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opencc-by-4.0Mar 2024View details →

Excel mapping tool for 2023 avian influenza data reporting

Data collection is an important task of the European Food Safety Authority (EFSA) and a fundamental component of risk assessment (Articles 22 and 23 of Regulation (EC) No 178/2002). EFSA receives a large volume of data from Member States (MSs) that is used in support of its risk assessment mission. Council Directive 2005/94/EC and Commission Decision 2010/367/EU lay down the guidelines for monitoring and reporting avian influenza surveillance data on poultry and wild birds by European Union (EU) MSs. EFSA has been assigned the task of collating, validating, analysing, and summarising in an annual report the results from the avian influenza surveillance programmes in poultry and wild birds. For the reporting of data, EFSA provides a Data Collection Framework that allows data providers to submit data in eXtensible Markup Language (XML) format through a web interface or a web service. Here, a data model describing the format, and the content requested when submitting data through the DCF, is provided. The data model supports the reporting of laboratory testing results for avian influenza in both wild birds, and poultry. The use of this reporting standard ensures that reported results are comparable between reporting countries. Data reported in this format will be used to generate epidemiological updates on the avian influenza surveillance testing carry out in Europe, and to provide scientific advice to the European Commission.

opencc-by-4.0Mar 2024View details →

DailySense: a Daily Self-reports and Physiological Signals Sensing Dataset for Subjective Health Research in the Wild

Description: This is a daily self-reports and physiological signals sensing dataset for subjective health research in the wild (DailySense). This is a dataset from a consecutive 14-day experiment in real-life settings composed of smartphone-based subjective psychological evaluation and physiological sensing. A Total of 36 healthy Japanese adult remote workers (mean±SD, 35.8±7.5; range, 27–58 years; 21 male and 15 female participants) participated in the experiment through two terms (1st term [1], 18 participants from a Japanese company without rewards; 2nd term, 18 participants from a participant's pool with rewards). The study protocol was approved by the internal review board of Research & Development Group, Hitachi, Ltd., and was conducted in accordance with the Declaration of Helsinki. All participants provided informed consent prior to enrollment in this study. The permission to share the raw data with participants' anonymization was included in this approval and explicitly obtained in that informed consent. This dataset contains the following data:  - pre- and post-term data of     - responses to self-reporting questionnaires (i.e., the Japanese versions of NEO-FFI, STAI, CES-D, CFS, PSQI, WHO-QOL, and SF-36v2©).     - demographics     - survey regarding this experiment - mid-term data of     - responses to emotional self-reports (i.e., Affective Slider and I-PANAS-SF) and their behavior in ESM 6 times/day at maximum     - responses to subjective health (i.e., degree of fatigue, stress, anxiety, depression, and sleeplessness), wake-up/in-bed times, and work style 1time/day     - continuously monitored physiological data (i.e., EDA, PPG, Acc) and event tags obtained by a wristband sensor (E4 wristband, Empatica Inc.) during their waking hours     - response profile data estimated using the proposed method     - log data of an experience sampling support system (exkuma, Japan Experience Sampling Method Association) Details of data are mentioned in an xlsx file of the root directory. Due to the limitation of questionnaires, descriptions of original instructions of items in each questionnaire are omitted. The details of the experiment are described in [1][2]. Note that, in [1], participant #29 was excluded due to insufficient physiological data quality. In addition, in [2], participant #47 was excluded since he did not complete a personality questionnaire, but #29 was included since he completed responses to all the questionnaires.   License: This dataset is made available by Hitachi, Ltd. under a Creative Commons Attribution 4.0 International (CC BY 4.0) license.   References: If you use this dataset, please cite the following papers: [1] Shunsuke Minusa, Chihiro Yoshimura, and Hiroyuki Mizuno "Emodiversity evaluation of remote workers through health monitoring based on intra-day emotion sampling," Front. Public Heal., vol. 11, no. August, pp. 1–12, 2023, doi: <a href="https://doi.org/10.3389/fpubh.2023.1196539" target="_blank" rel="noopener">10.3389/fpubh.2023.1196539</a> [2] Shunsuke Minusa, Tadayuki Matsumura, Kanako Esaki, Yang Shao, Chihiro Yoshimura, and Hiroyuki Mizuno, "Response Style Characterization for Repeated Measures Using the Visual Analogue Scale," arXiv preprint <a href="https://arxiv.org/abs/2403.10136" target="_blank" rel="noopener">arXiv:2403.10136</a>, 2024.   Contact: If there is any problem, please contact us: <ul> <li>Shunsuke Minusa, <a href="mailto:shunsuke.minusa.hd@hitachi.com" target="_blank" rel="noopener">shunsuke.minusa.hd@hitachi.com</a></li> </ul>

opencc-by-4.0Oct 2023View details →

Fig. 3 in Report of a Feather Mite Species (Acariformes: Astigmata) from the Oriental White Stork, Ciconia boyciana (Ciconiiformes: Ciconiidae), Belonging to the Japanese Native Population

Fig. 3. Pelargolichus orientalis, male (A) and female (B). A, right setae se and si on prodorsal shield, dorsal view; B, posterior part of hysterosoma, dorsal view. Scale bars: 10 µm.

opencc-by-4.0Oct 2023View details →

Fig. 1 in Report of a Feather Mite Species (Acariformes: Astigmata) from the Oriental White Stork, Ciconia boyciana (Ciconiiformes: Ciconiidae), Belonging to the Japanese Native Population

Fig. 1. The taxidermy specimen of the Oriental White Stork Ciconia boyciana sampled in Toyooka City, Hyogo Prefecture, Japan.

Figure 1. Collection localities, 1 in First report of two ark shells, Anadara consociata (E.A. Smith, 1885) and A. troscheli (Dunker, 1882) (Arcidae: Anadarinae) from Indian waters with notes on morpho-taxonomy of some related species from east coast of India

Figure 1. Collection localities, 1-Bokhali, 2-Sagar Island, 3-Junput, 4-Jalda (Tajpur), 5-Digha, 6-Udaypur & Talsari, 7-Chandipur, 8-Paradip, 9-Chandrabhaga, 10-Puri, 11-Chilka New Mouth, 12-Gopalpur, 13-Vishakhapatnam, 14-Kakinada, 15-Pulicat lake, 16-Chennai, 17-Rameswaram, 18-Tuticorin.

Figure 5. a-b in First report of two ark shells, Anadara consociata (E.A. Smith, 1885) and A. troscheli (Dunker, 1882) (Arcidae: Anadarinae) from Indian waters with notes on morpho-taxonomy of some related species from east coast of India

Figure 5. a-b,Mosambicarca erythraneonensis (Jonas in Philippi, 1851), a-exterior of left valve, b- interior of left valve, c-d, Tegillarca granosa (Linnaeus, 1758); c- exterior of right valve, d- internal view of right valve; e-f, T. nodifera (Martens, 1860); e-exterior of left valve, f- interior of left valve; g-h, T. rhombea (Born, 1778); g-exterior of left valve, h-interior of left valve.

Figure 4. a-g,A in First report of two ark shells, Anadara consociata (E.A. Smith, 1885) and A. troscheli (Dunker, 1882) (Arcidae: Anadarinae) from Indian waters with notes on morpho-taxonomy of some related species from east coast of India

Figure 4. a-g,A. troscheli (Dunker, 1882); a-b, interior right & left valve, c- exterior right valve, d- umbo, e- anterior, f- posterior & g- ventral view of shell.

Figure 2. a-b in First report of two ark shells, Anadara consociata (E.A. Smith, 1885) and A. troscheli (Dunker, 1882) (Arcidae: Anadarinae) from Indian waters with notes on morpho-taxonomy of some related species from east coast of India

Figure 2. a-b,Anadara antiquata (Linnaeus, 1758); a- exterior of right valve, b- interior of right valve; c-e, A. consociata (E.A. Smith, 1885), c- exterior of left valve, d- interior of left valve & e- dorsal view of umbo; f-g, A.eherenbergi (Dunker, 1868), f- exterior of left valve, g- interior of left valve.

Figure 3. a-b,A in First report of two ark shells, Anadara consociata (E.A. Smith, 1885) and A. troscheli (Dunker, 1882) (Arcidae: Anadarinae) from Indian waters with notes on morpho-taxonomy of some related species from east coast of India

Figure 3. a-b,A. ferriginea (Reeve, 1844), a- exterior of left valve, b- exterior of right valve; c-e, A. inaequivalvis (Bruguière, 1789); c-exterior of left valve, d- exterior of left valve & left valve overlapping the right valve along postero-ventral region, e- umbo; f-g, A. pilula (Reeve, 1843); f- exterior of right valve, g- interior of right valve.

Fig. 5 in First report of Schistosoma sinensium infecting Tupaia belangeri and Tricula sp. LF

Fig. 5. Molecular phylogenetic analyses of the Tricula sp. LF (◆) by the maximum likelihood method (ML) and maximum parsimony method (MP). Phylogenetic tree depicting relationships among Tricula species inferred from: A. 28S nucleotide data analyses using ML (Ai) and MP (Aii). [Tricula ludongbini AY207037.1, Tricula bambooensis AY207036.1, Tricula xiaolongmenensis AY207040.1, Neotricula aperta AY207034.1 and Delavaya dianchiensis AY207038.1 were cited from Attwood et al. (2004); Gammatricula shini AB611797.1 was cited from Kameda and Kato (2011)]. Outgroup taxon Potamopyrgus antipodarum-JF960454.1. B. 16S nucleotide data analyses using ML (Bi) and MP (Bii). [Tricula ludongbini AY207031.1, Tricula bambooensis AY207030.1, Delavaya dianchiensis AY207033.1 and Tricula xiaolongmenensis AY207032.1 were cited from Attwood et al. (2004); Tricula hudiequanensis KC832712.1 and Jinghongia jinghongensis KC832728.1 were cited from Liu et al. (2014); Neotricula aperta EU306250.1 was cited from Attwood et al. (2008); Gammatricula shini AB611798.1 was cited from Kameda and Kato (2011)]. Outgroup taxon Potamopyrgus antipodarum-AY314009.1. Other sequences were from GenBank.

opencc-by-4.0Apr 2022View details →

Fig. 1. a in First report on Phyllobothrium delphini infection and Crassicauda sp. parasitism resulting in osseous metaplasia in a Cuvier's beaked whale (Ziphius cavirostris) from the Brazilian region

Fig. 1. a Infected adipous tissue. Phyllobothrium delphini located in the center of the well-delimited parasitic cyst. Inset: Phyllobothrium delphini displaying a whitish coloration and shiny appearance. Bar, 2 cm b Thoracic aorta artery displaying bone metaplasia. Radiographic image highlighting the strong radiopacity, similar to bone radiopacity, observed along all the artery walls. Bar, 15 cm c Parasitic cyst located in adipose tissue. Proliferating and reacting fibrous tissue with a moderate number of lymphocytes and plasmocytes located along the parasitic cyst wall. Numerous activated macrophages and multinucleated giant cell (black arrow) are visible around the P. delphini specimen displaying a degenerated cuticle (red arrow). Insert: Hight power field of inflammatory infiltrate with lymphocytes (black arrow) and plasma cells (red arrow). d Thoracic aorta artery displaying bone metaplasia. Mature bone tissue is organized as circumferential lamellae and cement line (red arrow). Note the erythrocytes within the blood vessel and adipose tissue in the medullar region of the detected bone metaplasia. Inset: Hight power field of bone metaplasia with osteocytes allocated in lacunae (black arrow). e Parasitized kidney. Crassicauda sp. involved by reactive fibrous tissue associated with inflammatory infiltrate. f Parasitized Kidney. High power field of nephritis associated with Crassicauda sp. Note the fibrosis and inflammatory infiltrate formed by macrophages (red arrow) and plasma cells (black arrow).. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 4 in First report of Schistosoma sinensium infecting Tupaia belangeri and Tricula sp. LF

Fig. 4. Shell morphology of Tricula sp. LF. A. Shape. B–C. Scanning electron micrograph of the radula.

Fig. 3 in First report of Schistosoma sinensium infecting Tupaia belangeri and Tricula sp. LF

Fig. 3. Molecular phylogenetic analyses of the present Schistosoma sinensium (◆) by the maximum likelihood method (ML) and maximum parsimony method (MP). Phylogenetic tree depicting relationships among Schistosoma species inferred from: A. 18S nucleotide data analyses using ML (Ai) and MP (Aii). [Schistosoma malayensis AY157227.1, Schistosoma mekongi AY157228.1, Schistosoma sinensium AY157225.1, Schistosoma indicum AY157231.1 and Schistosoma japonicum AY157226.1 were cited from Lockyer et al. (2003); Schistosoma incognitum JQ408706.1 was cited from Webster and Littlewood (2012); Schistosoma.spindale Z11979.1 was cited from Johnston et al. (1993)]. B. CO1 nucleotide data analyses using ML (Bi) and MP (Bii). [Schistosoma malayensis AY157198.1, Schistosoma mekongi AY157199.1, Schistosoma sinensium AY157197.1 and Schistosoma incognitum AY157201.1 were cited from Lockyer et al. (2003); Schistosoma indicum NC_047240.1 was cited from Jones et al. (2020); Schistosoma nasale KR607232.1 was cited from Devkota et al. (2015)]. C.12S nucleotide data analyses using ML (Ci) and MP (Cii). [Schistosoma mekongi AF217449.1 was cited from Le et al. (2000); Schistosoma sinensium AF465918.1 and Schistosoma ovuncatum AF465917.1 were cited from Attwood et al. (2002a); Schistosoma incognitum EF534279.1 was cited from Attwood et al. (2007); Schistosoma nasale KR607261.1 was cited from Devkota et al. (2015); Schistosoma mansoni MN593407.1 was cited from Catalano et al. (2020); Schistosoma indicum NC_047240.1 and Schistosoma spindale MN637820.1 were cited from Jones et al. (2020)]. Other sequences were from GenBank.

Fig. 2. Enlarged worm picture. A in First report of Schistosoma sinensium infecting Tupaia belangeri and Tricula sp. LF

Fig. 2. Enlarged worm picture. A. Male, showing oral sucker (os), ventral sucker (vs), constriction (pac), testes (te), gut caeca (int) and gynecophoral canal (gyn). B. Female, showing oral sucker (os), ventral sucker (vs), utero (ut), ovary(ov), vitellarium (vg) and gut caeca (int).

Fig. 1 in First report of Schistosoma sinensium infecting Tupaia belangeri and Tricula sp. LF

Fig. 1. Morphology of S. sinensium at different life cycle stages. Miracidia and cercariae were stained with iodine. A. Egg. B. Miracidium. C. Cercaria. D. Male and female adult worms.

opencc-by-4.0Apr 2024View details →

Data supplementing Einhäuser, W., Neubert, C. R., Grimm, S., & Bendixen, A. (2024). High visual salience of alert signals can lead to a counterintuitive increase of reaction times. Scientific Reports, 14, 8858.

These files supplement the publication  Einhäuser, W., Neubert, C. R., Grimm, S., & Bendixen, A. (2024). High visual salience of alert signals can lead to a counterintuitive increase of reaction times. Scientific Reports, 14, 8858. https://doi.org/10.1038/s41598-024-58953-4 The files data_expX.mat, where X is the experiment number (1-4), contain the data as described below.  The files dataTraining_expX.mat contain the data of the first (training) block of each experiment. They are needed only for the supplemental material.  To exemplify the usage, the functions figure2and3.m, figure4.m, figure5.m, figure6.m and Table1.m output the paper's figures and the data of Table 1, respectively; figureS2.m, figureS3.m, figureS4.m and figureS5.m output the figures of the supplemental material (figure S1 needs substantial amounts of external source code to compute the salience maps and is therefore not included). data_exp1.mat contains the following variables For alert trials, variable of dimensions subjects x blocks x alert trials (20x10x64); note that only used participants and blocks with alert trials (2 through 11) are included in the data set: alert_aud - the salience level of the alert tone (1-8, corresponding to 54dB(A) through 89 dB(A)) alert_vis - the salience level of the alert frame (1-8, corresponding to 0.10 to 8.50 Weber contrasts in logarithmic steps) alert_side - the side on which the alert frame and the tone were presented (1-left, 2-right) alert_fixOk - derived from eye movement data, was the first fixation closer to the alert square than to the center? alert_primaryRT - primary-task reaction time (for alert trials) alert_alertRT - alert-task reaction time  alert_correctAlert - was the response (up/down) to the alert correct? alert_intrusionAlert - was there an intrusion (left/right pressed before up or down)? alert_correctPrimary - was the primary task conducted correctly? alert_intrusionPrimary - was there an intrusion for the primary task? alert_timeToFixation - time to first fixation on alert square  alert_fixationToResp - time from beginning of fixation to response to the alert  alert_fixDur - duration of first fixation after trial onset For no-alert trials, variable of dimensions subjects x blocks x no-alert trials (20x10x448): noalert_correctPrimary - was the primary task conducted correctly? noalert_intrusionPrimary - was there an intrusion for the primary task? (i.e., up/down pressed before left/right)? For all trials, variable of dimensions subjects x blocks x no-alert trials (20x10x512): all_correctPrimary - was the primary task conducted correctly? all_intrusionPrimary - was there an intrusion for the primary task? (i.e., up/down pressed before left/right)? all_RT - reaction time in the primary task all_isAlertTrial - was the trial an alert trial? (useful to map no-alert trials and alert trials on all trials) In addition, there are some raw eye movement data for the alert blocks: alert_eyeX, alert_eyeY - dimension 20 x 10 x 64 x 6000; x and y position in pixel coordinates relative to trial (and alert) onset, 1ms/sample, ends at conclusion of trials, filled up with NaN if duration was less than 6000ms  alert_eyeFixX, alert_eyeFixY, alert_eyeFixTon, alert_eyeFixDur - 20 x 10 x 64 x 15; x and y position, onset (in ms relative to trial onset) and duration of fixations during the trial (from onset to primary-task response), filled with NaN when less than 15 fixations were made. Note that the first entry of alert_eyeFixDur along the forth dimension will usually equal the alert_fixDur data_exp2.mat contains the same variables as data_exp1.mat with the following exceptions: alert_vis - contains only two levels (1 and 2) corresponding to Weber contrasts of 0.10 and 2.39, respectively alert_dur - the level of duration of the alert frame (1 through 8, corresponding to 25ms, 50ms, 100ms, 200ms, 300ms, 400ms, 600ms, 800ms) alert_aud is not included (all tones were at 54 dB(A)) there are only 19 participants; hence the variables are of size 19 x ... note: block 8 for subject 6 contains only 450 trials (57 alert trials), the remainder is filled with NaN. data_exp3.mat contains the same variables as data_exp1.mat with the following exceptions: alert_aud - contains only two levels (1 and 2) corresponding to sound levels of 54 dB(A) and 79 dB(A) respectively alert_dur - the level of duration of the alert tone (1 through 8, corresponding to 25ms, 50ms, 100ms, 200ms, 300ms, 400ms, 600ms, 800ms) alert_vis is not included (all alert frames were at 0.10 contrast)   data_exp4.mat contains the same variables as data_exp1.mat with the following exceptions: alert_aud - contains only two levels (1 and 2) corresponding to sound levels of 54 dB(A) and 79 dB(A) respectively alert_vis is not included and replaced by alert_condBefore - alert frame contrast level before the saccade (1 - 0.10 contrast, 2 - 2.39 contrast) alert_condAfter - alert frame contrast level after the saccade (1 - 0.10 contrast, 2 - 2.39 contrast) dataTraining_expX.mat contains for the first (training) block of experiment X (X being 1, 2, 3 or 4) the following variables of size 20x512 (participant x trial) [19x512 in case of Experiment 2]: all_correctPrimary - was the primary task conducted correctly? all_RT - reaction time in the primary task [Note that there are no alert trials in this block and these data are only used in the supplementary material (part 4)]

opencc-by-4.0Mar 2020View details →

Figure 1 in Description of Nanorana conaensis (Fei and Huang, 1981) (Amphibia: Anura: Dicroglossidae) reported from Arunachal Pradesh, India

Figure 1. Maximum Likelihood (ML) tree for the species of Nanorana based on 570 bp of mitochondrial 16S rRNA (*represents the bootstrap values above 50%).

opencc-by-4.0Apr 2024View details →

From Generalist to Specialist: Incorporating Domain-Knowledge into Flamingo for Chest X-Ray Report Generation

This subset of the MIMIC-CXR split file contains the study identifiers and paths to the chest X-ray images used for training, validation and testing of all models presented in the paper: "From Generalist to Specialist: Incorporating Domain-Knowledge into Flamingo for Chest X-Ray Report Generation".

opencc-by-4.0Apr 2024View details →

Code for generating figures and analyzing amplicon sequencing of human mRNA and reporter mRNA targeted with type III-A CRISPR complex from Streptococcus thermophiles

This dataset contains code for analyzing amplicon sequencing data and generating figures in the manuscript by Anna Nemudraia, Artem Nemudryi, and Blake Wiedenheft (2024), "Repair of CRISPR-guided RNA breaks enables site-specific RNA excision in human cells."  Amplicon sequencing data has been deposited to NCBI Sequence Read Archive (SRA) under BioProject PRJNA1099688. The description of read files deposited to SRA can be found in the spreadsheet ./code_for_sequencing_data_analysis/SRA_read_files_description.xlsx The code for analyzing amplicon sequencing data can be found in the archive "code_for_sequencing_data_analysis.tar.gz." Output files from this analysis were used to generate figures. Figures were generated using the ggplot2 package in R and finalized in CorelDRAW. Code for generating figures can be found in the archive "code_for_generating_figures.tar.gz".  Any questions or requests regarding the data or the code should be addressed to Dr. Artem Nemudryi at artem.nemudryi@gmail.com.