bluuebunny/crossref_metadata_2025_split huggingface dataset:
A De-Novo Genome Analysis Pipeline (DeNoGAP) for large-scale comparative prokaryotic genomics studies
Authors: Thakur Shalabh , Guttman David S. 
Published: June 2016

Abstract
Background
Comparative analysis of whole genome sequence data from closely related prokaryotic species or strains is becoming an increasingly important and accessible approach for addressing both fundamental and applied biological questions. While there are number of excellent tools developed for performing this task, most scale poorly when faced with hundreds of genome sequences, and many require extensive manual curation.

Results
We have developed a de-novo genome analysis pipeline (DeNoGAP) for the automated, iterative and high-throughput analysis of data from comparative genomics projects involving hundreds of whole genome sequences. The pipeline is designed to perform reference-assisted and de novo gene prediction, homolog protein family assignment, ortholog prediction, functional annotation, and pan-genome analysis using a range of proven tools and databases. While most existing methods scale quadratically with the number of genomes since they rely on pairwise comparisons among predicted protein sequences, DeNoGAP scales linearly since the homology assignment is based on iteratively refined hidden Markov models. This iterative clustering strategy enables DeNoGAP to handle a very large number of genomes using minimal computational resources. Moreover, the modular structure of the pipeline permits easy updates as new analysis programs become available.

Conclusion
DeNoGAP integrates bioinformatics tools and databases for comparative analysis of a large number of genomes. The pipeline offers tools and algorithms for annotation and analysis of completed and draft genome sequences. The pipeline is developed using Perl, BioPerl and SQLite on Ubuntu Linux version 12.04 LTS. Currently, the software package accompanies script for automated installation of necessary external programs on Ubuntu Linux; however, the pipeline should be also compatible with other Linux and Unix systems after necessary external programs are installed. DeNoGAP is freely available at https://sourceforge.net/projects/denogap/.
Light-sheet microscopy for everyone? Experience of building an OpenSPIM to study flatworm development
Authors: Girstmair Johannes , Zakrzewski Anne , Lapraz François , Handberg-Thorsager Mette , Tomancak Pavel , Pitrone Peter Gabriel , Simpson Fraser , Telford Maximilian J. 
Published: June 2016

Abstract
Background
Selective plane illumination microscopy (SPIM a type of light-sheet microscopy) involves focusing a thin sheet of laser light through a specimen at right angles to the objective lens. As only the thin section of the specimen at the focal plane of the lens is illuminated, out of focus light is naturally absent and toxicity due to light (phototoxicity) is greatly reduced enabling longer term live imaging. OpenSPIM is an open access platform (Pitrone et al. 2013 and OpenSPIM.org) created to give new users step-by-step instructions on building a basic configuration of a SPIM microscope, which can in principle be adapted and upgraded to each laboratory’s own requirements and budget. Here we describe our own experience with the process of designing, building, configuring and using an OpenSPIM for our research into the early development of the polyclad flatworm Maritigrella crozieri – a non-model animal.

Results
Our OpenSPIM builds on the standard design with the addition of two colour laser illumination for simultaneous detection of two probes/molecules and dual sided illumination, which provides more even signal intensity across a specimen. Our OpenSPIM provides high resolution 3d images and time lapse recordings, and we demonstrate the use of two colour lasers and the benefits of two color dual-sided imaging. We used our microscope to study the development of the embryo of the polyclad flatworm M. crozieri. The capabilities of our microscope are demonstrated by our ability to record the stereotypical spiral cleavage pattern of M. crozieri with high-speed multi-view time lapse imaging. 3D and 4D (3D + time) reconstruction of early development from these data is possible using image registration and deconvolution tools provided as part of the open source Fiji platform. We discuss our findings on the pros and cons of a self built microscope.

Conclusions
We conclude that home-built microscopes, such as an OpenSPIM, together with the available open source software, such as MicroManager and Fiji, make SPIM accessible to anyone interested in having continuous access to their own light-sheet microscope. However, building an OpenSPIM is not without challenges and an open access microscope is a worthwhile, if significant, investment of time and money. Multi-view 4D microscopy is more challenging than we had expected. We hope that our experience gained during this project will help future OpenSPIM users with similar ambitions.
A note on recent cyclic fixed point results in dislocated quasi-b-metric spaces
Authors: Dolićanin-Ðekić Diana , Došenović Tatjana , Huang Huaping , Radenović Stojan 
Published: June 2016

AbstractThe purpose of this paper is to establish some fixed point results for cyclic contractions in the setting of dislocated quasi-b-metric spaces. We verify that some previous cyclic contraction results in dislocated quasi-b-metric spaces are just equivalent to the non-cyclic ones in the same spaces. Moreover, by using two examples, we highlight the superiority of the results obtained.
O absenteísmo da equipe de enfermagem de um hospital universitário público<br>The absenteeism of the team of nursing of a public university hospital
Authors: Silva Larissa Gutierrez de Carvalho , Buss Adeline Aparecida Queiroz , Haddad Maria do Carmo Lourenço , Vannuchi Marli Terezinha de Oliveira 
Published: June 2016

Introdução: A identificação do absenteísmo da enfermagem no contexto hospitalar constitui-se em um importante indicador de análise para a gestão de pessoas e para a qualificação e segurança da assistência aos clientes. Objetivo: Analisar o absenteísmo dos trabalhadores da equipe de enfermagem de um hospital público universitário. Metodologia: Pesquisa de abordagem quantitativa, tendo como população os atestados dos profissionais da equipe de enfermagem do ano de 2009. Os dados foram coletados com um instrumento que continha informações sobre o perfil sóciodemográfico e ocupacional, a causa e o período da ausência dos profissionais. A análise descritiva foi realizada, agrupando-se em distribuição de frequências e gráficos. Resultados: O perfil dos trabalhadores que apresentaram atestados são mulheres casadas, com idade entre 41 a 50 anos, auxiliares, vínculo empregatício público, tempo de trabalho de 11 a 15 anos, lotados no centro cirúrgico em período integral. O número de atestados foi 3.149, 72,46% por justificativas médicas, o que resultou na ausência de 71,6 trabalhadores de enfermagem por semana. Conclusão: O número elevado de atestados médicos pode sugerir um processo de trabalho que deve ser reavaliado sob o enfoque na preservação da saúde dentro do ambiente de trabalho e da subjetividade do cuidar de si e do próximo.
Efeitos do treinamento físico em mulheres com síndrome dos ovários policísticos: Revisão Sistemática<br>Effects of exercise training in women with polycystic ovary syndrome: Systematic review
Authors: Ribeiro Victor Barbosa , Lopes Iris Palma , Oliveira Arthur Marques Zecchin , Santiago Hildemberg Agostinho Rocha de , Kogure Gislaine Satyko , Reis Rafael Menezes 
Published: June 2016

Introdução: A síndrome dos ovários policísticos (SOP) é uma doença que atinge cerca de 15% das mulheres. Esta é caracterizada por oligomenorreia ou anovulação, por sinais clínicos e/ou bioquímicos de hiperandrogenismo; e, por último, pela identificação de ovários policísticos. Em decorrência da doença, essas mulheres apresentam maiores chances de aumento de peso e gordura corporal e de desenvolver desordens metabólicas e hormonais. Dessa forma, o objetivo é identificar os principais efeitos do treinamento físico sobre composição corporal, em parâmetros endócrinos e metabólicos em mulheres com a síndrome dos ovários policísticos. Métodos: Foi realizada uma revisão bibliográfica dos artigos publicados entre julho de 2010 e julho de 2015 na base de dados PubMed. Os artigos selecionados deveriam investigar os efeitos do treinamento físico na composição corporal, nos parâmetros endócrinos e metabólicos de mulheres com SOP. Resultados: Após a leitura dos títulos e resumos, foram selecionados inicialmente 43 artigos para leitura. Desses, 23 foram excluídos, sendo selecionados 20. Conclusão: Os resultados dos estudos avaliados demonstraram claramente que o treinamento físico promove melhorias na composição corporal, nos parâmetros metabólicos e endócrinos em mulheres com SOP. Além disso, é um método de baixo custo e de baixo ou nenhum risco. Portanto, é relevante que ele seja indicado para os cuidados com a SOP.
Mesozooplankton biomass and abundance in Cyprus coastal waters and comparison with the Aegean Sea (eastern Mediterranean)
Authors: HANNIDES C. C.S. , SIOKOU I. , ZERVOUDAKID S. , FRANGOULIS C. , LANGE M. A. 
Published: June 2016

Here we conduct the first comprehensive assessment of mesozooplankton abundance, biomass, and taxa composition in Cyprus coastal waters (Levantine Sea). Mesozooplankton abundance and biomass sampled at several locations around the island ranged from 153 – 498 individuals m-3 and 0.7 – 5.2 mg dry weight m-3, respectively, with significantly larger biomass observed in winter-early spring (March) than in summer (September). The community was dominated by calanoid and cyclopoid copepods throughout the year (80% of total numbers), with higher abundances of predatory taxa (chaetognaths and medusae) in winter and cladocerans in summer. Overall, we find that coastal mesozooplankton communities around Cyprus appear to be more similar to communities in offshore waters or those around the island of Rhodes than to communities along the mainland Levantine coast. We further highlight regional differences in the eastern Mediterranean by comparing our data with mesozooplankton in the western Aegean (Saronikos Gulf) and northeastern Aegean Sea (NEA). Distinct spatial differences were observed, for example anthropogenic influences in the Saronikos Gulf and the outflow of Modified Black Sea Water in the NEA drove generally greater biomass and abundance in these regions. Overall, our comparison supports the concept of a latitudinal gradient in oligotrophy in the eastern Mediterranean, with ultra-oligotrophic conditions found in the Levantine Sea.
New Mediterranean Biodiversity Records (April 2015)
Authors: ΖΕΝΕΤΟΣ Α. , AKEL E.H.KH. , APOSTOLIDIS C. , BILECENOGLU M. , BITAR G. , BUCHET V. , CHALARI N. , CORSINI-FOKA M. , CROCETTA F. , DOGRAMMATZI A. , DRAKULIĆ M. , FANELLI G. , GIGLIO G. , IMSIRIDOU A. , KAPIRIS K. , PKARACHLE P.K. , KAVADAS S. , KONDYLATOS G. , LEFKADITOU E. , LIPEJ L. , MAVRIČ B. , MINOS G. , MOUSSA R. , PANCUCCI-PAPADOPOULOU M.A. , PRATO E. , RENDA W. , RÍOS N. , RIZKALLA S.I. , RUSSO F. , SERVONNAT M. , SIAPATIS A. , SPERONE E. , THEODOROU J.A. , TIRALONGO F. , TZOVENIS I. 
Published: June 2016

The Collective Article ‘New Mediterranean Biodiversity Records’ of the Mediterranean Marine Science journal offers the means to publish biodiversity records in the Mediterranean Sea. The current article is divided in two parts, for records of native and alien species respectively. The new records of native fish species include: the slender sunfish Ranzania laevis and the scalloped ribbonfish Zu cristatus in Calabria; the Azores rockling Gaidropsarus granti in Calabria and Sicily; the agujon needlefish Tylosurus acus imperialis in the Northern Aegean; and the amphibious behaviour of Gouania willdenowi in Southern Turkey. As regards molluscs, the interesting findings include Ischnochiton usticensis in Calabria and Thordisa filix in the bay of Piran (Slovenia). The stomatopod Parasquilla ferussaci was collected from Lesvos island (Greece); the isopod Anilocra frontalis was observed parasitizing the alien Pteragogus trispilus in the Rhodes area. The asteroid Tethyaster subinermis and the butterfly ray Gymnura altavela were reported from several localities in the Greek Ionian and Aegean Seas. The new records of alien species include: the antenna codlet Bregmaceros atlanticus in Saronikos Gulf; three new fish records and two decapods from Egypt; the establishment of the two spot cardinal fish Cheilodipterus novemstriatus and the first record of the Indo-Pacific marble shrimp Saron marmoratus in semi-dark caves along the Lebanese coastline; the finding of Lagocephalus sceleratus, Sargocentron rubrum, Fistularia commersonii and Stephanolepis diaspros around Lipsi island (Aegean Sea, Greece); the decapod Penaeus hathor in Aegean waters; the decapod Penaeus aztecus and the nudibranch Melibe viridis in the Dodecanese islands; the finding of Pinctada imbricata radiata in the Mar Grande of Taranto (Ionian Sea, Italy) and the Maliakos Gulf (Greece).
Blood loss predictive factors and transfusion practice during percutaneous nephrolithotomy of kidney stones: a prospective study
Authors: Syahputra Firtantyo Adi , Birowo Ponco , Rasyid Nur , Matondang Faisal Abdi , Noviandrini Endrika , Huseini Maruto Harjanggi 
Published: June 2016

Objectives Bleeding is the most common complication of percutaneous nephrolithotomy (PCNL). Injudicious transfusion is frequently performed in current practice, even though it is not always needed. This study aimed to identify the predictive factors of blood loss in the PCNL procedure and evaluate the perioperative transfusion practice. Methods A prospective study of PCNL was randomly performed by two consultants of endo-urology at our institution. The inclusion criteria were adults with kidney pelvic stones >20 mm or stone in inferior calyx >10 mm or staghorn stone. Those with coagulopathy, under anti-coagulant treatment or open conversion were excluded. A full blood count was taken at baseline and during 12, 24, 36, 72-hours post-operatively. Factors such as stone burden, sex, body surface area, shifting of hematocrit level and amount of blood transfused were analyzed statistically using line regression to identify the predictive factors of total blood loss (TBL). Results Eighty-five patients were enrolled in this study. Mean TBL was 560.92 ± 428.43 mL for both endo-urology surgeons. Stone burden was the most influential factor for TBL (p=0.037). Our results revealed that TBL (mL) = -153.379 + 0.229 × stone burden (mm2) + 0.203 x baseline serum hematocrit (%); thus considerably predicted the need for blood transfusion. A total of 87.1% patients did not receive perioperative transfusion, 3.5% received intra-operative transfusion, 7.1% received post-operative transfusion, 23% had both intra and post-operative transfusion, resulting in a cross-matched transfusion ratio of 7.72. Mean perioperative blood transfused was 356.00 ± 145.88 mL.
Peculiarities in use of cutting- electromotive force signal under conditions of computer-aided machine manufacturing
Authors: Сергеев Александр , Sergeyev Aleksandr , Плотников Александр , Plotnikov Aleksandr , Тихонова Жанна , Tikhonova Zhanna 
Published: June 2016

In the paper there is considered a problem of properties heterogeneity in a terminal pair under conditions of computer-aided manufacturing. It is emphasized that this circumstance results in decrease of stability and quality of machining on the whole. The existence of tolerances for the content of chemical elements in steel is caused by a complexity in control of metallurgical processes.
It is offered to use a parameter of thermo-electromotive force of a terminal pair “tool-blank” obtained in strictly definite modes of a calibrating cut for the further definition and optimization of cutting modes for machining. Drawbacks and possible variants for their solution at the realization of a method to measure cutting-electromotive force under production conditions are emphasized. A complex approach to the assessment of the influence of cutter geometrical parameters and technological factors of production upon the value of a thermo-electromotive force signal of a natural thermocouple “tool-part” is presented. It is established experimentally the influence of the antiwear coating state upon a thermo-electromotive force signal.
Quality increase in assembly joints of mechanical engineering objects by ultrasonic vibrations superposition
Authors: Малкина Ирина , Malkina Irina 
Published: June 2016

This paper reports the problem of quality increase in the assembly of riveted connections. The basic methods for the creation of permanent connections are considered, the computation procedures for durability are analyzed, advantages and disadvantages of hot and cold riveting are revealed. A basic part of the paper deals with of common assembly processes updating. In particular, to the introduction of ultrasonic vibrations in the area of a contact of parts surfaces when together with basic motions envisaged by a technological scheme of assembly the vibrations of ultrasonic frequency are imparted to the parts additionally.
The author shows the main positive results obtained due to the introduction of an ultrasonic method of product processing: the improvement of a surface layer quality in a product, increase of fatigue resistance, contact endurance, contact rigidity and machine parts and tool wear resistance.
In the experimental part there are considered three different procedures of USC feed in the area of rivet head formation. The diagrams of value changes in static efforts of rivet material deformation caused by oscillation amplitude of the end of a thickener are shown.
Infection in total elbow arthroplasty with stable components
Authors: Streubel P. N. , Simone J. P. , Morrey B. F. , Sanchez-Sotelo J. , Morrey M. E. 
Published: June 2016

AimsWe describe the use of a protocol of irrigation and debridement (I& D) with retention of the implant for the treatment of periprosthetic infection of a total elbow arthroplasty (TEA). This may be an attractive alternative to staged re-implantation.Patients and MethodsBetween 1990 and 2010, 23 consecutive patients were treated in this way. Three were lost to follow-up leaving 20 patients (21 TEAs) in the study. There were six men and 14 women. Their mean age was 58 years (23 to 76). The protocol involved: component unlinking, irrigation and debridement (I& D), and the introduction of antibiotic laden cement beads; organism-specific intravenous antibiotics; repeat I& D and re-linkage of the implant if appropriate; long-term oral antibiotic therapy.ResultsThe mean follow-up was 7.1 years (2 to 16). The infecting micro-organisms were Staphylococcus aureus in nine, coagulase-negative Staphylococcus in 13, Corynebacterium in three and other in six cases. Re-operations included three repeat staged I& Ds, two repeat superficial I& Ds and one fasciocutaneous forearm flap. One patient required removal of the implant due to persistent infection. All except three patients rated their pain as absent or mild. Outcome was rated as good or excellent in 15 patients (mean Mayo Elbow Performance Score 78 points, (5 to 100) with a mean flexion-extension arc of 103° (40° to 150°)).ConclusionA staged protocol can be successful in retaining stable components of an infected TEA. Function of the elbow may compare unfavourably to that after an uncomplicated TEA. Cite this article: Bone Joint J 2016;98-B:976–83.
The effect of using components from different manufacturers on the rate of wear and corrosion of the head–stem taper junction of metal-on-metal hip arthroplasties
Authors: Whittaker R. K. , Hothi H. S. , Meswania J. M. , Berber R. , Blunn G. W. , Skinner J. A. , Hart A. J. 
Published: June 2016

Aims Surgeons have commonly used modular femoral heads and stems from different manufacturers, although this is not recommended by orthopaedic companies due to the different manufacturing processes. We compared the rate of corrosion and rate of wear at the trunnion/head taper junction in two groups of retrieved hips; those with mixed manufacturers (MM) and those from the same manufacturer (SM). Materials and Methods We identified 151 retrieved hips with large-diameter cobalt-chromium heads; 51 of two designs that had been paired with stems from different manufacturers (MM) and 100 of seven designs paired with stems from the same manufacturer (SM). We determined the severity of corrosion with the Goldberg corrosion score and the volume of material loss at the head/stem junction. We used multivariable statistical analysis to determine if there was a significant difference between the two groups. Results We found no significant difference in the corrosion scores of the two groups. The median rate of material loss at the head/stem junction for the MM and SM groups were 0.39 mm3/year (0.00 to 4.73) and 0.46 mm3/year (0.00 to 6.71) respectively; this difference was not significant after controlling for confounding factors (p = 0.06). Conclusion The use of stems with heads of another manufacturer does not appear to affect the amount of metal lost from the surfaces between these two components at total hip arthroplasty. Other surgical, implant and patient factors should be considered when determining the mechanisms of failure of large diameter metal-on-metal hip arthroplasties. Cite this article: Bone Joint J 2016;98-B:917–24.
The clinical implications of metal debris release from the taper junctions and bearing surfaces of metal-on-metal hip arthroplasty
Authors: Sidaginamale R. P. , Joyce T. J. , Bowsher J. G. , Lord J. K. , Avery P. J. , Natu S. , Nargol A. V. F. , Langton D. J. 
Published: June 2016

Aims We wished to investigate the influence of metal debris exposure on the subsequent immune response and resulting soft-tissue injury following metal-on-metal (MoM) hip arthroplasty. Some reports have suggested that debris generated from the head-neck taper junction is more destructive than equivalent doses from metal bearing surfaces. Patients and Methods We investigated the influence of the source and volume of metal debris on chromium (Cr) and cobalt (Co) concentrations in corresponding blood and hip synovial fluid samples and the observed agglomerated particle sizes in excised tissues using multiple regression analysis of prospectively collected data. A total of 199 explanted MoM hips (177 patients; 132 hips female) were analysed to determine rates of volumetric wear at the bearing surfaces and taper junctions. Results The statistical modelling suggested that a greater source contribution of metal debris from the taper junction was associated with smaller aggregated particle sizes in the local tissues and a relative reduction of Cr ion concentrations in the corresponding synovial fluid and blood samples. Metal debris generated from taper junctions appears to be of a different morphology, composition and therefore, potentially, immunogenicity to that generated from bearing surfaces. Conclusion The differences in debris arising from the taper and the articulating surfaces may provide some understanding of the increased incidence of soft-tissue reactions reported in patients implanted with MoM total hip arthroplasties compared with patients with hip resurfacings. Cite this article: Bone Joint J 2016;98-B:925–33.