bluuebunny/crossref_metadata_2025 huggingface dataset:
Developing data interoperability using standards: A wheat community use case
Authors: Dzale Yeumo Esther , Alaux Michael , Arnaud Elizabeth , Aubin Sophie , Baumann Ute , Buche Patrice , Cooper Laurel , Ćwiek-Kupczyńska Hanna , Davey Robert P. , Fulss Richard Allan , Jonquet Clement , Laporte Marie-Angélique , Larmande Pierre , Pommier Cyril , Protonotarios Vassilis , Reverte Carmen , Shrestha Rosemary , Subirats Imma , Venkatesan Aravind , Whan Alex , Quesneville Hadi
Published: October 2017

In this article, we present a joint effort of the wheat research community, along with data and ontology experts, to develop wheat data interoperability guidelines. Interoperability is the ability of two or more systems and devices to cooperate and exchange data, and interpret that shared information. Interoperability is a growing concern to the wheat scientific community, and agriculture in general, as the need to interpret the deluge of data obtained through high-throughput technologies grows. Agreeing on common data formats, metadata, and vocabulary standards is an important step to obtain the required data interoperability level in order to add value by encouraging data sharing, and subsequently facilitate the extraction of new information from existing and new datasets.

During a period of more than 18 months, the RDA Wheat Data Interoperability Working Group (WDI-WG) surveyed the wheat research community about the use of data standards, then discussed and selected a set of recommendations based on consensual criteria. The recommendations promote standards for data types identified by the wheat research community as the most important for the coming years: nucleotide sequence variants, genome annotations, phenotypes, germplasm data, gene expression experiments, and physical maps. For each of these data types, the guidelines recommend best practices in terms of use of data formats, metadata standards and ontologies. In addition to the best practices, the guidelines provide examples of tools and implementations that are likely to facilitate the adoption of the recommendations.

To maximize the adoption of the recommendations, the WDI-WG used a community-driven approach that involved the wheat research community from the start, took into account their needs and practices, and provided them with a framework to keep the recommendations up to date. We also report this approach’s potential to be generalizable to other (agricultural) domains.
The use of dexmedetomidine and intravenous acetaminophen for the prevention of postoperative delirium in cardiac surgery patients over 60 years of age: a pilot study
Authors: Susheela Ammu T. , Packiasabapathy Senthil , Gasangwa Doris-Vanessa , Patxot Melissa , O’Neal Jason , Marcantonio Edward , Subramaniam Balachundhar
Published: October 2017

Background: Delirium is associated with many negative health outcomes. Postoperative sedation and opioid administration may contribute to delirium. We hypothesize that the use of dexmedetomidine and Intravenous acetaminophen (IVA) may lead to reduced opioid consumption and decreased incidence of postoperative delirium. This pilot study aims to assess feasibility of using dexmedetomidine and IVA in cardiac surgical patients, and obtain effect size estimates for incidence and duration of delirium.

Methods: A total of 12 adult patients >60 years of age undergoing cardiac surgery were recruited for the study after IRB approval and randomized into 4 groups: Propofol only (P), Propofol with IVA (P+A), Dexmedetomidine only (D), Dexmedetomidine with IVA (D+A). Preoperative baseline cognition and postoperative delirium was assessed daily until discharge. The feasibility was assessed by the number of patients who successfully completed the study.

Results: All patients completed the study protocol successfully. The total incidence of delirium in the study population was 42% (5/12):  67% (2/3) in the group P, and 67% (2/3) in the group D, 33% (1/3) in  D+A group and 0%(0/3)  P+A group. The incidence of delirium was 17% (1/6) in the group receiving IVA compared to 67% (4/6) that did not receive IVA. The mean duration of delirium was 0-1 days. One patient expired after surgery, unrelated to the study protocol. One patient in the D group experienced hypotension with systolic blood pressure <90 mm of Hg.

Conclusions: The feasibility of performing a large-scale project is ascertained by the study. Patients receiving IVA had lower incidence of delirium compared to patients not receiving IVA which suggests that IVA may have a role in reducing the incidence of delirium. A prospective randomized, placebo-controlled trial will be the next step in investigating the role of dexmedetomidine and IVA in reducing the incidence of delirium.
Measuring evolutionary rates of proteins in a structural context
Authors: Sydykova Dariya K. , Jack Benjamin R. , Spielman Stephanie J. , Wilke Claus O.
Published: October 2017

We describe how to measure site-specific rates of evolution in protein-coding genes and how to correlate these rates with structural features of the expressed protein, such as relative solvent accessibility, secondary structure, or weighted contact number. We present two alternative approaches to rate calculations, one based on relative amino-acid rates and the other based on site-specific codon rates measured as dN/dS. In addition to describing the specific analysis protocols we recommend, we also provide a code repository containing scripts to facilitate these kinds of analyses.
Hospital Privileging Practices for Bedside Procedures: A Survey of Hospitalist Experts
Authors: Jensen Trevor P. , Soni Nilam J. , Tierney David M. , Lucas Brian P.
Published: October 2017

Many hospitalists are routinely granted hospital privileges to perform invasive bedside procedures, but criteria for privileging are not well described. We conducted a survey of 21 hospitalist procedure experts from the Society of Hospital Medicine Point‐of‐Care Ultrasound Task Force to better understand current privileging practices for bedside procedures and how those practices are perceived. Only half of all experts reported their hospitals require a minimum number of procedures performed to grant initial (48%) and ongoing (52%) privileges for bedside procedures. Regardless, most experts thought minimums should be higher than those in current practice and should exist alongside direct observation of manual skills. Experts reported that the use of ultrasound guidance was nearly universal for paracentesis, thoracentesis, and central venous catheter placement, but only 10% of hospitals required the use of ultrasound for initial privileging of these procedures.
Introducing Troubleshooting for Model Formulation, Spreadsheet Development, and Memo Communication with Feedforward
Authors: Williams Julie Ann Stuart , Reid Randall , Gallamore Kristine , Rankin Maxwell
Published: October 2017

Novices need to learn how to recognize and correct formulation, spreadsheet, and writing mistakes. Yet quantitative business courses historically focus on examples of model formulation and more recently spreadsheet solution. This paper presents a feedforward example for formal instruction of troubleshooting issues for three domains, i.e., model formulation, spreadsheet development, and professional memo writing. The example is provided in a format for an active learning exercise.
Obesity and Cancer: Evidence, Impact, and Future Directions
Authors: Colditz Graham A , Peterson Lindsay L
Published: October 2017

BACKGROUND

Mounting evidence, particularly from prospective epidemiologic studies but with additional support from animal models and mechanistic studies, supported conclusions in 2016 by the International Agency for Research on Cancer (IARC) in their review of the preventive effects of weight control on cancer risk.

CONTENT

The workgroup concluded that obesity is causally related to cancer at 13 anatomic sites (esophagus: adenocarcinoma; gastric cardia; colon and rectum; liver; gallbladder; pancreas; breast: postmenopausal; uterine endometrial; ovary; kidney: renal cell; meningioma; thyroid; and multiple myeloma). Further, avoiding weight gain and excess body fat will prevent cancer. Evidence on weight loss and reduction in risk of cancer is more limited. Ongoing clinical trials address the benefits of weight loss interventions after diagnosis.

Here, we review the evidence from the 2016 IARC that obesity is causally related to cancer at 13 anatomic sites and identify areas for future research, including the consequences of childhood adiposity, the relation between velocity of weight gain and cancer risk, and improved methods for analysis of life-course adiposity and cancer risk. Refining understanding of mechanisms may further inform prevention strategies.
Anti-angiogenic and anti-lymphangiogenic role of praziquantel and artemether in experimental mansoniasis
Authors: Abd El-Aal Naglaa Fathy , Hamza Rania Said , Magdy Mona
Published: October 2017

Angiogenesis is one of the pillars of neoplasia. Lymphangiogenesis in context of granulomas is not yet understood. This study aimed to evaluate the role of praziquantel (PZQ) and artemether (ART) as anti-angiogenic and anti-lymphangiogenic drugs in
Measurement of Gas Released during Blast Densification
Authors: Gallant Aaron P. , Finno Richard J.
Published: October 2017

The introduction of nitrogen and carbon dioxide gases into the ground during blasting increases pore fluid compressibility and thus affects the postblast mechanical behavior of densified sand. This study presents the techniques used to sample pore fluid in situ with the BAT probe at a full-scale blast densification site. Special emphasis is given to the importance of preparing sample containers prior to collecting pore fluid. In addition, a methodology to evaluate gas concentrations and the degree of saturation in situ is provided. Measurements of postblast gas concentrations reveal that gas generated by explosives significantly increases both nitrogen gas and carbon dioxide concentrations relative to preblast levels. In addition, groundwater flow is likely responsible for increased gas concentrations outside the zone after a blast. However, nitrogen gas is responsible, almost exclusively, for the saturation of groundwater with dissolved gas and introduction of free gas into the soil matrix.
Estimation of Damage Location of Rock Based on Denoised Acoustic Emission Signals Using Wavelet Packet Algorithm
Authors: Kang Yumei , Ni Pengpeng , Fu Chuang , Zhang Penghai
Published: October 2017

The damage source location of acoustic emission (AE) signals is studied in this investigation. Noises can influence the accuracy of calculation significantly as the compressive wave velocity in rock is very fast. A novel fractional power model is proposed for use in wavelet packet transform analysis to decompose, filter, and reconstruct AE signals. Analysis of uniaxial compression testing data on sandstone samples has revealed that the denoising scheme can result in a higher signal to noise ratio (SNR) and a lower root mean square error (RMSE) compared with the conventional soft and hard thresholding functions. The arrival time of AE signals needs to be determined to perform the time difference of arrival (TDOA) analysis. A combined maximum likelihood estimation and Akaike’s information criterion (MLE–AIC) approach is initially used to compute the arrival time. To locate the damage source, a combined least squares–particle swarm optimization (LSPSO) method is originally proposed, which can reduce the number of iterations compared to the conventional particle swarm optimization (PSO) analysis. Two techniques have been evaluated based on either a predefined wave velocity range or interval theory to improve the accuracy of damage source location. Simulated artificial signals and AE signals obtained from pencil-lead breakage tests and uniaxial compression tests are analyzed using the LSPSO algorithm. The comparison of located damage source obtained from the current approach and the PCI-2 AE system has demonstrated the efficacy of the proposed analysis scheme.
Exploring Caenorhabditis elegans Behavior: An Inquiry-Based Laboratory Module for Middle or High School Students
Authors: Deffit Sarah N. , Neff Cori , Kowalski Jennifer R.
Published: October 2017

The use of primary scientific inquiry and experimentation to develop students’ understanding of methodologies used by scientists and the nature of science is a key component of the Next-Generation Science Standards (NGSS). Introduction to inquiry-based experimentation also has been shown to improve students’ attitudes and interest in science. However, implementing scientific inquiry activities that include experimental design and data analysis in a classroom of middle or high school students can be daunting for teachers with limited experimental experience. Here, we present a four- to five-day, inquiry-based laboratory activity designed to teach students about the scientific process and excite them about scientific discovery while providing opportunities for interactions of both teachers and students with scientists in the field. Within this laboratory module, students make observations and develop their own research questions, then design, execute, analyze, and present the results of their hypothesis-driven experiments investigating the behavior of Caenorhabditis elegans, a relatively inexpensive and tractable model organism. Our experience running this module in a middle school biology classroom suggests students enjoyed the opportunity to investigate their own research questions, and post-course surveys indicated that students’ fear of biology decreased and their interest in biology-related careers increased following participation in the module.
The prevalence of KRAS mutation in colorectal cancer patients in Iranian population: A systematic review and meta-analysis study
Authors: Payandeh Mehrdad , Amirifard Nasrin , Sadeghi Masoud , Shazad Babak , Farshchian Negin , Sadeghi Edris , Dayani Malihe
Published: October 2017

Colorectal cancer (CRC) is one of the most common cancers in the World that KRAS mutations are considered as a key step in the progression of CRC. This meta-analysis study aimed to evaluate the prevalence of KRAS mutations in CRC patients in Iran. Six online databases including PubMed, Science direct, Scopus, Web of science, Cochran Library, and Scientific Information Database (SID) were searched systematically up to January 2017. A random-effects meta-analysis was used to calculate the estimation of the prevalence of KRAS mutations in CRC patients by the event rate (ER) with 95% confidence interval (95%CI). Out of 82 articles identified from the search, eleven studies included and analyzed for meta-analysis study. The studies included 1814 CRC patients that mean age of the patients was 57.5 years. The pooled ER of the studies for estimation of the prevalence of KRAS mutation in CRC patients was 32.8% (95%CI=28.7-37.3%). The pooled ER of the studies for the prevalence of codon 12 mutation was 72.5% (95%CI=59.8-82.3%) and for codon 13 mutation was 20% (95%CI=14.6-26.7%). The results showed that the prevalence of KRAS mutation in Iran was different with more studies that therefore the geographical area and race can impact on the prevalence of KRAS mutation in CRC patients. Also, codon 12 had the most prevalence among mutant codons, followed by codon 13 that Gly to Asp and Gly to Val were the most mutations in codon 12.
 
Peer Review Details

Peer review method: Single-Blind (Peer-reviewers: 02) Peer-review policy
Plagiarism software screening?: Yes
Date of Original Submission: 07 September 2017
Date accepted: 02 October 2017
Peer reviewers approved by: Dr. Lili Hami
Editor who approved publication: Dr. Phuc Van Pham
Satysfakcja i zaangażowanie kadry kierowniczej w innowacyjnych przedsiębiorstwach – wyniki badań
Authors: Rakowska Anna , Mendryk Iwona
Published: October 2017

Managerial engagement plays an important role in achieving organisational performance. Three types of behaviors and attitudes related to managers’ performance should be considered: job engagement, work involvement, and organizational commitment. The literature indicates that numerous factors are relevant to high engagement, with satisfaction playing a particularly important role among them. The purpose of this article is to assess the level of commitment and satisfaction among managers, compare their results with those of non-management employees, and determine the strength of the relationships between the engagement (three types) and managerial job satisfaction with: economic conditions, their responsibilities, interpersonal relations and the physical environment. Organisational factors including perceived support and a sense of justice are also highlighted. The relationships between the three types of satisfaction and different types of engagement are identified; the strength of these relationships varied. The results obtained can be used to shape the commitment of managers and hence make more effective use of their potential.
Style uczenia się i umiejętności pracowników w kontekście wybranych segmentów rynku pracy
Authors: Sitko-Lutek Agnieszka , Jakubiak Monika
Published: October 2017

The paper examines learning styles and employee skills at innovative companies. These were evaluated in the context of selected segments of the labour market. The modern labour market may be analyzed using numerous criteria. The focus here was on the division of positions in organizations. The authors sought to determine whether positions occupied by respondents affected their learning styles and skills. The results of the study can be applied by HR managers and specialists in designing human resource management systems that can be adjusted to the needs of employees representing particular position types.The empirical study was conducted by means of a diagnostic survey based on a questionnaire. 1365 employees of innovative companies located in Poland replied and the questionnaires were analyzed with statistical methods. The results enabled recommendations for HR managers and specialists to be formulated. The recommendations pertain to the management of teams in modern enterprises.
Imigracja zarobkowa w Polsce. Stan i perspektywy emigracji z Ukrainy do Polski
Authors: Jarecki Wojciech
Published: October 2017

Changes on the labour market due to immigration are an important element of the business environment. This phenomenon affects companies in Poland as well. The present paper provides an answer to several questions concerning the amount of labour immigration to Poland, the professions immigrants engage in and the predicted amount of labour immigration. The analysis revealed that the number of immigrants, mostly from Ukraine, oscillates around 1 million and that the majority of them perform simple jobs. It is to be expected that in the near term, migration from Ukraine will not change considerably.
Mundos Plurales. Revista Latinoamericana de Políticas y Acción Pública
Authors: Universidad Nacional de Colombia Flacso Ecuador
Published: October 2017

La importancia creciente de las políticas públicas en los discursos políticos y académicos en América Latina urge la difusión de los principales aportes, propuestas, debates y discusiones en un campo de gran heterogeneidad. Este interés contrasta con la aún limitada disponibilidad en idioma castellano de numerosos autores considerados como referencias indispensables en el campo de las políticas públicas así como en la escasa producción regional de aportes a los debates en este campo, a pesar de la reciente multiplicación de programas de formación en políticas públicas en la región.
La política y las políticas en Latinoamérica: importancia de un modelo de análisis regional. Diálogo con Pedro Medellín
Authors: Montenegro Vanessa , Zabala Tania , Izquierdo Juan Diego , Zamora Edgar Alberto
Published: October 2017

Pedro Medellín es economista de la Universidad Nacional de Colombia donde hizo una maestría en Política Económica, es doctor en Ciencias Políticas de la Universidad de París III, cuya tesis doctoral versó sobre las políticas de justicia en Colombia como caso de estudio de la política pública en países de frágil institucionalidad, actualmente es candidato a Doctor en Ciencias Económicas de la Universidad de París XIII.
Mundos Plurales
Authors: MUNDOS PLURALES Revista
Published: October 2017

La importancia creciente de las políticas públicas en los discursos políticos y académicos en América Latina urge la difusión de los principales aportes, propuestas, debates y discusiones en un campo de gran heterogeneidad. Este interés contrasta con la aún limitada disponibilidad en idioma castellano de numerosos autores considerados como referencias indispensables en el campo de las políticas públicas así como en la escasa producción regional de aportes a los debates en este campo, a pesar de la reciente multiplicación de programas de formación en políticas públicas en la región.
Desarrollo y Libertad
Authors: Rivera Jairo
Published: October 2017

El libro tiene como objetivo principal analizar al desarrollo como un proceso de expansión de las libertades reales que disfrutan los individuos. La hipótesis que el texto defiende es que el desarrollo consiste en la eliminación de algunos tipos de ausencias de libertad que dejan a los individuos pocas opciones y escasas oportunidades para ejercer su agencia1. La tesis que plantea el autor radica en concebir la libertad individual como compromiso social.
Acceso y equidad a la educación superior y posgrado en el Ecuador, un enfoque descriptivo
Authors: Ponce Juan , Carrasco Fernando
Published: October 2017

Se analiza el acceso a la educación superior en el Ecuador con un enfoque de equidad donde se muestra en términos descriptivos la relación con la pobreza y, aunque no se considera el tema de la calidad de la educación, todos, de los muchos estudios realizados y teorías, plantean una fuerte sinergia educación-pobreza. Es por eso el interés de este análisis a través de indicadores de cobertura de educación y niveles de consumo. El enfoque teórico de Sen es usado para analizar ladesigualdad en el acceso a la educación superior como una medida relevante de inequidad.
Gratitud y felicidad en estudiantes del segundo al quinto año de una universidad privada de Lima este, 2016
Authors: Leon Lopez Susana Thalia , Hidalgo Gómez Ethel Priscilla , Mendoza Galarza Maritza
Published: October 2017

Objetivo: Determinar la relación entre las variables gratitud y felicidad en los estudiantes de una universidad privada de Lima este. El diseño de investigación es no experimental, de corte trasversal y de alcance correlacional. Materiales y Métodos: Los participantes fueron 404 estudiantes de ambos sexos entre las edades de 20 a 30 años. El instrumento empleado para la medición de la gratitud fue la Escala de gratitud, elaborada por Alarcón (2014) en Lima, Perú. Para medir la felicidad se utilizó la Escala de felicidad, elaborada por Alarcón (2006) en Lima, Perú, conformada por cuatro dimensiones: sentido positivo de la vida, satisfacción con la vida, realización personal y alegría de vivir. Resultados: Se relaciona significativamente con felicidad (rho=,324; p<0.01), y con cada una de sus dimensiones. Conclusiones: Por lo tanto, se concluye que las personas que presentan un nivel elevado de gratitud tienen más probabilidad de experimentar la felicidad plena.
Relación entre conocimientos, actitudes y prácticas en la prevención de los riesgos ergonómicos de los profesionales de enfermería de la Clínica Good Hope, Lima, 2016
Authors: Tipantuña Malte Paulina , Reyes Miguel Wendy , Paredes Aguirre Angela
Published: October 2017

Objetivo: Determinar la relación entre conocimientos, actitudes y prácticas en la prevención de riesgos ergonómicos de los profesionales de Enfermería de la Clínica Good Hope. Materiales y Métodos: Diseño correlacional de corte transversal. La muestra fue no probabilística y por conveniencia, conformada por 130 profesionales de Enfermería. Los instrumentos utilizados para la recolección de datos fueron de elaboración propia contando con una validez de 1 a través de la V de Aiken y una confiabilidad de 0,890 con Alfa de Cronbach. Resultados: A través de la prueba chi cuadrado se encontró que existe relación entre los conocimientos y prácticas (p= 0.025)en la prevención de riesgos ergonómicos. Sin embargo no existe relación entre los conocimientos y actitudes (p=0.076) y entre las actitudes y prácticas (p= 0.133). Conclusiones: Se encontró relación entre los conocimientos y prácticas hacia la prevención de riesgos ergonómicos.
Gene expression analysis for browning in murine subcutaneous and gonadal fat tissues and for steatosis and fibrosis in liver tissues. v1
Authors: Hemmeryckx Bianca , Bauters Dries , Roger Lijnen H.
Published: October 2017

ADAMTS5, the main aggrecanase, is a protein that appears to play a functional role in development ofwhite adipose tissue (WAT)and brown adipose tissue (BAT) and in browning of WAT. ADAMTS5 deficient or knockout (ADAMTS5-/- or KO) mice indeed showed lower WAT mass, higher mass of interscapular BAT and enhanced browning of WAT, as indicated by elevated uncoupling-protein-1 (UCP-1) levels. In addition, ADAMTS5-/- mice appeared to be protected from non-alcoholic steatohepatitis (NASH) when kept on a Western type diet. These observations were made with the ADAMTS5-/--P mice originally generated by Pfizer, in collaboration with Lexicon Genetics. To provide confirmation of these observations, we have obtained a second strain of ADAMTS5 deficient mice, generated independently by Deltagen Inc.
DNA extraction of Nephila clavipes using the Wizard Genomic DNA Purification kit (Promega) v1
Authors: Filipe Bartoleti Luiz , Filipe Bartoleti Luiz
Published: October 2017

Protocol used to extract whole genome DNA from Nephila clavipes (Araneae: Araneidae) specimens.
Treatment of Severely Resorbed Maxilla Due to Peri-Implantitis by Guided Bone Regeneration Using a Customized Allogenic Bone Block: A Case Report
Authors: Blume Oliver , Hoffmann Lisa , Donkiewicz Phil , Wenisch Sabine , Back Michael , Schnettler Reinhard , Barbeck Mike
Published: October 2017

The objective of this case report is to introduce a customized CAD/CAM freeze-dried bone allograft (FDBA) block for its use in Guided Bone Regeneration (GBR) procedures for severely deficient maxillary bones. Additionally, a special newly developed remote incision technique is presented to avoid wound dehiscence. The results show an optimal integration behaviour of the FDBA block after six months and the formation of new vital bone. Thus, the results of the present case report confirm the use of the customized CAD/CAM bone block for augmentation of complex defects in the maxillary aesthetic zone as a successful treatment concept.
Combining Spherical-Cap and Taylor Bubble Fluid Dynamics with Plume Measurements to Characterize Basaltic Degassing
Authors: Pering Tom D. , McGonigle Andrew J. S.
Published: October 2017

Basaltic activity is the most common class of volcanism on Earth, characterized by magmas of sufficiently low viscosities such that bubbles can move independently of the melt. Following exsolution, spherical bubbles can then expand and/or coalesce to generate larger bubbles of spherical-cap or Taylor bubble (slug) morphologies. Puffing and strombolian explosive activity are driven by bursting of these larger bubbles at the surface. Here, we present the first combined model classification of spherical-cap and Taylor bubble driven puffing and strombolian activity modes on volcanoes. We furthermore incorporate the possibility that neighboring bubbles might coalesce, leading to elevated strombolian explosivity. The model categorizes behavior in terms of the temporal separation between the arrival of successive bubbles at the surface and bubble gas volume or length, with the output presented on visually intuitive two-dimensional plots. The categorized behavior is grouped into the following regimes: puffing from a) cap bubbles; and b) non-overpressurised Taylor bubbles; and c) Taylor bubble driven strombolian explosions; each of these regimes is further subdivided into scenarios whereby inter-bubble interaction does/doesn't occur. The model performance is corroborated using field data from Stromboli (Aeolian Islands, Italy), Etna (Sicily, Italy) and Yasur (Vanuatu), representing one of the very first studies, focused on combining high temporal resolution degassing data with fluid dynamics, as a means of deepening our understanding of the processes which drive basaltic volcanism.
Application of Multi Network Alignment Algorithms for Connectomes Study
Authors: Milano Marianna , Guzzi Pietro Hiram , Cannataro Mario
Published: October 2017

A growing area in neurosciences is focused on the modeling and analysis the complex system of connections in neural systems, i.e. the connectome. Here we focus on the representation of connectomes by using graph theory formalisms. The human brain connectomes are usually derived from neuroimages; the analyzed brains are co-registered in the image domain and brought to a common anatomical space. An atlas is then applied in order to define anatomically meaningful regions that will serve as the nodes of the network - this process is referred to as parcellation. Recently, it has been proposed to perform atlas-free random brain parcellation into nodes and align brains in the network space instead of the anatomical image space to define network nodes of individual brain networks. In the network domain, the question of comparison of the structure of networks arises. Such question is tackled by modeling the comparison of brain network as a network alignment (NA) problem. In this paper, we first defined the NA problem formally, then we applied three existing state of the art of multiple alignment algorithms (MNA) on diffusion MRI-derived brain networks and we compared the performances. The results confirm that MNA algorithms may be applied in cases of atlas-free parcellation for a fully network-driven comparison of connectomes.
Global Calibration of Multi-Cameras Based on Refractive Projection and Ray Tracing
Authors: Feng Mingchi , Jia Xiang , Wang Jingshu , Feng Song , Zheng Taixiong
Published: October 2017

Multi-cameras system is widely applied in 3D computer vision especially when multiple cameras are distributed on both sides of the measured object. The calibration methods of multi-cameras system are critical to the accuracy of vision measurement and the key is to find an appropriate calibration target. In this paper, a high-precision camera calibration method for multi-cameras system based on transparent glass checkerboard and ray tracing is described, which is used to calibrate multiple cameras distributed on both sides of the glass checkerboard. Firstly, the intrinsic parameters of each camera is obtained by Zhang’s calibration method. Then, multiple cameras capture several images from the front and back of the glass checkerboard with different orientations, and all images contain distinct grid corners. As the cameras on one side are not affected by the refraction of glass checkerboard, extrinsic parameters can be directly calculated. However, the cameras on another side are influenced by the refraction of glass checkerboard, and the direct use of projection model will produce calibration error. A multi-cameras calibration method using refractive projection model and ray tracing is developed to eliminate this error. Furthermore, both synthetic and real data are employed to validate the proposed approach. The experimental results of refractive calibration show that the error of the 3D reconstruction is smaller than 0.2 mm, the relative errors of both rotation and translation are less than 0.014%, and the mean and standard deviation of reprojection error of 4-cameras system are 0.00007 and 0.4543 pixel. The proposed method is flexible, high accurate, and simple to carry out.
Pyplis - A Python Software Toolbox for the Analysis of SO2 Camera Data
Authors: Gliß Jonas , Stebel Kerstin , Kylling Arve , Dinger Anna Solvejg , Sihler Holger , Sudbø Aasmund
Published: October 2017

UV SO2 cameras have become a common tool to measure and monitor SO2-emission-rates, mostly from volcanoes but also from anthropogenic sources (e.g. power plants or ships). In the past years, the analysis of UV SO2 camera data has seen many improvements. As a result, for many of the required analysis steps, several alternatives exist today. This inspired the development of Pyplis, an open-source software toolbox written in Python 2.7, which aims to unify the most prevalent methods from literature within a single, cross-platform analysis framework. Pyplis comprises a vast collection of algorithms relevant for the analysis of UV SO2 camera data. These include several routines to retrieve plume background radiances as well as routines for cell and DOAS based camera calibration. The latter includes two independent methods to identify the DOAS field-of-view within the camera images. Plume velocities can be retrieved using an optical flow algorithm as well as signal cross-correlation. Furthermore, Pyplis includes a routine to perform a first order correction of the signal dilution effect. All required geometrical calculations are performed within a 3D model environment allowing for distance retrievals to plume and local terrain features on a pixel basis. SO2-emission-rates can be retrieved simultaneously for an arbitrary number of plume intersections. Pyplis has been extensively and successfully tested using data from several field campaigns. Here, the main features are introduced using a dataset obtained at Mt. Etna, Italy on 16 September 2015.
New Cassane Diterpenoids from Caesalpinia sappan and Their Antiplasmodial Activity
Authors: Zhu Nai-Liang , Sun Zhong-Hao , Hu Mei-Geng , Wu Tong-Yu , Yuan Jing-Quan , Wu Hai-Feng , Tian Yu , Li Peng-Fei , Yang Jun-Shan , Ma Guo-Xu , Xu Xu-Dong
Published: October 2017

One new cassane diterpene possessing an unusual N bridge between C-19 and C-20 named caesalsappanin R (1), as well as another new diterpene caesalsappanin S (2), were isolated from the seeds of Caesalpinia sappan with methanol extract. Their structures were determined by spectroscopic analysis and examined alongside existing data from prior studies. Their biological activities were profiled by their antiplasmodial activity.
Potensi dan Prospek Pemanfaatan Lahan Pekarangan untuk Mendukung Ketahanan Pangan
Authors: Ashari NFN , Saptana NFN , Purwantini Tri Bastuti
Published: October 2017

English
Food security remains as a fundamental problem in most countries along with population increase, purchasing power improvement, and climate change. To support national food security, it is necessary to implement it at the households’ level such as farming on backyard land (pekarangan) areas. This paper aims to review the potencies, policies and programs, as well as constraints related with use of backyard land in supporting food security at households’ level. Backyard land is potential for farming in order to supply family food needs, especially vegetables, to reduce household food expenditure, and to increase the household income. Some constrains are found in backyard farming, such as less intensive cultivation, not a core business, lack of specific technology, and less field workers’ of assistance. Support from various stakeholders is necessary in order to improve backyard farming.

 

Indonesian
Ketahanan pangan akan tetap menjadi permasalahan pokok di sebagian besar negara di dunia seiring dengan semakin besar jumlah penduduk, peningkatan daya beli dan dinamika iklim global. Upaya membangun ketahanan pangan keluarga, salah satunya dapat dilakukan dengan memanfaatkan sumberdaya yang tersedia, diantaranya melalui pemanfaatan lahan pekarangan.Tulisan ini bertujuan untuk mengulas potensi, kebijakan dan program, serta kendala pemanfaatan lahan pekarangan untuk mendukung ketahanan pangan, terutama di tingkat rumah tangga. Lahan pekarangan memiliki potensi dalam penyediaan bahan pangan keluarga, mengurangi pengeluaran rumah tangga untuk pembelian pangan dan meningkatkan pendapatan rumah tangga petani. Sejumlah kendala terkait masalah sosial, budaya, dan ekonomi masih dijumpai dalam program pemanfaatan  lahan pekarangan, diantaranya belum membudayanya budidaya pekarangan secara intensif, masih bersifat sambilan dan belum berorientasi pasar, kurang tersedianya teknologi budidaya spesifik pekarangan, serta proses pendampingan dari petugas yang belum memadai. Oleh karena itu diperlukan perencanaan yang matang dan dukungan lintas sektoral dalam pemanfaatan lahan pekarangan sehingga mampu lebih optimal dalam mendukung ketahanan pangan.
Konsep Efisiensi Usahatani Pangan dan Implikasinya bagi Peningkatan Produktivitas
Authors: Saptana NFN
Published: October 2017

English
Basic problems for farm business improvement are lack of types, quantity, quality, and continuity of agricultural products supply in accordance with market demand dynamics. Improving agricultural productivity can be carried out through efficiency enhancement and technology breakthrough. Empirical studies on technical efficiency (TE) show that Indonesian farming TE values for some food commodities are moderate to high (0.50-0.80) suggesting that the food-crop farm business are not fully technically efficient.  Meanwhile, the allocative efficiencies (AE) of some food-crop farm businesses range from 0.45 to 0.70, and economic efficiencies (EE) vary from 0.35 to 0.60 indicating low to moderate efficiency levels. Socio-economic factors affecting the lower technical inefficiencies are: (a) land size, (b) household income, (c) formal education of household heads, and (d) household heads’ experience in farming. Strategies to improve farm business efficiency are through transformation of traditional farming to modern one In the future the farming should be driven by innovation in science and technology and skilled human resources.

 

Indonesian
Permasalahan-permasalahan pokok yang dihadapi dalam pengembangan usahatani adalah belum terwujudnya ragam, kuantitas, kualitas, dan kesinambungan pasokan berbagai produk pertanian yang sesuai dengan dinamika permintaan pasar.  Berkaitan dengan permasahan tersebut maka upaya peningkatan produktivitas pertanian dapat dilakukan dengan peningkatan efisiensi dan terobosan teknologi baru.  Hasil review studi empiris pencapaian efisiensi teknis (TE) usahatani pangan di Indonesia tergolong moderat hingga tinggi (0,50-0,80) yang menunjukkan usahatani beberapa komoditas belum sepenuhnya efisien secara teknis.  Sementara itu, tingkat efisiensi alokatif (AE) beberapa usahatani pangan berkisar (0,45-0,70) dan efisiensi ekonomi (EE) berkisar (0,35-0,60), berada pada level rendah hingga moderat. Faktor sosial-ekonomi yang berpengaruh menurunkan inefisiensi teknis pada usahatani pangan adalah : (a) variabel luas garapan, (b) variabel pendapatan rumah tangga, (c) variabel pendidikan formal KK,  dan (d) Variabel pengalaman KK dalam usahatani. Pilihan strategi peningkatan efisiensi usahatani dapat di lakukan dengan transformasi usahatani dari usahatani tradisional ke arah kebudayaan industrial, selanjutnya ke depan harus mengarah pada usahatani yang digerakkan oleh inovasi ilmu pengetahuan dan teknologi serta SDM yang terampil.
Pemahaman terhadap Petani Kecil sebagai Landasan Kebijakan Pembangunan Pertanian
Authors: Syahyuti NFN
Published: October 2017

English
Improving the farmers’ welfare is one of goals in agricultural development policy. Inadequate government’s concern to farmers is observed from the definition of farmers in various regulations and understanding of small farmers’ existence, role and characters. Lacks of understanding and taking side to small farmers are indicated by absence of using the term of "small farmers" in various government policies. This paper reviews various thoughts, as well as development and implementation of agricultural policies with respect to farmers’ welfare improvement. The results show the weak understanding on, no partiality, and even unfair treatment to small farmers. Thus, in the future the concept of "small farmers" must be unequivocally expressed in order to make their potential more environmentally friendly and independently.

 

Indonesian
Peningkatan kesejahteraan petani hanya menjadi sub tujuan dalam kebijakan pembangunan pertanian. Perhatian yang belum memadai kepada petani terlihat dari definisi petani dalam berbagai regulasi dan pemahaman tentang keberadaan, peran serta karakter petani kecil. Pemahaman dan keberpihakan yang rendah ditunjukkan dengan tidak adanya penggunaan istilah “petani kecil” dalam berbagai kebijakan pemerintah. Tulisan ini merupakan review dari berbagai pemikiran, serta kebijakan dan pelaksanaan pembangunan pertanian yang berkenaan dengan peningkatan kesejahteraan petani. Hasilnya menunjukkan masih lemahnya pemahaman, belum ada pemihakan, dan bahkan perlakuan yang tidak adil kepada petani kecil. Dengan demikian, ke depan semestinya konsep “petani kecil” dicantumkan secara tegas, sehingga potensinya yang lebih ramah lingkungan dan mandiri dapat dioptimalkan. Hanya dengan pendekatan ini akan memberikan jaminan perhatian kepada petani kecil di masa mendatang.
Potensi Pengembangan Pupuk Organik Insitu Mendukung Percepatan Penerapan Pertanian Organik
Authors: Darwis Valeriana , Rachman Benny
Published: October 2017

English
Organic fertilizer in-situ application is the beginning of organic farming. In-situ organic fertilizer raw materials can be obtained from straw and dung. National straw production is 30.4 million tons per year and cow’s dung production is 3.8 million tons per month. Technology for organic fertilizer production is simple, namely through stacking the straw and flipping it. Solid fertilizer organic fertilizer cost is Rp 417 per kg and that of liquid organic fertilizer is Rp 3,510 per liter. Accelerating organic farming implementation can be carried out through: (1)  use of straw, (2) sustainable cattle and livestock integration program, (3) price subsidy policy, (4) provision of organic fertilizer processing equipments, composting houses, and organic fertilizer processing units, and (5) standardization and labeling of farmers-produced organic fertilizer.

 

Indonesian
Pemakaian pupuk organik in-situ di tingkat petani merupakan awal dalam mewujudkan pertanian organik. Bahan pupuk organik in-situ dapat diperoleh dari jerami dan kotoran hewan (kohe). Potensi jerami secara nasional dalam satu tahun sebesar 30,4 juta ton dan kohe sapi 3,8 juta ton per bulan. Teknologi membuat pupuk organik sangat sederhana yaitu dengan cara menumpuk dan membalik-baliknya. Biaya yang dikeluarkan dalam membuat satu kilogram pupuk organik padat sebesar Rp 417 dan Rp 3.510 per liter untuk pupuk organik cair. Percepatan implementasi pertanian organik dapat dilaksanakan melalui : (1) kebijakan pemakaian jerami secara bijak, (2) program integrasi sapi dan ternak secara berkelanjutan, (3) penerapan kebijakan subsidi harga pupuk organik yang lebih menarik, (4) memberikan bantuan pembuatan pupuk organik secara berjenjang dimulai dari pemberian alat pengolah pupuk organik, kemudian diteruskan ke pemberian Rumah Kompos dan terakhir ke pemberian unit pengolah pupuk organik, (dan 5) standarisasi dan pelabelan pupuk organik produksi petani.
Penataan Ruang Daerah Aliran Sungai Ciliwung dengan Pendekatan Kelembagaan dalam Perspektif Pemantapan Pengelolaan Usahatani
Authors: Saridewi Tri Ratna , Hadi Setia , Fauzi Akhmad , Rusastra I Wayan
Published: October 2017

English
Rapid development on Ciliwung watershed converts farmland to other uses causing decreased catchment area and flood. Flood occurrence on Ciliwung watershed indicates that current land use planning is not in accordance with its carrying capacity. Currently, most of the policies issued to manage watershed are dominated by structural approach. Moreover, land use planning often leads regional and sectoral conflicts. Based on a literature study, a non-structural approach should be done prior to a structural approach. Land use planning using an institutional approach is part of a non-structural approach. An institutional approach in managing Ciliwung watershed could be based on Ostrom’s Institutional Analysis and Development (IAD). Payment mechanism for environmental services and compensation can be carried out through the operation and maintenance of irrigation and watershed management simultaneously. Good watershed quality is able prevent flood incidence and to guarantee continuity of irrigation water supply resulting in farming productivity improvement. Optimum allocation of Ciliwung watershed can be achieved by accommodating both conservation and economic requirements simultaneously. Effective institutional interaction is the appropriate way to ensure implementation of integrated watershed management.

 

Indonesian
Pembangunan yang sangat pesat di Daerah Aliran Sungai Ciliwung mendorong terjadinya konversi lahan pertanian menjadi lahan terbangun. Hal ini menyebabkan berkurangnya daerah resapan air sehingga terjadi banjir. Banjir tersebut merupakan indikasi bahwa tata ruang saat ini tidak sesuai dengan daya dukung wilayah. Selama ini, kebijakan pemerintah untuk penyelesaian pengelolaan kawasan DAS lebih didominasi oleh penyelesaian secara struktural. Selain itu, perencanaan penataan ruang yang telah disusun seringkali menimbulkan adanya konflik sektoral dan kewilayahan. Melalui studi literatur, dapat diketahui bahwa pendekatan yang bersifat nonstruktural harus dilakukan terlebih dahulu sebelum pendekatan struktural. Penataan ruang menggunakan pendekatan kelembagaan merupakan bagian dari pendekatan nonstruktural. Pendekatan kelembagaan dalam pengelolaan kawasan DAS Ciliwung dapat mengacu pada Ostrom’s Institutional Analysis and Development (IAD). Mekanisme imbal jasa lingkungan dan pemberian kompensasi dapat dilakukan melalui operasi dan pemeliharaan irigasi serta pengelolaan DAS secara bersamaan. Kualitas DAS yang terjaga dengan baik mampu menanggulangi banjir sekaligus menjaga kontinuitas air irigasi sehingga produktivitas usahatani meningkat. Alokasi tata ruang kawasan DAS Ciliwung yang optimum dapat diperoleh dengan mengakomodir kebutuhan konservasi dan ekonomi secara bersamaan. Interaksi kelembagaan yang efektif merupakan langkah yang tepat untuk menjamin implementasi pengelolaan DAS secara terpadu.
Kedaulatan Pangan sebagai Basis untuk Mewujudkan Ketahanan Pangan Nasional
Authors: Syahyuti NFN , Sunarsih NFN , Wahyuni Sri , Sejati Wahyuning Kusuma , Azis Miftahul
Published: October 2017

English
The concept of food sovereignty officially becomes an objective and an approach in national food development such as depicted in Law No. 18/2012 on Food along with food self-sufficiency and food security. However, up to now formulation and understanding of food sovereignty is various and unclear. This article aims to review the concept of food sovereignty at international and national levels. Food sovereignty is a strategy to improve food security as the ultimate goal of food development because the concept is in fact consistent and complementary. Food sovereignty is related with farmers' rights and access to the entire agricultural resources including land, water, production factors, technology, and marketing as well as on consumption. This condition is measurable at various levels at individual, household, community, regional, and national levels.

 

Indonesian
Konsep kedaulatan pangan secara resmi telah menjadi tujuan dan juga pendekatan dalam pembangunan pangan nasional, sebagaimana tercantum dalam UU No. 18 Tahun 2012 tentang Pangan, bersama-sama dengan kemandirian pangan dan ketahanan pangan. Namun demikian, sampai saat ini perumusan dan pemahaman tentang kedaulatan pangan masih beragam dan kurang jelas. Tulisan ini bertujuan melakukan review konsep kedaulatan pangan yang berlangsung di dunia internasional dan dalam kebijakan-kebijakan pemerintah di Indonesia. Hasil penelusuran menunjukkan bahwa kedaulatan pangan merupakan suatu strategi dasar untuk melengkapi ketahanan pangan sebagai tujuan akhir pembangunan pangan, karena kedua konsep ini sesungguhnya sejalan dan saling melengkapi. Hasil dari pendalaman terhadap berbagai konsep, dirumuskan bahwa kedaulatan pangan berkenaan dengan hak dan akses petani kepada seluruh sumber daya pertanian mencakup lahan, air, sarana produksi, teknologi, pemasaran, serta terhadap konsumsi. Kondisi ini dapat diukur pada berbagai level baik level individu, rumah tangga, komunitas, wilayah, dan juga nasional.