bluuebunny/crossref_metadata_2025_split huggingface dataset:
A fungal avirulence factor encoded in a highly plastic genomic region triggers partial resistance to septoria tritici blotch
Authors: Meile Lukas , Croll Daniel , Brunner Patrick C. , Plissonneau Clémence , Hartmann Fanny E. , McDonald Bruce A. , Sánchez-Vallet Andrea 
Published: February 2018

SummaryCultivar-strain specificity in the wheat-Zymoseptoria tritici pathosystem determines the infection outcome and is controlled by resistance genes on the host side, of which many have been identified. However, on the pathogen side, the molecular determinants of specificity are largely unknown.We used genetic mapping, targeted gene disruption and allele swapping to characterize the recognition of the new avirulence factor Avr3D1. We then combined population genetic and comparative genomic analyses to estimate the evolutionary trajectory of Avr3D1.Avr3D1 is specifically recognized by cultivars harboring the resistance gene Stb7 and triggers a strong defence response without preventing pathogen infection and reproduction. Avr3D1 resides in a cluster of putative effector genes located in a region populated by independent transposable element insertions. The gene is present in all 132 investigated strains and is highly polymorphic, with a total of 30 different protein variants. We demonstrated that certain amino acid mutations in Avr3D1 led to evasion of recognition.These results demonstrate that quantitative resistance and gene-for-gene interactions are not mutually exclusive per se. Location of avirulence genes in highly plastic genomic regions likely facilitates accelerated evolution that enables escape from recognition by resistance proteins.
Does impedance matter when recording spikes with polytrodes?
Authors: Neto Joana P. , Baião Pedro , Lopes Gonçalo , Frazão João , Nogueira Joana , Fortunato Elvira , Barquinha Pedro , Kampff Adam R. 
Published: February 2018

ABSTRACTExtracellular microelectrodes have been widely used to measure brain activity, yet there are still basic questions about the requirements for a good extracellular microelectrode. One common source of confusion is how an electrode’s impedance affects the amplitude of extracellular spikes and background noise.Here we discuss how an electrode’s impedance affects data quality in extracellular recordings, which is crucial for both the detection of spikes and their assignment to the correct neurons. This study employs commercial polytrodes containing 32 electrodes (177 μm2) arranged in a dense array. This allowed us to directly compare, side-by-side, the same extracellular signals measured by modified low impedance (~100 kOhm) microelectrodes with unmodified high impedance (~1 MOhm) microelectrodes. We begin with an evaluation of existing protocols to lower the impedance of the electrodes. The poly(3,4-ethylenedioxythiophene)-polystyrene sulfonate (PEDOT-PSS) electrodeposition protocol is a simple, stable, and reliable method for decreasing the impedance of a microelectrode up to tenfold. We next record in vivo using polytrodes that are modified in a ‘chess board’ pattern, such that the signal of one neuron is detected by multiple coated and non-coated electrodes. The performance of the coated and non-coated electrodes is then compared on measures of background noise and amplitude of the detected action potentials.If the proper recording system is used, then the impedance of a microelectrode within the range of standard polytrodes (~ 0.1 to 2 MOhm) does not significantly affect data quality and spike sorting. This study should encourage neuroscientists to stop worrying about one more unknown.
Best Practices for Benchmarking Germline Small Variant Calls in Human Genomes
Authors: Krusche Peter , Trigg Len , Boutros Paul C. , Mason Christopher E. , De La Vega Francisco M. , Moore Benjamin L. , Gonzalez-Porta Mar , Eberle Michael A. , Tezak Zivana , Lababidi Samir , Truty Rebecca , Asimenos George , Funke Birgit , Fleharty Mark , Salit Marc , Zook Justin M ,   the Global Alliance for Genomics and Health Benchmarking Team
Published: February 2018

AbstractAssessing accuracy of NGS variant calling is immensely facilitated by a robust benchmarking strategy and tools to carry it out in a standard way. Benchmarking variant calls requires careful attention to definitions of performance metrics, sophisticated comparison approaches, and stratification by variant type and genome context. The Global Alliance for Genomics and Health (GA4GH) Benchmarking Team has developed standardized performance metrics and tools for benchmarking germline small variant calls. This team includes representatives from sequencing technology developers, government agencies, academic bioinformatics researchers, clinical laboratories, and commercial technology and bioinformatics developers for whom benchmarking variant calls is essential to their work. Benchmarking variant calls is a challenging problem for many reasons:Evaluating variant calls requires complex matching algorithms and standardized counting because the same variant may be represented differently in truth and query callsets.Defining and interpreting resulting metrics such as precision (aka positive predictive value = TP/(TP+FP)) and recall (aka sensitivity = TP/(TP+FN)) requires standardization to draw robust conclusions about comparative performance for different variant calling methods.Performance of NGS methods can vary depending on variant types and genome context; and as a result understanding performance requires meaningful stratification.High-confidence variant calls and regions that can be used as “truth” to accurately identify false positives and negatives are difficult to define, and reliable calls for the most challenging regions and variants remain out of reach.We have made significant progress on standardizing comparison methods, metric definitions and reporting, as well as developing and using truth sets. Our methods are publicly available on GitHub (https://github.com/ga4gh/benchmarking-tools) and in a web-based app on precisionFDA, which allow users to compare their variant calls against truth sets and to obtain a standardized report on their variant calling performance. Our methods have been piloted in the precisionFDA variant calling challenges to identify the best-in-class variant calling methods within high-confidence regions. Finally, we recommend a set of best practices for using our tools and critically evaluating the results.
Yield of Universal Testing for DNA Mismatch Repair Protein Deficiency in Colorectal Carcinoma From an Australian Community-based Practice
Authors: Miller Gregory C. , Bettington Mark L. , Brown Ian S. , Rosty Christophe 
Published: February 2018

AbstractLynch syndrome is the most common cause of inherited colorectal carcinoma (CRC). Testing all newly diagnosed CRC for MMR protein deficiency, known as universal testing, has recently emerged as the preferred approach to identify potential Lynch syndrome individuals. All newly diagnosed CRCs were screened for MMR protein expression by immunohistochemistry. A 2-step approach was used: PMS2 and MSH6 testing followed by the testing of the respective MMR protein partner if one of the proteins is lost. We retrospectively searched our pathology database for MMR protein expression results across a 5-year period (2012-2016) when universal testing was performed. Clinical and pathological data were extracted from the pathology report. A total of 2077 consecutive CRCs were tested for MMR protein expression. Mean age at diagnosis was 68.4 years. MMR protein deficiency was identified in 399 cases (19.2%). The vast majority of CRC with MLH1/PMS2 loss were diagnosed in patients older than 70 years (84%), most of them are likely to be secondary to sporadic MLH1 methylation. MMR protein deficiency patterns suggestive of a defect in MSH2, MSH6 or PMS2 comprised 42 cases, of which 37 were found in individuals aged 50 years or older. CRCs with MSH2/MSH6 loss were most commonly found in patients older than 70 years (57%). In summary, universal testing for MMR protein deficiency in CRC identifies abnormal patterns of expression suggestive of Lynch syndrome in all age groups. Further studies are needed to demonstrate the actual rate of Lynch syndrome individuals identified from this initial screening.
The TMEM16A Channel Mediates the fast polyspermy block in Xenopus Laevis
Authors: Wozniak Katherine L. , Phelps Wesley A. , Tembo Maiwase , Lee Miler T. , Carlson Anne E. 
Published: February 2018

ABSTRACTIn externally fertilizing animals, such as sea urchins and frogs, prolonged depolarization of the egg immediately after fertilization inhibits the entry of additional sperm – a phenomenon known as the fast block to polyspermy. In the African clawed frog, Xenopus laevis, this depolarization is driven by a Ca2+-activated Cl− efflux. Although the prominent Ca2+-activated Cl− currents generated by immature X. laevis oocytes are conducted by xTMEM16A channels, little is known about which channels contribute to fertilization-competency in mature eggs. Moreover, the gamete undergoes a gross transformation as it matures from an immature oocyte into a fertilization-competent egg. Here we report the results of our approach to identify the Ca2+-activated Cl− channel that triggers the fast block. Querying published proteomics and RNA-seq data, we identified two Ca2+-activated Cl− channels expressed in fertilization-competent X. laevis eggs: xTMEM16A and xBEST2A. Furthermore, transcripts for these channels increase in abundance during gamete maturation. To determine if either of these mediates the fast block, we characterized exogenously expressed xTMEM16A and xBEST2A using pharmacologic inhibitors. None of the inhibitors tested blocked xBEST2A currents specifically. However, Ani9 and MONNA each reduced xTMEM16A currents by more than 70%, while only nominally inhibiting those generated by xBEST2A. Using whole-cell recordings during fertilization, we found that Ani9 and MONNA effectively diminished fertilization-evoked depolarizations. These results indicate that fertilization activates TMEM16A channels in X. laevis eggs and induces the earliest known event triggered by fertilization: the fast block to polyspermy.HIGHLIGHTSProtein for the channels xBEST2A and xTMEM16A is present in X. laevis eggs.The inhibitors MONNA and Ani9 effectively block xTMEM16A compared to xBEST2A.Xenopus laevis fertilization opens TMEM16A to trigger egg depolarization.The TMEM16A-mediated depolarization is critical for the fast block to polyspermy.
Elongation during segmentation shows axial variability, low mitotic rates, and synchronized cell cycle domains in the crustacean,Thamnocephalus platyurus
Authors: Constantinou Savvas J , Duan Nicole , Chipman Ariel D. , Nagy Lisa M. , Williams Terri A. 
Published: February 2018

AbstractSegmentation in arthropods typically occurs by sequential addition of segments from a posterior growth zone, but cell behaviors producing posterior elongation are not well known. Using precisely staged larvae of the crustacean,Thamnocephalus platyurus, we systematically examined cell division patterns and morphometric changes associated with posterior elongation during segmentation. We show that cell division is required for normal elongation but that cells in the growth zone need only divide ~1.5 times to meet that requirement; correspondingly, direct measures of cell division in the growth zone are low. Morphometric measurements of the growth zone and of newly formed segments suggest tagma-specific features of segment generation. Using methods for detecting two different phases in the cell cycle, we show distinct domains of synchronized cells in the posterior. Borders of cell cycle domains correlate with domains of segmental gene expression, suggesting an intimate link between segment generation and cell cycle regulation.Summary StatementPosterior growth zone has synchronized cell cycle domains but shows little cell division during segment addition in a crustacean. Dimensions of the shrinking posterior growth zone change at tagma boundaries.
A microtubule-based mechanism predicts cell division orientation in plant embryogenesis
Authors: Chakrabortty Bandan , Willemsen Viola , de Zeeuw Thijs , Liao Che-Yang , Weijers Dolf , Mulder Bela , Scheres Ben 
Published: February 2018

AbstractOriented cell divisions are significant in plant morphogenesis because plant cells are embedded in cell walls and cannot relocate. Cell divisions follow various regular orientations, but the underlying mechanisms have not been clarified. We show that cell-shape dependent self-organisation of cortical microtubule arrays is crucial for determining planes of early tissue-generating divisions and forms the basis for robust control of cell division orientation in the embryo. To achieve this, we simulate microtubules on actual cell surface shapes from which we derive a minimal set of three rules for proper array orientation. The first rule captures the effects of cell shape alone on microtubule organisation, the second rule describes the regulation of microtubule stability at cell edges and the third rule includes the differential effect of auxin on local microtubule stability. These rules explain early embryonic division plane orientations and offer a framework for understanding patterned cell divisions in plant morphogenesis.
YopT domain of the PfhB2 toxin from Pasteurella multocida: protein expression, characterization, crystallization and crystallographic analysis
Authors: Kumar Sanjeev , Hedrick Victoria , Mattoo Seema 
Published: February 2018

Pasteurella multocida causes respiratory-tract infections in a broad range of animals, as well as opportunistic infections in humans. P. multocida secretes a multidomain toxin called PfhB2, which contains a YopT-like cysteine protease domain at its C-terminus. The YopT domain of PfhB2 contains a well conserved Cys–His–Asp catalytic triad that defines YopT family members, and shares high sequence similarity with the prototype YopT from Yersinia sp. To date, only one crystal structure of a YopT family member has been reported; however, additional structural information is needed to help characterize the varied substrate specificity and enzymatic action of this large protease family. Here, a catalytically inactive C3733S mutant of PfhB2 YopT that provides enhanced protein stability was used with the aim of gaining structural insight into the diversity within the YopT protein family. To this end, the C3733S mutant of PfhB2 YopT has been successfully cloned, overexpressed, purified and crystallized. Diffraction data sets were collected from native crystals to 3.5 Å resolution and a single-wavelength anomalous data set was collected from an iodide-derivative crystal to 3.2 Å resolution. Data pertaining to crystals belonging to space group P31, with unit-cell parameters a = 136.9, b = 136.9, c = 74.7 Å for the native crystals and a = 139.2, b = 139.2, c = 74.7 Å for the iodide-derivative crystals, are discussed.
Expression, purification and crystallization of phosphoribosyl transferase from a mycobacteriophage
Authors: Li Lei , Lee Eungyu , Shaw Neil 
Published: February 2018

Tuberculosis (TB) continues to remain a leading cause of death globally. Of particular concern is the emergence and rise in incidence of multidrug-resistant and extremely drug-resistant cases of TB. To counter this threat, it is important to explore alternative therapies, including phage therapy. Phage BTCU-1 specifically infectsMycobacteriumspp. and kills the majority of them. Intriguingly, many proteins from the phage do not share high amino-acid sequence identity with proteins from species other than phages. Here, the expression, purification and crystallization of one such protein, a putative phosphoribosyl transferase from phage BTCU-1, is reported. The crystals belonged to space groupC2221, with unit-cell parametersa= 59.71,b= 64.42,c = 65.32 Å, α = β = γ = 90°. The crystals diffracted X-rays to 2.2 Å resolution.
Analysis of deburring effectiveness and surface layer properties around edges of workpieces made of 7075 aluminium alloy
Authors: Matuszak Jakub , Zaleski Kazimierz 
Published: February 2018

Purpose
This paper aims to present a comprehensive analysis of deburring effectiveness and surface layer properties after deburring process by wire brushing from milled 7075 aluminium alloys objects. Edge states (rounding, chamfering), surface roughness around the edge, microhardness and residual stress distribution were analyzed.

Design/methodology/approach
During the machining process, undesirable phenomenon occurs, which is the formation of burrs at the edges of workpieces. They occur in most elements formed by machining. There are many methods that can be used for deburring, but in the case of large components, typical of aerospace industry, using certain methods becomes difficult or uneconomic. Taking advantage of the fact that a part is mounted on the machine, it is advisable to make deburring operation the last action. This operation can be carried out by wire brushing.

Findings
On the basis of conducted studies, it was demonstrated that it was possible to choose such technological brushing conditions as to ensure an effective process of deburring, form appropriate edge state and generate the desired surface layer properties.

Practical implications
The method presented in the article allows for efficient, automatic deburring, especially for large components made of 7075 aluminium alloy. This eliminates manual, time-consuming methods of removing burrs by locksmiths. Moreover, the results allow to evaluate changes occurring in the surface layer after brushing process.

Originality/value
Results of brushing experiment provide full information on selection of technological parameters to obtain the required surface roughness and edge state. Moreover, analysis of surface layer properties (microhardness, residual stress) allows to assess the degree of impact hitting fibre on the workpiece.
Study of low-cycle fatigue of glass-hybrid laminates
Authors: Majerski Krzysztof , Surowska Barbara , Bienias Jaroslaw , Szusta Jaroslaw 
Published: February 2018

Purpose
The purpose of this study is to investigate the results of reinforcing fibre metal laminates with glass fibres under low-cycle fatigue conditions in a limited number of cycles.

Design/methodology/approach
The tests were carried out on open-hole rectangular specimens loaded in tension-tension at high load ranges of 80 and 85 per cent of maximum force determined in static test, correspondingly. The number of cycles for destruction has been determined experimentally.

Findings
By means of microscopic observations, it was possible to determine the moment of crack initiation and their growth rate. Furthermore, it was possible to identify the impact of reinforcing fibre orientation in composite layers, material creating the metal layers, on fatigue life and on nature of crack propagation.

Practical implications
This work validates the possibility of increasing the resistance of fibre metal laminates to low-cycle fatigue by modifying the structure of the laminate.

Originality/value
The resistance of fibre metal laminates on low-cycle fatigue is not widely described and the phenomena occurring during degradation are poorly understood.
Influence of ethnic values on public sector performance management
Authors: Lam Newman M.K. , MacGregor James 
Published: February 2018

Purpose
The purpose of this paper is to examine whether deeply rooted ethnic values persist in public administration in spite of strong foreign influence in education and administrative culture.

Design/methodology/approach
This paper presents the theories and concepts on ethnic values, in particular Chinese and Canadian administrative values in order to examine their differences. Victoria of Canada and Hong Kong of China, both former British colonies, have been selected as the study sites due to their similarity in British education and administrative culture. Comparable samples of human subjects were drawn from the public sectors of Hong Kong and Victoria, who were either students or graduates of a master of public administration program. A questionnaire containing questions on program evaluation and staff promotion was administered to participants.

Findings
The survey results show that, while organizations may have similar administrative systems and cultures, employees revert to their ethnic values for matters concerning their immediate well-being – staff promotion in this case. The findings also suggest that employees endorse good practices and reject bad ones more often than they believe their organizations do.

Research limitations/implications
The purpose of this study is to examine whether lengthy foreign influence can change deeply rooted ethnic culture. The research results are not aimed at and may not be relevant to explaining a current situation.

Practical implications
The research findings may help improve public administration, in particular regarding issues of human resources management.

Social implications
The research findings may provide a better understanding of social behavior in the work place.

Originality/value
This paper contains original data for a comparative analysis that appears to have never been done before. It provides empirical proof that deeply rooted ethnics values are very difficult to change in spite of a long history of foreign influence.
Domestic and overseas doctorates and their academic entry-level jobs in South Korea
Authors: Jung Jisun 
Published: February 2018

PurposeThe purpose of this paper is to explore the development and challenges of doctoral education in Korea. In particular, it focusses on the differences between overseas and domestic doctorates in terms of training, supply and demand in the academic workforce, their academic entry-level jobs and employment status.Design/methodology/approachThis study applied document analysis to mainly secondary data sources. The data were drawn from the Statistical Yearbooks of Education, Annual Science and Technology Statistics, the Database for Overseas Doctorates Registration and the Organisation for Economic Co-operation and Development.FindingsThe findings indicate that the doctoral education system in Korea, in terms of both size and quality, has demonstrated significant development for last four decades. However, the results also show that overseas doctorates have relative advantages for their academic job entry over domestic doctorates, and the major research universities are more likely to hire those with overseas doctorates than domestic doctorates.Originality/valueThis study presents the evolution of the doctoral education system in Korea, which has not yet been considered in the international research.