bluuebunny/crossref_metadata_2025_split 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.
Obesity and Cancer: Evidence, Impact, and Future Directions
Authors: Colditz Graham A , Peterson Lindsay L 
Published: October 2017

Abstract

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.

SUMMARY
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

AbstractAngiogenesis 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

Abstract
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

AbstractThe 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.
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
Potensi dan Prospek Pemanfaatan Lahan Pekarangan untuk Mendukung Ketahanan Pangan
Authors: Ashari NFN , Saptana NFN , Purwantini Tri Bastuti 
Published: October 2017

<p><strong>English</strong><br />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.</p><p> </p><p><strong>Indonesian</strong><br />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.</p>
Konsep Efisiensi Usahatani Pangan dan Implikasinya bagi Peningkatan Produktivitas
Authors: Saptana NFN 
Published: October 2017

<p><strong>English</strong><br />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.</p><p> </p><p><strong>Indonesian</strong><br />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.</p>
Pemahaman terhadap Petani Kecil sebagai Landasan Kebijakan Pembangunan Pertanian
Authors: Syahyuti NFN 
Published: October 2017

<p><strong>English</strong><br />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. </p><p> </p><p><strong>Indonesian</strong><br />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.</p>
Potensi Pengembangan Pupuk Organik Insitu Mendukung Percepatan Penerapan Pertanian Organik
Authors: Darwis Valeriana , Rachman Benny 
Published: October 2017

<p><strong>English</strong><br />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.</p><p> </p><p><strong>Indonesian</strong><br />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.</p>
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

<p><strong>English</strong><br />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. </p><p> </p><p><strong>Indonesian</strong><br />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.</p>