At present, no core outcome set exists specifically for radial dysplasia, and the literature is dominated by retrospective case series. A recent systematic review by this group demonstrated significant heterogeneity in both which outcomes are measured, and how they are measured. Methods: The RADIATE study will conduct a three-round online Delphi process, involving adult radial dysplasia patients, the parents of children with radial dysplasia, hand surgeons and hand therapists. The initial list of outcomes is drawn from our recent systematic review and will be supplemented by suggestions from the stakeholder groups. Following the Delphi process, outcomes which meet the ‘consensus in’ definition will be ratified at a final consensus meeting. We will then follow the COSMIN guidelines to select outcome measurement instruments; where appropriate, these will overlap with the outcome measures specified in the forthcoming ICHOM congenital upper limb anomalies standard set. Discussion: The Radial Dysplasia Assessment, Treatment and Aetiology (RADIATE) study aims to address the uncertainty in the treatment of radial dysplasia, and to begin to answer the question “what is the most appropriate treatment for children with radial dysplasia?” by establishing a core outcome set. Trial registration: COMET initiative study 902, registered May 2016 http://www.comet-initiative.org/studies/details/902
Comparison of five point-of-use drinking water technologies using a specialized comparison framework
Authors: Siwila Stephen , Brink Isobel C. 
Published: April 2019

Abstract
Three novel and two commercially available low-cost point-of-use (PoU) water treatment technologies were comparatively evaluated using a specialized comparison framework targeted at them. The comparison results and specialized framework have been discussed. The PoU systems were evaluated principally in terms of performance, flow rate and cost per volume of water treated (quantitatively), ease of use, potential acceptability and material availability (qualitatively) with main focus on rural and suburban settings. The three novel systems assessed were developed in an ongoing research project aimed at developing a multibarrier low-cost PoU water treatment system. The comparative evaluation and analysis revealed that the commercially available systems may often produce water free of pathogens (with an apparent 100% removal for Escherichia coli and fecal coliforms) but may not be affordable for application to the poorest groups in much of the developing world. The novel systems, which were principally constructed from local materials, were more affordable, can supply relatively safe water and can be constructed by users with minimal training. Overall, bacterial removal effectiveness, ease of use, flow rate, material availability, cost and acceptability aspects of water were identified as key to potential adoption and sustainability of the evaluated low-cost PoU systems.
Removal of metals from water using a novel high-rate algal pond and submerged macrophyte pond treatment reactor
Authors: Wang Yuhui , Song Xinshan , Li Hongwei , Ding Yi 
Published: April 2019

Abstract
A combined high-rate algal pond and submerged macrophyte pond (APMP) reactor was introduced as a novel biotechnique for efficient heavy metals (HMs) removal from wastewater. The role of water temperature, light regime, and N:P mass ratio on algae growth and HMs removal as well as effects of macrophyte species and densities on algae extermination were investigated through batch experiments. Results showed that water temperature significantly affected algae proliferation and HMs removal. Effects of light regime and N:P only showed obvious influences on HMs removal performance at high temperature. HMs removal efficiency reached 75.8% (Cr), 63.6% (Pb), and 61.1% (Zn) at 5-day hydraulic retention time (HRT) in APMP. Positive correlation existed closely between HMs removal and algal growth with long HRT. Algae were strongly inhibited by Ceratophyllum demersum and Vallisneria natans at plant density of 20–30 rhizomes m−2 with effluent algae concentration about 1,000 cells mL−1 at 7-day HRT. Results suggested that the APMP reactor was efficient for HMs removal from wastewater, indicating a possible effective metals removal technique by using APMP.
Metal Complexes as Promising Agents for Biomedical Applications
Authors: Loginova Natalia V. , Harbatsevich Hleb I. , Osipovich Nikolai P. , Ksendzova Galina A. , Koval’chuk Tatsiana V. , Polozov Genrikh I. 
Published: April 2019

Background::
In this review article, a brief overview of novel metallotherapeutic agents
(with an emphasis on the complexes of essential biometals) promising for medical application is
presented. We have also focused on the recent work carried out by our research team, specifically
the development of redox-active antimicrobial complexes of sterically hindered diphenols with some
essential biometals (copper, zinc, nickel).

Results::
The complexes of essential metals (manganese, iron, cobalt, nickel, copper, zinc) described
in the review show diverse in vitro biological activities, ranging from antimicrobial and antiinflammatory
to antiproliferative and enzyme inhibitory. It is necessary to emphasize that the type of
organic ligands in these metal complexes seems to be responsible for their pharmacological
activities. In the last decades, there has been a significant interest in synthesis and biological
evaluation of metal complexes with redox-active ligands. A substantial step in the development of
these redox-active agents is the study of their physicochemical and biological properties, including
investigations in vitro of model enzyme systems, which can provide evidence on a plausible
mechanism underlying the pharmacological activity. When considering the peculiarities of the
pharmacological activity of the sterically hindered diphenol derivatives and their nickel(II),
copper(II) and zinc(II) complexes synthesized, we took into account the following: (i) all these
compounds are potential antioxidants and (ii) their antimicrobial activity possibly results from their
ability to affect the electron-transport chain.

Conclusion::
We obtained novel data demonstrating that the level of antibacterial and antifungal
activity in the series of the above-mentioned metal-based antimicrobials depends not only on the
nature of the phenolic ligands and complexing metal ions, but also on the lipophilicity and reducing
ability of the ligands and metal complexes, specifically regarding the potential biotargets of their
antimicrobial action – ferricytochrome c and the superoxide anion radical. The combination of
antibacterial, antifungal and antioxidant activity allows one to consider these compounds as
promising substances for developing therapeutic agents with a broad spectrum of activities.