Miracle-dz/UniFAR-FTUs huggingface dataset:
Radial spoke proteins regulate otolith formation during early zebrafish development

Radial spokes are structurally conserved, macromolecular complexes that are essential for the motility of 9 + 2 motile cilia. In Chlamydomonas species, mutations in radial spoke proteins result in ciliary motility defects. However, little is known about the function of radial spoke proteins during embryonic development. Here, we investigated the role of a novel radial spoke protein, leucine‐rich repeat containing protein 23 (Lrrc23), during zebrafish embryonic development. Mutations in lrrc23 resulted in a selective otolith formation defect during early ear development. Similar otolith defects were also present in the radial spoke head 3 homolog (rsph3)and radial spoke head 4 homolog A (rsph4a) radial spoke mutants. Notably, the radial spoke protein mutations specifically affected ciliary motility in the otic vesicle (OV), whereas motile cilia in other organs functioned normally. Via highspeed video microscopy, we found that motile cilia formation was stochastic and transient in the OV. Importantly, all the motile cilia in the OV beat circularly, in contrast to the planar beating pattern of typical 9 + 2 motile cilia. We identified the key time frame for motile cilia formation during OV development. Finally, we showed that the functions of radial spoke proteins were conserved between zebrafish and Tetrahymena. Together, our results suggest that radial spoke proteins are essential for ciliary motility in the OV and that radial spoke‐regulated OV motile cilia represent a unique type of cilia during early zebrafish embryonic development. —Han, X. , Xie, H. , Wang, Y. , Zhao, C. Radial spoke proteins regulate otolith formation during early zebrafish development. FASEB J. 32, 3984–3992 (2018). www.fasebj. org
Acoustic streaming: an arbitrary Lagrangian–Eulerian perspective

We analyse acoustic streaming flows using an arbitrary Lagrangian Eulerian (ALE) perspective. The formulation stems from an explicit separation of time scales resulting in two subproblems: a first-order problem, formulated in terms of the fluid displacement at the fast scale, and a second-order problem, formulated in terms of the Lagrangian flow velocity at the slow time scale. Following a rigorous time-averaging procedure, the second-order problem is shown to be intrinsically steady, and with exact boundary conditions at the oscillating walls. Also, as the second-order problem is solved directly for the Lagrangian velocity, the formulation does not need to employ the notion of Stokes drift, or any associated post-processing, thus facilitating a direct comparison with experiments. Because the first-order problem is formulated in terms of the displacement field, our formulation is directly applicable to more complex fluid–structure interaction problems in microacoustofluidic devices. After the formulation’s exposition, we present numerical results that illustrate the advantages of the formulation with respect to current approaches.
Wireless Information Surveillance via Proactive Eavesdropping with Spoofing Relay

Wireless information surveillance, by which suspicious wireless communications are closely monitored by legitimate agencies, is an integral part of national security. To enhance the information surveillance capability, we propose in this paper a new proactive eavesdropping approach via a spoofing relay, where the legitimate monitor operates in a full-duplex manner with simultaneous eavesdropping and spoofing relaying to vary the source transmission rate in favor of the eavesdropping performance. To this end, a power splitting receiver is proposed, where the signal received at each antenna of the legitimate monitor is split into two parts for information eavesdropping and spoofing relaying, respectively. We formulate an optimization problem to maximize the achievable eavesdropping rate by jointly optimizing the power splitting ratios and relay precoding matrix at the multiantenna monitor. Depending on the suspicious and eavesdropping channel conditions, the optimal solution corresponds to three possible spoofing relay strategies, namely constructive relaying, jamming, and simultaneous jamming and destructive relaying. Numerical results show that the proposed technique significantly improves the eavesdropping rate of the legitimate monitor as compared to the existing passive eavesdropping and jamming-assisted eavesdropping schemes.
Clinicopathological and prognostic significance of platelet to lymphocyte ratio in patients with gastric cancer

The present study was aim to investigate the prognostic role of platelet to lymphocyte ratio (PLR) for patients with gastric cancer (GC) using meta-analysis. A total of 13 studies (14 cohorts) with 6,280 subjects were included. By pooling hazard ratios (HRs) and 95% confidence intervals (CIs) and odds ratios (ORs) and 95% CIs from each study, we found that elevated PLR was significantly associated with poorer overall survival (OS) (HR: 1.3, 95% CI: 1.1–1.52, p = 0.001; I2 = 68.5%, Ph < 0.001) but not with poor disease-free survival (DFS) (HR: 1.6, 95% CI: 0.88–2.9, p = 0.122; I2 = 87.8%, Ph < 0.001). Subgroup analysis showed that a high PLR significantly predicted poor OS in Caucasian populations, patients receiving chemotherapy and patients at advanced stage. In addition, the cut-off value of PLR > 160 showed adequately prognostic value. Furthermore, elevated PLR was associated with lymph node metastasis and CEA levels in GC. Our meta-analysis showed that elevated PLR could be a significant prognostic biomarker for poor OS in patients with GC.
Quality assessment of long-term stored formalin-fixed paraffin embedded tissues for histopathological evaluation

Histopathological examination of formalin-fixed paraffin-embedded (FFPE) tissues that had been stored for 30 years was conducted, and reconstructivity of the results was verified. These FFPE tissues, which were from all organs of male and female rats, were re-sectioned and histopathologically examined using hematoxylin and eosin (HE) staining. In particular, the stainability and morphology of HE sections and reproducibility of microscopic findings in the liver and kidney demonstrated in the original final reports were evaluated. Although the stainability of hematoxylin was slightly weaker and some morphological artifacts were observed in tissues in re-prepared slides, these deteriorations in the quality of HE sections were considered to be permissible for histopathological examination so long as control sections were also prepared. Most microscopic findings recorded in the original final reports were confirmed using re-prepared HE sections in the present study. While some focal findings, which were judged to be either incidental or spontaneous in nature, were not observed in the sections as expected, this was not considered to be a problem in reconstructing the results of the original histopathological examination because most findings related to the test articles were generally observed diffusely or multifocally in each organ. We concluded that results of the original histopathological examinations could be reconstructed using paraffin blocks that had been stored for up to 30 years.
In Pursuit of Protein Targets: Proteomic characterization of Bacterial Spore Outer Layers

Bacillus cereus, responsible for food poisoning and Clostridium difficile, causative agent of Clostridium difficile-associated diarrhoea (CDAD) are both spore forming pathogens involved in food spoilage, food intoxication and other infections in humans and animals. The proteinaceous coat and the exosporium layers from spores are important for their resistance and pathogenicity characteristics. The exosporium additionally provides an ability to adhere to surfaces eventually leading to spore survival in food. Thus studying these layers and identifying suitable protein targets for rapid detection and removal of spores is of utmost importance. In this study, we identified 100 proteins from B. cereus spore coat, exosporium and 54 proteins from the C. difficile coat insoluble protein fraction. In an attempt to define a universal set of spore outer layer proteins we identified 11 superfamily domains common to the identified proteins from two Bacilli and a Clostridium species. The evaluated orthologue relationships of identified proteins across different spore formers resulted in a set of 13 coat proteins conserved across the spore formers and 12 exosporium proteins conserved in the B. cereus group which could be tested for quick and easy detection or targeted in strategies aimed at removal of spores from surfaces.
Assessing Performance of Spore Samplers in Monitoring Aeromycobiota and Fungal Plant Pathogen Diversity in Canada

ABSTRACT Spore samplers are widely used in pathogen surveillance but not so much for monitoring the composition of aeromycobiota. In Canada, a nationwide spore-sampling network (AeroNet) was established as a pilot project to assess fungal community composition in air and rain samples collected using three different spore samplers in the summers of 2010 and 2011. Metabarcodes of the internal transcribed spacer (ITS) were exhaustively characterized for three of the network sites, in British Columbia (BC), Québec (QC), and Prince Edward Island (PEI), to compare performance of the samplers. Sampler type accounted for ca. 20% of the total explainable variance in aeromycobiota compositional heterogeneity, with air samplers recovering more Ascomycota and rain samplers recovering more Basidiomycota. Spore samplers showed different abilities to collect 27 fungal genera that are plant pathogens. For instance, Cladosporium spp. , Drechslera spp. , and Entyloma spp. were collected mainly by air samplers, while Fusarium spp. , Microdochium spp. , and Ustilago spp. were recovered more frequently with rain samplers. The diversity and abundance of some fungi were significantly affected by sampling location and time (e.g., Alternaria and Bipolaris) and weather conditions (e.g., Mycocentrospora and Leptosphaeria), and depended on using ITS1 or ITS2 as the barcoding region (e.g., Epicoccum and Botrytis). The observation that Canada's aeromycobiota diversity correlates with cooler, wetter conditions and northward wind requires support from more long-term data sets. Our vision of the AeroNet network, combined with high-throughput sequencing (HTS) and well-designed sampling strategies, may contribute significantly to a national biovigilance network for protecting plants of agricultural and economic importance in Canada. IMPORTANCE The current study compared the performance of spore samplers for collecting broad-spectrum air- and rain-borne fungal pathogens using a metabarcoding approach. The results provided a thorough characterization of the aeromycobiota in the coastal regions of Canada in relation to the influence of climatic factors. This study lays the methodological basis to eventually develop knowledge-based guidance on pest surveillance by assisting in the selection of appropriate spore samplers.
Experimental Investigation on the Detection of Multiple Surface Cracks Using Vibrothermography with a Low-Power Piezoceramic Actuator

Vibrothermography often employs a high-power actuator to generate heat on a specimen to reveal damage, however, the high-power actuator brings inconvenience to the application and possibly introduces additional damage to the inspected objects. This study uses a low-power piezoceramic transducer as the actuator of vibrothermography and explores its ability to detect multiple surface cracks in a metal part. Experiments were conducted on a thin aluminum beam with three cracks in different orientations. Detailed analyses of both thermograms and temperature data are presented to validate the proposed vibrothermography method. To further investigate the performance of the proposed vibrothermography method, we experimentally studied the effects of several critical factors, including the amplitude of excitation signal, specimen constraints, relative position between the transducer and cracks (the transducer is mounted on the same or the opposite side with the cracks). The results demonstrate that all cracks can be detected conveniently and simultaneously by using the proposed low-power vibrothermography. We also found that the magnitude of excitation signal and the specimen constraints have a great influence on detection results. Combined with effective data processing methods, such as Fourier transformation employed in this study, the proposed method provides a promising potential to detect multiple cracks on a metal surface in a safe and effective manner.
Characterisation of potentially probiotic vaginal lactobacilli isolated from Argentinean women

Abstract This study aims to evaluate potentially beneficial properties of 20 strains of vaginal lactobacilli isolated from women in Tucumán, Argentina, by determining acid and hydrogen peroxide production and auto-aggregation ability. The microorganisms were characterised genetically by amplified ribosomal 16S-DNA restriction analysis (ARDRA). Lactobacillus gasseri and L. rhamnosus were the predominant species identified among the 20 vaginal lactobacilli strains. Most achieved low pH values after 12 h incubation at 37°C and produced hydrogen peroxide in static culture. However, pH decrease and semi-quantitative hydrogen peroxide production of most homofermentative lactobacilli were significantly higher than those of heterofermentative lactobacilli. Of the 20 strains studied, only three demonstrated remarkable auto-aggregation patterns. Four strains were selected for possible use in a probiotic product for vaginal application; however, further in vitro study of other potentially probiotic characteristics is required before attempting clinical trials.
Quality of life of high-functioning children and youth with autism spectrum disorder and typically developing peers: Self- and proxy-reports

Studies have shown parents to report lower quality of life for their children with autism spectrum disorder than children’s self-report scores and the same applies for data on typically developing children. Our objectives were to: (1) explore how high-functioning children with autism spectrum disorder rate their quality of life compared with paired controls without autism spectrum disorder; (2) explore how parents of high-functioning children with autism spectrum disorder rate their children’s quality of life compared with parents of paired controls; and (3) compare child self-reports of quality of life with their parent’s proxy-reports for both groups of children. Data were collected with the Icelandic self- and proxy-reported versions of the KIDSCREEN-27. Reports of 96 children with autism spectrum disorder, 211 controls and their parents were included in the analyses. Compared with controls, children with autism spectrum disorder had lower means on all quality of life dimensions. Parents of children with autism spectrum disorder evaluated their children’s quality of life lower on all dimensions than did parents of controls. On four out of five dimensions, children with autism spectrum disorder reported better quality of life than did their parents. Despite differences in ratings children with autism spectrum disorder and their parents agreed on the most problematic dimensions, namely, social support and peers and physical well-being. Our results highlight the importance of seeking the viewpoints of both children and their parents.
Measuring Stratigraphic Congruence Across Trees, Higher Taxa, and Time

The congruence between the order of cladistic branching and the first appearance dates of fossil lineages can be quantified using a variety of indices. Good matching is a prerequisite for the accurate time calibration of trees, while the distribution of congruence indices across large samples of cladograms has underpinned claims about temporal and taxonomic patterns of completeness in the fossil record. The most widely used stratigraphic congruence indices are the stratigraphic consistency index (SCI), the modified Manhattan stratigraphic measure (MSM*), and the gap excess ratio (GER) (plus its derivatives; the topological GER and the modified GER). Many factors are believed to variously bias these indices, with several empirical and simulation studies addressing some subset of the putative interactions. This study combines both approaches to quantify the effects (on all five indices) of eight variables reasoned to constrain the distribution of possible values (the number of taxa, tree balance, tree resolution, range of first occurrence (FO) dates, center of gravity of FO dates, the variability of FO dates, percentage of extant taxa, and percentage of taxa with no fossil record). Our empirical data set comprised 647 published animal and plant cladograms spanning the entire Phanerozoic, and for these data we also modeled the effects of mean age of FOs (as a proxy for clade age), the taxonomic rank of the clade, and the higher taxonomic group to which it belonged. The center of gravity of FO dates had not been investigated hitherto, and this was found to correlate most strongly with some measures of stratigraphic congruence in our empirical study (top-heavy clades had better congruence). The modified GER was the index least susceptible to bias. We found significant differences across higher taxa for all indices; arthropods had lower congruence and tetrapods higher congruence. Stratigraphic congruence—however measured—also varied throughout the Phanerozoic, reflecting the taxonomic composition of our sample. Notably, periods containing a high proportion of arthropods had poorer congruence overall than those with higher proportions of tetrapods. [Fossil calibration; gap excess ratio; manhattan stratigraphic metric; molecular clocks; stratigraphic congruence. ]
A Structural Framework for Analyzing Information Technology

With the rise of technological advance, organizations require methods and tools to analyze technologies regarding their fit to the needs of an institution. Research on the evaluation and selection of technologies has mainly adopted a process perspective so far. We argue that it is crucial to consider the inner structure of technologies as well and describe its elements and connections. Hence, in this paper we propose a framework for analyzing information technology by reconstructing its inner structure. We transfer concepts of philosophical Structuralism to technologies by analyzing the striking proximity in the assembly of theories and technologies as conceptual networks. By describing technologies in such a way, we are able to formulate a set of questions which allows for analyzing and evaluating the suitability of technologies for specific requirements. In order to demonstrate the utility of such theoretizied technologies we apply our approach to the technology . NET.
Forms of Rubber as Indicated by Temperature-Volume Relationship

Abstract This paper describes measurements of the change of volume of rubber with change of temperature, which have been used as a means for determining the forms in which rubber may exist and ascertaining the conditions under which transition from one form to another may occur. This work is part of a study of the basic thermodynamic properties of rubber which is being conducted at the cryogenic laboratory of the National Bureau of Standards. In this study, an attempt was first made to measure the heat capacity of rubber over a wide range of temperature, but under some circumstances anomalies due to change in phase were encountered which took place so slowly that it was impracticable t0 follow them through by calorimetric methods. These anomalies have been studied by the measurement of the changes in volume or coefficient of expansion associated with them, it being possible to follow changes in volume over as long a period of time as desired. At temperatures at which rubber is relatively stiff and rigid, .
A Comprehensive Health Profile of Youths Living with a “Hikikomori” Lifestyle

To understand the health impacts of “hikikomori” lifestyle and to establish its first 16 comprehensive health profile, a cross-sectional study was designed to measure how well the cases 17 of hikikomori youths of Hong Kong were living, in terms of social, mental and physical aspects. 18 This study involved 104 eligible participants at age 19.02 year-old who had completed the set of 19 questionnaires and a series of anthropometric and physical health measurements. Despite SF36 20 score of 84.0 indicated good physical functioning in general, participants were lived sedentarily 21 with high incidence of hypertension at 15.4% and prehypertension at 31.7%. Occurrence of 22 hypertension in cases living as hikikomori >6 months was 3-times higher than those newly onset 23 cases. The blood pressure levels were correlated with age and all obesity index parameters 24 measured including waist circumference and body mass index. Half of the hypertensive cases 25 involved the elevation of systolic blood pressure, which suggested higher odds of cardiovascular 26 complications. Participants were mentally stable living with moderate levels of perceived stress and 27 state anxiety, but borderline clinical depression. In conclusion, the hikikomori lifestyle could be a 28 risk behavior that may harm the younger generation physically by promoting obesity and 29 hypertension and probably other chronic illnesses. 30
Discovering Unwarranted Associations in Data-Driven Applications with the FairTest Testing Toolkit

In today's data-driven world, programmers routinely incorporate user data into complex algorithms, heuristics, and application pipelines. While often beneficial, this practice can have unintended and detrimental consequences, such as the discriminatory effects identified in Staples' online pricing algorithm and the racially offensive labels recently found in Google's image tagger. We argue that such effects are bugs that should be tested for and debugged in a manner similar to functionality, performance, and security bugs. We describe FairTest, a testing toolkit that detects unwarranted associations between an algorithm's outputs (e.g., prices or labels) and user subpopulations, including protected groups (e.g., defined by race or gender). FairTest reports any statistically significant associations to programmers as potential bugs and ranks them by their strength while accounting for known explanatory factors. We designed FairTest for ease of use by programmers and integrated it into the evaluation framework of SciPy, a popular library for data analytics. We used FairTest experimentally to identify unfair disparate impact, offensive labeling, and disparate rates of algorithmic error in six applications and datasets. As examples, our results reveal subtle biases against older populations in the distribution of error in a real predictive health application, and offensive racial labeling in an image tagger.