bluuebunny/crossref_metadata_2025_split huggingface dataset:
TRaCE+: Ensemble inference of gene regulatory networks from transcriptional expression profiles of gene knock-out experiments
Authors: Ud-Dean S.M. Minhaz , Heise Sandra , Klamt Steffen , Gunawan Rudiyanto 
Published: June 2016

Abstract
Background
The inference of gene regulatory networks (GRNs) from transcriptional expression profiles is challenging, predominantly due to its underdetermined nature. One important consequence of underdetermination is the existence of many possible solutions to this inference. Our previously proposed ensemble inference algorithm TRaCE addressed this issue by inferring an ensemble of network directed graphs (digraphs) using differential gene expressions from gene knock-out (KO) experiments. However, TRaCE could not deal with the mode of the transcriptional regulations (activation or repression), an important feature of GRNs.

Results
In this work, we developed a new algorithm called TRaCE+ for the inference of an ensemble of signed GRN digraphs from transcriptional expression data of gene KO experiments. The sign of the edges indicates whether the regulation is an activation (positive) or a repression (negative). TRaCE+ generates the upper and lower bounds of the ensemble, which define uncertain regulatory interactions that could not be verified by the data. As demonstrated in the case studies using Escherichia coli GRN and 100-gene gold-standard GRNs from DREAM 4 network inference challenge, by accounting for regulatory signs, TRaCE+ could extract more information from the KO data than TRaCE, leading to fewer uncertain edges. Importantly, iterating TRaCE+ with an optimal design of gene KOs could resolve the underdetermined issue of GRN inference in much fewer KO experiments than using TRaCE.

Conclusions
TRaCE+ expands the applications of ensemble GRN inference strategy by accounting for the mode of the gene regulatory interactions. In comparison to TRaCE, TRaCE+ enables a better utilization of gene KO data, thereby reducing the cost of tackling underdetermined GRN inference. TRaCE+ subroutines for MATLAB are freely available at the following website: http://www.cabsel.ethz.ch/tools/trace.html.
CerealsDB 3.0: expansion of resources and data integration
Authors: Wilkinson Paul A. , Winfield Mark O. , Barker Gary L. A. , Tyrrell Simon , Bian Xingdong , Allen Alexandra M. , Burridge Amanda , Coghill Jane A. , Waterfall Christy , Caccamo Mario , Davey Robert P. , Edwards Keith J. 
Published: June 2016

Abstract
Background
The increase in human populations around the world has put pressure on resources, and as a consequence food security has become an important challenge for the 21st century. Wheat (Triticum aestivum) is one of the most important crops in human and livestock diets, and the development of wheat varieties that produce higher yields, combined with increased resistance to pests and resilience to changes in climate, has meant that wheat breeding has become an important focus of scientific research. In an attempt to facilitate these improvements in wheat, plant breeders have employed molecular tools to help them identify genes for important agronomic traits that can be bred into new varieties. Modern molecular techniques have ensured that the rapid and inexpensive characterisation of SNP markers and their validation with modern genotyping methods has produced a valuable resource that can be used in marker assisted selection. CerealsDB was created as a means of quickly disseminating this information to breeders and researchers around the globe.

Description
CerealsDB version 3.0 is an online resource that contains a wide range of genomic datasets for wheat that will assist plant breeders and scientists to select the most appropriate markers for use in marker assisted selection. CerealsDB includes a database which currently contains in excess of a million putative varietal SNPs, of which several hundreds of thousands have been experimentally validated. In addition, CerealsDB also contains new data on functional SNPs predicted to have a major effect on protein function and we have constructed a web service to encourage data integration and high-throughput programmatic access.

Conclusion
CerealsDB is an open access website that hosts information on SNPs that are considered useful for both plant breeders and research scientists. The recent inclusion of web services designed to federate genomic data resources allows the information on CerealsDB to be more fully integrated with the WheatIS network and other biological databases.
Genome sequence of the organohalide-respiring Dehalogenimonas alkenigignens type strain (IP3-3T)
Authors: Key Trent A. , Richmond Dray P. , Bowman Kimberly S. , Cho Yong-Joon , Chun Jongsik , da Costa Milton S. , Rainey Fred A. , Moe William M. 
Published: June 2016

AbstractDehalogenimonas alkenigignens IP3-3T is a strictly anaerobic, mesophilic, Gram negative staining bacterium that grows by organohalide respiration, coupling the oxidation of H2 to the reductive dehalogenation of polychlorinated alkanes. Growth has not been observed with any non-polyhalogenated alkane electron acceptors. Here we describe the features of strain IP3-3T together with genome sequence information and its annotation. The 1,849,792 bp high-quality-draft genome contains 1936 predicted protein coding genes, 47 tRNA genes, a single large subunit rRNA (23S-5S) locus, and a single, orphan, small unit rRNA (16S) locus. The genome contains 29 predicted reductive dehalogenase genes, a large majority of which lack cognate genes encoding membrane anchoring proteins.
Combining escitalopram and cognitive–behavioural therapy for social anxiety disorder: Randomised controlled fMRI trial
Authors: Gingnell Malin , Frick Andreas , Engman Jonas , Alaie Iman , Björkstrand Johannes , Faria Vanda , Carlbring Per , Andersson Gerhard , Reis Margareta , Larsson Elna-Marie , Wahlstedt Kurt , Fredrikson Mats , Furmark Tomas 
Published: June 2016

BackgroundSelective serotonin reuptake inhibitors (SSRIs) and cognitive–behavioural therapy (CBT) are often used concomitantly to treat social anxiety disorder (SAD), but few studies have examined the effect of this combination.AimsTo evaluate whether adding escitalopram to internet-delivered CBT (ICBT) improves clinical outcome and alters brain reactivity and connectivity in SAD.MethodDouble-blind, randomised, placebo-controlled neuroimaging trial of ICBT combined either with escitalopram (n = 24) or placebo (n = 24), including a 15-month clinical follow-up (trial registration: ISRCTN24929928).ResultsEscitalopram+ICBT, relative to placebo+ICBT, resulted in significantly more clinical responders, larger reductions in anticipatory speech state anxiety at post-treatment and larger reductions in social anxiety symptom severity at 15-month follow-up and at a trend-level (P = 0.09) at post-treatment. Right amygdala reactivity to emotional faces also decreased more in the escitalopram+ICBT combination relative to placebo+ICBT, and in treatment responders relative to non-responders.ConclusionsAdding escitalopram improves the outcome of ICBT for SAD and decreased amygdala reactivity is important for anxiolytic treatment response.
Compassion fatigue: A Study of critical care nurses in Turkey
Authors: Dikmen Yurdanur , Aydın Yasemin , Tabakoğlu Pınar 
Published: June 2016

This study was conducted to determine the level of compassion fatigue which experienced by nurses who work in intensive care units and factors that affecting it.In a cross sectional design, critical nurses were surveyed by using questionnaire and compassion fatigue (CF) subscale of the Professional Quality of Life Scale (ProQOL R-IV) to measure levels of compassion fatigueat a large National Education and ResearchHospital located in northwestof Turkey. A total of 69 critical care nurses participated in the study, for a response rate of 78%.A series of cross tab analyses examined the relationship between nurses demographics and compassion fatigue (CF) subscale. To analyze the data further, participants were recategorized into 2 groups for CF scores: (1) higher than 17: high risk and (2) lower than 17: low risk.Findings show that critical care nurses were at high risk (52.7%) and low risk (47.3%) for CF. Nurses informed significant differences in compassion fatigue on the basis of age, years of critical care experience, working hours (weekly).
Adnexal masses: Clinical approach and pathological findings<p> Adneksiyal kitleler: Klinik yaklaşım ve patolojik bulgular
Authors: Şık Bulat Aytek , Erdem Baki , Aba Yılda Arzu , Kumbasar Serkan 
Published: June 2016

Our study aims to investigate patients with adnexal masses without known pathologies in conjunction with their demographic data, patient history, length of hospitalization, complications, ratio of approaching patients laparoscopically or with laparotomy, and pathological findings. Patient data were collected retrospectively by browsing patient filed. Besides clinical information such as length of hospitalization, used surgical technique, whether there was a transition to laparotomy, whether there was a perioperative complication, and pathological examination results of the sample taken, data like the radiological size of the mass, number of previous operations, circumstances that lead to comorbidity, age, and state of menopause during surgery were collected. Among 110 patients, 48 (43.6%) were applied laparoscopy, while 56 (50.9) were applied laparotomy. The mean length of surgery was 107.4±53.8 minutes (40-181 mins.). Most seen surgery indications were persistent cyst seen in 55 patients (50%) and complex cyst seen in 16 patients (14.5%). In patients diagnosed with adnexal masses, distinguishing benign and malign masses by simultaneous usage of history, physical therapy, laboratory tests, and transvaginal ultrasonography, and deciding for laparoscopy and/or laparotomy based on this for treatment, is a highly reliable method. ÖzetÇalışmamız da patolojisi bilinmeyen adneksiyal kitlesi olan hastaların, sosyodemografik verileri, hasta özellikleri, hastanede yatış süreleri, komplikasyonları, hastalara laparoskopik veya laparotomi ile yaklaşım oranları, patolojik bulguları ile birlikte değerlendirilmesi amaçlanmıştır. Hasta bilgileri retrospektif olarak hasta dosyalarının taranması sonucu elde edilmiştir. Hastanede kalış süresi, perioperatif komplikasyon, kullanılan cerrahi teknik, laparotomiye geçiş olup olmadığı, alınan materyalin patolojik inceleme sonucu gibi klinik bilgilerin yanında radyolojik olarak kitlenin boyutu, daha önce geçirilmiş ameliyat sayısı, komorbidite oluşturan durumlar, cerrahi esnasında menopoz durumu ve yaş gibi bilgiler değerlendirilmiştir. 110 hastanın 48 (%43,6) ine laparoskopi, 56 (%50,9) sına laparotomi yapılmıştır. Ameliyat süresi ortalaması 107,4±538 dakikadır (40-181 dk.). En sık ameliyat endikasyonu, 55 hastada (%50) saptanan persiste kist ve ikinci sıklıkta 16 hastada (%14,5) komplike kisttir. Adneksiyal kitle tanısı alan hastalarda, öykü, fizik muayene, laboratuvar tetkikleri, transvaginal ultrasonografi ile bir arada kullanılarak benign-malign ayırımının yapılması ve buna göre laparoskopi ve/veya laparotomi ile tedavisi oldukça yüksek güvenilirliğe sahiptir.
Trends in the Production of Castings in the World and in Poland in the XXI Century
Authors: Soiński M.S. , Kordas P. , Skurka K. 
Published: June 2016

Abstract
The paper presents data concerning the total production of castings over the 2000-2014 period, both on a global scale, and in Poland. The basic types of casting alloys were taken into account. Changes in the production volume and structure over the period of the analysed 15 years were pointed out with respect to countries leading in foundry production. The topmost position in the world foundry industry is held by China for several years (with almost 45% share in the foundry market), the second place is taken by India (with almost 9% share). A distinct reduction in the shares of the once significant producers of castings, such as USA, Japan, Germany, Russia, Italy, or France, was observed over the 2000-2014 period. Poland had a share of 1.16% in 2000, and of 1.02% in 2014. Comparing the detailed data concerning the years 2000 and 2014, one can see that the fractions of castings made of ductile iron, cast steel, aluminium alloys, or magnesium alloys increase on a global scale, while such alloys as grey cast iron or malleable are in decline.
Numerical Simulation of Solidification Microstructure based on Adaptive Octree Grids
Authors: Yin Y. , Li Y. , Wu K. , Zhou J. 
Published: June 2016

Abstract
The main work of this paper focuses on the simulation of binary alloy solidification using the phase field model and adaptive octree grids. Ni-Cu binary alloy is used as an example in this paper to do research on the numerical simulation of isothermal solidification of binary alloy. Firstly, the WBM model, numerical issues and adaptive octree grids have been explained. Secondary, the numerical simulation results of three dimensional morphology of the equiaxed grain and concentration variations are given, taking the efficiency advantage of the adaptive octree grids. The microsegregation of binary alloy has been analysed emphatically. Then, numerical simulation results of the influence of thermophysical parameters on the growth of the equiaxed grain are also given. At last, a simulation experiment of large scale and long-time has been carried out. It is found that increases of initial temperature and initial concentration will make grain grow along certain directions and adaptive octree grids can effectively be used in simulations of microstructure.
Application of ALSV(FD) logic and XTT knowledge representation in the range of ADI properties
Authors: Regulski K. , Wilk-Kołodziejczyk D. , Rojek G. , Kluska-Nawarecka S. , Adrian W.T. 
Published: June 2016

Abstract
The objective of studies presented in this publication was structuring of research knowledge about the ADI functional properties and changes in these properties due to material treatment. The results obtained were an outcome of research on the selection of a format of knowledge representation that would be useful in further work aiming at the design, application and implementation of an effective system supporting the decisions of a technologist concerning the choice of a suitable material (ADI in this case) and appropriate treatment process (if necessary). ALSV(FD) logic allows easy modelling of knowledge, which should let addressees of the target system carry out knowledge modelling by themselves. The expressiveness of ALSV (FD) logic allows recording the values of attributes from the scope of the modelled domain regarding ADI, which is undoubtedly an advantage in the context of further use of the logic. Yet, although the logic by itself does not allow creating the rules of knowledge, it may form a basis for the XTT format that is rule-based notation. The difficulty in the use of XTT format for knowledge modelling is acceptable, but formalism is not suitable for the discovery of rules, and therefore the knowledge of technologist is required to determine the impact of process parameters on values that are functional properties of ADI. The characteristics of ALSV(FD) logic and XTT formalism, described in this article, cover the most important aspects of a broadly discussed, full evaluation of the applicability of these solutions in the construction of a system supporting the decisions of a technologist.
Cardiac War Wounds
Authors: Ždrale Slavko , Vuković Marko 
Published: June 2016

Summary
The paper presents myocardial contusion and penetrating cardiac war wounds. The authors report their experience with thirteen cases of penetrating wounds, out of which only two were treated in the conditions acceptable for surgery. The other 11 wounds were treated in war hospitals which were mostly improvised, and in mobile surgical teams. The basic, exclusively physical examination methods are described here, with the emphasis that “it is better to open and see than wait and see”. Such procedure gave the results that could be compared with the best ones in the literature (only one death). Three, conditionally speaking, specific cases are presented: one tangential wound with relapsing hemorrhage and two spontaneously sanitized ventricle wounds followed by other kinds of complications.
Perforation of the Right Ventricle as a Complication of Pericardiocentesis: A Case report
Authors: Stojanović Milovan , Ilić Bojan , Stojanović Sanja , Ilić Stevan , Ilić Marina Deljanin 
Published: June 2016

Summary
Pericardial effusion represents the accumulation of larger amounts of fluid in the pericardial cavity. If not timely diagnosed and adequately treated, it can lead to cardiac tamponade. The treatment of pericardial effusion includes primarily the use of drugs like aspirin, NSAIDs, corticosteroids, and/or colchicine followed by invasive procedures such as pericardiocentesis or pericardiectomy. Pericardiocentesis complications are extremely rare but very serious especially in the case of the rupture of the right ventricle or the coronary arteries. Patient S.V, born in 1938, from Svrljig, was examined because of suffocating and swollen shin. The medical reports showed that the patient previously had had a permanent pacemaker implanted and that he had undergone a triple coronary artery bridging. Medical reports also showed that two months before the examination he was hospitalized due to pericardial effusion at the reference institution. The ultrasonographic examination registered large circular effusion with the motion of the right ventricle and the patient underwent urgent pericardiocentesis. During pericardiocentesis, the rupture of the right ventricle occurred and the patient was sent to the cardiac surgery clinic where he had catheter extraction performed. The control ultrasound examination of the heart showed no pericardial effusion, and no signs of damage to the right ventricle.
Evaluation of Usefulness of the Designed Laboratory Photobioreactor for Microalgae Cultivation in Controlled Conditions
Authors: Brzychczyk Beata , Kowalczyk Zbigniew , Giełżecki Jan 
Published: June 2016

Abstract
The objective of the paper was to analyse the use of the designed photobioreactor for freshwater microalgae cultivation in the controlled laboratory conditions. The work covered the design and construction of photobioreactors (PBR) and setting up comparative cultivations of freshwater microalgae chlorelli vulgaris along with determination of the biomass growth intensity for a varied amount of supplied culture medium. It was found out that the constructed PBR may be used for microalgae cultivation in the controlled conditions. The impact of the culture medium amount on the growth of chlorelli vulgaris was proved. As a result of the increase of culture medium concentration to 30.1-120.4 ml·l−1 of water, dry mass in photobioreactorsincreased respectively from 1.33 g·dm−3 to 4.68 g·dm−3.
Changes of Organoleptic Quality in Potato Tubers after Application of Natural Sprout Inhibitors
Authors: Grudzińska Magdalena , Czerko Zbigniew , Borowska-Komenda Monika 
Published: June 2016

Abstract
The aim of this study was to evaluate changes in the sensory properties of the table potato in relation to the use of natural sprout inhibitors during long-term storage. The material for the study consisted in four varieties of potato of the medium early group. The research was carried out in the Plant Breeding and Acclimatization Institute – National Research Institute Branch in Jadwisin in 2014-2015. After harvest potatoes were stored from the end of October to April at 5°C, at the relative humidity of 90-95%, without application of natural sprout inhibitors (control) and using the natural sprout inhibitors (essential oils). After storage, the potatoes were boiled and sensory evaluation was carried out, which includes qualities such as: over-cooking of the surface, texture, mealiness, flesh texture, taste and smell. Study results showed that long-term storage of potatoes treated with natural sprout inhibitors – peppermint, caraway and clove essential oils is significant for the changes in overcooking the surface, structure of potatoes and mealiness of tubers after cooking. The taste and smell of potato tubers depended only on the variety.
Limiting Odour Emission from Piggery through Application of Heat Recovery System
Authors: Rzeźnik Wojciech , Mielcarek Paulina , Rzeźnik Ilona 
Published: June 2016

Abstract
The aim of the study was to determine the effect of manure cooling by the use of the heat recovery system on odour emission from a deep litter piggery. Annual comparative research was carried out in a twin-room deep litter piggery located in Wielkopolska Voivodeship. The recovered heat was transferred to central heating and domestic hot water systems of a residential building. The study showed that the average odour emission rate from the room, where heat was recovered (0.192±0.083 ouE·s−1·kg m.c.−1) was lower than in the room without heat recovering (0.273±0.138 ouE·s−1·kg m.c. −1) (p<0.05). The difference was 27%. It was also found that there was statistically significant strong correlation (r =0.86) between the amount of the recovered heat and the percentage odour emission reduction (p <0.05). This relationship was described by the logarithmic regression line y=12.5ln(x)-21.5 (r2=0.74)
Effect of Osmotic Dehydration on Mechanical and Rheological Properties of Pumpkin Dried with Microwave Method in Reduced Pressure Conditions
Authors: Stępień Bogdan , Maślankowski Radosław , Pasławska Marta , Jałoszyński Klaudiusz , Surma Mariusz 
Published: June 2016

Abstract
The objective of the research was to indicate the impact of sirup type used for osmotic dehydration and the microwaves power for microwave and vacuum drying on the selected mechanical and rheological properties of dried pumpkin. Pumpkin cultivar Rugosa was osmotically dehydrated in three concentrates: apple, aronia and cherry. Initially prepared material was dried with microwave method in the reduced pressure conditions which was within 6-4 kPa at the microwave power which was 240 and 480 W. Dried material was subjected to compression tests and stresses relaxation tests. Compression work values (Pś), cutting work (Pp) and indicators describing material elasticity (a and b) were computed. An initial treatment in the form of osmotic dehydration carried out before microwave drying in the reduced pressure conditions allows obtaining dried pumpkin with a raised resistance to compression and cutting and the decreased elasticity in comparison to dried material obtained from a pumpkin which was not subjected to the initial treatment. Microwaves power influences the values of compression and cutting of dried pumpkin.
Assessment of Utilization Possibilities of Heat Conducted by Waste Gases Exhaust Pipe of SB 1.5 Drum Drier for Drying Wood Chips
Authors: Surma Mariusz , Zdrojewski Zbigniew , Peroń Stanisław , Jałoszyński Klaudiusz , Stępień Bogdan 
Published: June 2016

Abstract
Based on the exploitation research, the authors evaluated the possibilities of using the heat conducted through the side surface of the waste gases exhaust pipe of SB 1.5 drum drier for drying wood chips. According to the estimated calculations within one hour approximately 173 thousand of kJ of heat may be obtained from the external surface of the waste gases exhaust pipe with the height of 7 m and temperature of approximately 78°C which constitutes an equivalent of approximately 4 kilo of heating oil. In case the above mentioned heat source for drying wood chips in SPA 20 silo with a volume of 6800 kilo within 50% to 20% humidity is used, one may expect that the drying time will be approximately 100 hours.