bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diagnostic Importance of Hyphae on Heart Valve Tissue in Histoplasma Endocarditis and Treatment With Isavuconazole
Authors: Wiley Zanthia , Woodworth Michael H , Jacob Jesse T , Lockhart Shawn R , Rouphael Nadine G , Gullett Jonathan C , Guarner Jeannette , Workowski Kimberly 
Published: November 2017

Abstract
A patient who never resided in an endemic area for dimorphic fungi was diagnosed with Histoplasma capsulatum endocarditis. His diagnosis was suggested by yeast and hyphae on cardiac valve tissue pathology. Isavuconazole was an optimal therapeutic option due to renal dysfunction and anticoagulation with warfarin for mechanical valve replacement.
A new standard for crustacean genomes: the highly contiguous, annotated genome assembly of the clam shrimp Eulimnadia texana reveals HOX gene order and identifies the sex chromosome
Authors: Baldwin-Brown James G. , Weeks Stephen C. , Long Anthony D. 
Published: November 2017

AbstractVernal pool clam shrimp (Eulimnadia texana) are a promising model system due to their ease of lab culture, short generation time, modest sized genome, a somewhat rare stable androdioecious sex determination system, and a requirement to reproduce via desiccated diapaused eggs. We generated a highly contiguous genome assembly using 46X of PacBio long read data and 216X of Illumina short reads, and annotated using Illumina RNAseq obtained from adult males or hermaphrodites. 85% of the 120Mb genome is contained in the largest 8 contigs, the smallest of which is 4.6Mb. The assembly contains 98% of transcripts predicted via RNAseq. This assembly is qualitatively different from scaffolded Illumina assemblies: it is produced from long reads that contain sequence data along their entire length, and is thus gap free. The contiguity of the assembly allows us to order the HOX genes within the genome, identifying two loci that contain HOX gene orthologs, and which approximately maintain the order observed in other arthropods. We identified a partial duplication of the Antennapedia gene adjacent to the few genes homologous to the Bithorax locus. Because the sex chromosome of an androdioecious species is of special interest, we used existing allozyme and microsatellite markers to identify theE. texanasex chromosome, and find that it comprises nearly half of the genome of this species. Linkage patterns indicate that recombination is extremely rare and perhaps absent in hermaphrodites, and as a result the location of the sex determining locus will be difficult to refine using recombination mapping.
Cooperating H3N2 influenza virus variants are not detectable in primary clinical samples
Authors: Xue Katherine S. , Greninger Alexander L. , Pérez-Osorio Ailyn , Bloom Jesse D. 
Published: November 2017

ABSTRACTThe high mutation rates of RNA viruses lead to rapid genetic diversification, which can enable cooperative interactions between variants in a viral population. We previously described two distinct variants of H3N2 influenza virus that cooperate in cell culture. These variants differ by a single mutation, D151G, in the neuraminidase protein. The D151G mutation reaches a stable frequency of about 50% when virus is passaged in cell culture. However, it is unclear whether selection for the cooperative benefits of D151G is a cell-culture phenomenon, or whether the mutation is also sometimes present at appreciable frequency in virus populations sampled directly from infected humans. Prior work has not detected D151G in unpassaged clinical samples, but these studies have used methods like Sanger sequencing and pyrosequencing that are relatively insensitive to low-frequency variation. We identified nine samples of human H3N2 influenza collected between 2013 to 2015 in which Sanger sequencing had detected a high frequency of the D151G mutation following one to three passages in cell culture. We deep-sequenced the unpassaged clinical samples to identify low-frequency viral variants. The frequency of D151G did not exceed the frequency of library preparation and sequencing errors in any of the sequenced samples. We conclude that passage in cell culture is primarily responsible for the frequent observations of D151G in recent H3N2 influenza strains.IMPORTANCEViruses mutate rapidly, and recent studies of RNA viruses have shown that related viral variants can sometimes cooperate to improve each other’s growth. We previously described two variants of H3N2 influenza virus that cooperate in cell culture. The mutation responsible for cooperation is often observed when human samples of influenza virus are grown in the lab before sequencing, but it is unclear whether the mutation also exists in human infections or is exclusively the result of lab passage. We identified nine human isolates of influenza that had developed the cooperating mutation after being grown in the lab, and performed highly sensitive deep-sequencing of the unpassaged clinical samples to determine whether the mutation existed in the original human infections. We found no evidence of the cooperating mutation in the unpassaged samples, suggesting that the cooperation primarily arises in laboratory conditions.
Expressed Exome Capture Sequencing (EecSeq): a method for cost-effective exome sequencing for all organisms with or without genomic resources
Authors: Puritz Jonathan B. , Lotterhos Katie E 
Published: November 2017

AbstractExome capture is an effective tool for surveying the genome for loci under selection. However, traditional methods require annotated genomic resources. Here, we present a method for creating cDNA probes from expressed mRNA, which are then used to enrich and capture genomic DNA for exon regions. This approach, called “EecSeq”, eliminates the need for costly probe design and synthesis. We tested EecSeq in the eastern oyster, Crassostrea virginica, using a controlled exposure experiment. Four adult oysters were heat shocked at 36° C for 1 hour along with four control oysters kept at 14° C. Stranded mRNA libraries were prepared for two individuals from each treatment and pooled. Half of the combined library was used for probe synthesis and half was sequenced to evaluate capture efficiency. Genomic DNA was extracted from all individuals, enriched via captured probes, and sequenced directly. We found that EecSeq had an average capture sensitivity of 86.8% across all known exons and had over 99.4% sensitivity for exons with detectable levels of expression in the mRNA library. For all mapped reads, over 47.9% mapped to exons and 37.0% mapped to expressed targets, which is similar to previously published exon capture studies. EecSeq displayed relatively even coverage within exons (i.e. minor “edge effects”) and even coverage across exon GC content. We discovered 5,951 SNPs with a minimum average coverage of 80X, with 3,508 SNPs appearing in exonic regions. We show that EecSeq provides comparable, if not superior, specificity and capture efficiency compared to costly, traditional methods.
Neuronal resonance in the theta (4-10 Hz) frequency range is modulated by dynamic changes in the input resistance
Authors: Vera Jorge , Pereira Ulises , Reynaert Bryan , Bacigalupo Juan , Sanhueza Magdalena 
Published: November 2017

AbstractMost neurons of the mammalian brain display intrinsic resonance with frequency selectivity (fR) for inputs within the theta-range (4-10 Hz). Variations in network oscillation along this range depend on the animal behavior; however, whether neurons can dynamically tune their fR has not been addressed. Using slice electrophysiology, dynamic clamping and computer modeling we studied three types of cortical neurons, finding that the input resistance (Rin) inversely sets fR into the theta range, following a power law. We demonstrate that physiological changes in Rin modulate fR and response phase, serving as a mechanism that instantaneously tunes oscillatory responses. Moreover, these modulations are translated into spiking regimes, modifying spike frequency and timing. Since synaptic inputs reduce Rin, this modulation provides a mean for adjusting the frequency and timing of firing of individual neurons in interplay with the network fluctuations. This might be a widespread property among resonant neurons.
Allosteric effects in catalytic impaired variants of the enzyme cyclophilin A may be explained by changes in nano-microsecond time scale motions
Authors: Wapeesittipan Pattama , Mey Antonia S. J. S. , Walkinshaw Malcolm D. , Michel Julien 
Published: November 2017

AbstractThere is much debate about the mechanisms by which molecular motions influence catalysis in enzymes. This work investigates the connection between stochastic protein dynamics and function for the enzyme cyclophilin A (CypA) in wild-type (WT) form, and three variants that features several mutations that are distal from the active site. Previous biophysical studies have suggested that conformational exchange between a ‘major’ active and a ‘minor’ inactive state on millisecond time scales plays a key role in catalysis for CypA. Here this hypothesis was addressed by a variety of molecular dynamic (MD) simulation techniques. The simulations reproduce X-ray crystallography derived evidence for a shift in populations of major and minor active site conformations between the wild-type and mutant forms. Strikingly, exchange between these active site conformations occurs at a rate that is 5 to 6 orders of magnitude faster than previously proposed. Further analyses indicate that the minor active site conformation is catalytically impaired, and that decreased catalytic activity of the mutants may be explained by changes in Phe113 motions on a ns-μs time scale. Therefore previously described millisecond time scale motions may not be necessary to explain allosteric effects in CypA mutants.
The impact of food preservation on food waste
Authors: Martindale Wayne , Schiebel Walter 
Published: November 2017

Purpose
The purpose of this paper is to demonstrate the relationship between food preservation and reducing consumer waste is of value in developing sustainable meal options. The research reports insights into Austrian marketplace for frozen and fresh foods that have been obtained from a consumer survey.

Design/methodology/approach
The consumer survey methodologies indicate how preservation can change meal planning and lower food waste across frozen and fresh and ambient food purchases using freezing preservation methods.

Findings
The results show food waste can be reduced by six-fold when frozen foods are compared with fresh foods.

Research limitations/implications
This study highlights the requirement for a greater understanding of the probability that specific foods will be wasted with respect to the frequency of purchase. This is a limitation of the current study that has been investigated by other researchers.

Practical implications
This research has enabled the identification of different food waste amounts for different food product categories. The data presented could be used to guide food product development so that less consumer waste is produced.

Social implications
The research suggests a decision matrix approach can be used to can guide new product development and a model of this matrix is presented so that it may provide fit-for-purpose food preservation options for consumers.

Originality/value
This paper will continue to highlight the overlooked value of food preservation during processing and manufacturing of foods and their preparation in households.
What do students think of self-determined learning in entrepreneurship education?
Authors: Kapasi Isla , Grekova Galina 
Published: November 2017

Purpose
The purpose of this paper is to examine the perceptions and perspectives of students with regards to self-determined learning in an entrepreneurship education (EE) context and its potential contribution to employability.

Design/methodology/approach
This research used a mixed-methods approach with a sample of 25 students currently attending a UK higher education institute. The students had access to participation in EE modules but self-determined learning-informed modules or programmes were not currently offered. Students were invited to attend focus groups and as a result of emergent themes, a business school-wide survey was developed.

Findings
This research makes two tentative contributions to the EE field. First, the findings of this student cohort are similar to those found throughout the UK and the EU with regard to the perception of the value of a degree by students; its contribution to the hidden curriculum; and the importance of practical experience. The research also adds to the field by considering the value of a self-determined learning approach to developing the capabilities and competencies of graduates. This approach to learning in a context of EE was in general well received by potential students, particularly the applied aspect of the programme. However, there is a perception of risk about this approach to learning and students are concerned about the value of a programme like this to employers in general.

Originality/value
The study contributes to discussions on the value of EE on perceived employability and in particular self-determined learning through entrepreneurship activity.
Understanding international location decisions of poverty alleviation non-profit organizations
Authors: Sirisena Amila Buddhika , Shneor Rotem 
Published: November 2017

PurposeDespite the growing numbers of internationally active nonprofit organizations (NPOs), research on various facets of NPOs’ internationalization has been limited. The purpose of this paper is to investigate the impact of target-country related factors on international market selection of NPOs.Design/methodology/approachAnalysis is based on a logistic regression procedure using a self-compiled data set of 2,440 observations of de-facto entry or non-entry occurrences made by 19 large development-focused NPOs.FindingsThe study reveals that NPOs select target markets that are less developed, characterized by greater risk profiles, where other NPOs tend to cluster, and those that are preferred by their home-country governments. Moreover, findings suggest that with respect to institutional strength, NPOs balance mission to help strengthen institutions where needed, and avoidance of environments with extremely dysfunctional institutions, hence opting to operate in environments with medium levels of institutional strength.Research limitations/implicationsThe study only looked at external environmental factors, it must be acknowledged that a more complete understanding of NPO market selection decisions must also include variables internal to the organization. Further the study is based on a sample of NPOs dealing with poverty alleviation, which limits the generalization. Finally, the use of data from secondary sources creates its own limitations.Originality/valueThis study represents one of the few cross country studies done on the area, thus contributing for the development of the field.
Film thickness formation in nanoscale due to effects of elastohydrodynamic, electrostatic and surface force of solvation and van der Waals
Authors: Abd Alsamieh Mohamed 
Published: November 2017

Purpose
The purpose of this is to study the mechanism of an oil film thickness formation in the nanoscale. A polar lubricant of propylene carbonate is used as the intervening liquid between contiguous bodies in concentrated contacts. A pressure caused by the hydrodynamic viscous action in addition to the double-layer electrostatic force, van der Waals inter-molecular forces and solvation pressure owing to inter-surface forces is considered when calculating the ultrathin lubricating films.

Design/methodology/approach
Using the Newton–Raphson iteration technique applied for the convergence of the hydrodynamic pressure, a numerical solution has been ascertained.

Findings
The results show that, at separations beyond about five molecular diameters of the intervening liquid, the formation of a lubricant film thickness is governed by the combined effects of viscous action and surface force of an attractive van der Waals force and a repulsive double-layer force. At smaller separations below five molecular diameters of the intervening liquid, the effect of the solvation force is dominant in determining the oil film thickness.

Originality/value
This paper fulfils an identified need to study the behavior of polar lubricants in concentrated contacts in ultrathin conjunctions. The effect of the hydrodynamic action, electrostatic force and surface action of van der Waals and solvation forces is considered when calculating the lubricant oil film thickness.
Effect of recess depth on lubrication performance of annular recess hydrostatic thrust bearing by constant rate flow
Authors: Shao Jun-peng , Liu Guang-dong , Yu Xiao-dong , Zhang Yan-qin , Meng Xiu-li , Jiang Hui 
Published: November 2017

Purpose
The purpose of this paper is to describe a simulation and experimental research concerning the effect of recess depth on the lubrication performance of a hydrostatic thrust bearing by constant rate flow.

Design/methodology/approach
The computational fluid dynamics and finite volume method have been used to compute the lubrication characteristics of an annular recess hydrostatic thrust bearing with different recess depths. The performances are oil recess pressure, oil recess temperature and oil film velocity. The recess depth has been optimized. A test rig is established for testing the pressure field of the structure of hydrostatic thrust bearing after recess depth optimization, and experimental results show that experimental data are basically identical with the simulation results, which demonstrates the validity of the proposed numerical simulation method.

Findings
The results demonstrate that the oil film temperature decreases and the oil film pressure first increases and then decreases with an increase in the recess depth, but oil film velocity is constant. To sum up comprehensive lubrication performance, the recess depth of 3.5 mm is its optimal value for the annular recess hydrostatic thrust bearing.

Originality/value
The computed results indicate that to get an improved performance from a constant flow hydrostatic thrust bearing, a proper selection of the recess depth is essential.
Matching the relationship between rotational speed and load-carrying capacity on high-speed and heavy-load hydrostatic thrust bearing
Authors: Yu Xiao-dong , Geng Lei , Zheng Xiao-jun , Wang Zi-xuan , Wu Xiao-gang 
Published: November 2017

Purpose
Rotational speed and load-carrying capacity are two mutual coupling factors which affect high precision and stable operation of a hydrostatic thrust bearing. The purpose of this paper is to study reasonable matching relationship between the rotational speed and the load-carrying capacity.

Design/methodology/approach
A mathematical model of relationship between the rotational speed and the load-carrying capacity of the hydrostatic bearing with double-rectangle recess is set up on the basis of the tribology theory and the lubrication theory, and the load and rotational speed characteristics of an oil film temperature field and a pressure field in the hydrostatic bearing are analyzed, reasonable matching relationship between the rotational speed and the load-carrying capacity is deduced and a verification experiment is conducted.

Findings
By increasing the rotational speed, the oil film temperature increases, the average pressure decreases and the load-carrying capacity decreases. By increasing the load-carrying capacity, the oil film temperature and the average pressure increases and the rotational speed decreases; corresponding certain reasonable matching values are available.

Originality/value
The load-carrying capacity can be increased and the rotational speed improved by means of reducing the friction area of the oil recess by using low-viscosity lubricating oil and adding more oil film clearance; but, the stiffness of the hydrostatic bearing decreases.
Tribological characterization on friction brake in continuous braking
Authors: Bao Jiusheng , Yin Yan , Lu Lijian , Liu Tonggang 
Published: November 2017

Purpose
The purpose of this study is to establish an effective method for characterizing the tribological properties of friction brakes during continuous braking because they have direct influences on the reliable operation of transport vehicles and industrial equipments.

Design/methodology/approach
First, tribological tests were carried out with the X-DM type friction tester, and changing curves of friction coefficient and temperature were obtained. Second, a novel tribological characteristic parameter set characterizing the tribological properties of brake pair in continuous braking was extracted from some important experimental data such as friction coefficient, wear rate and temperature. Finally, the influence of law and mechanism of braking number on dynamic tribological parameters was studied through continuous braking experiments.

Findings
The extracted tribological characteristic parameter set includes two subsets: dynamic characteristic parameter subset and overall characteristic parameter subset, which is composed of ten parameters: dynamic parameters of friction coefficient (including average, trend coefficient and stability coefficient), dynamic wear rate, dynamic average temperature, dynamic temperature rise, overall average friction coefficient, overall wear rate, overall average temperature and overall temperature rise.

Originality/value
Conclusively, the novel tribological characteristic parameter set is more comprehensive and objective, and it can provide a theoretical basis for the study of tribological properties in continuous braking.
Dynamic analysis of a tapered roller bearing
Authors: Deng Sier , Gu Jinfang , Cui Yongcun , Zhang Wenhu 
Published: November 2017

Purpose
This study aims to analyze the roller dynamic characteristics and cage whirling of tapered roller bearing considering roller tilt and skew which provide a theoretical basis for the design and application of tapered roller bearing.

Design/methodology/approach
Based on rolling bearing dynamic analysis, the dynamic differential equations of tapered roller bearing are established. Fine integral method and predict correct Adams–Bashforth–Moulton multi-step method are used to solve the dynamic differential equations of tapered roller bearings.

Findings
Friction at the flange contact between roller and large flange is the chief factor of roller skew. In comparison to cone speed, axial loads have more visible effect on roller skew, and proper speed or axial load is beneficial to sustain cage motion and decrease cage instability. Under the combined effort of axial load and radial load, the distribution of roller skew is correlated to the roller-flange contact load. In addition, roller skew angle in loaded zone is larger than that in unloaded zone; hence, it is helpful for cage stability if an extent radial load is applied. The pocket clearance of cage has very small influence on roller skew; therefore, a reasonable pocket clearance is suggested to assure minimum instability of cage. Friction coefficient of flange contact has a large effect on roller skew, and cage whirl is found to demonstrate a circular orbit with increasing friction coefficient.

Originality/value
The dynamic differential equations of tapered roller bearing considering roller large end/inner ring back face rib contact under various lubrication states were established. The impact of flange friction working conditions and cage pocket clearance on cage instability and roller skew were focused on. It is the first time that the ratio of the standard deviation of the cage-center translational speed to its mean value is used to access the instability of cage in tapered roller bearing.