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opennotspecifiedJan 2022View details →

FIGURES 1–10. Carepalxis quasimodo n in Diagnostic notes on the spider orb-weaving genera Carepalxis and Ocrepeira (Araneae: Araneidae), with description of three new species from Central Brazil

FIGURES 1–10. Carepalxis quasimodo n. sp. 1–5, Epigynum (1, posterior; 1 ventral; 3, lateral; 4, ventral without scape; 5, posterior, cleared). 6–10, Female habitus; 6–8, female from Brasília (6, dorsal; 7, lateral; 8, frontal); 9–10, female from Jaborandi (9, dorsal; 10 lateral).

opennotspecifiedJan 2022View details →

FIGURES 22–29. Ocrepeira planalto n in Diagnostic notes on the spider orb-weaving genera Carepalxis and Ocrepeira (Araneae: Araneidae), with description of three new species from Central Brazil

FIGURES 22–29. Ocrepeira planalto n. sp. 22–25, Epigynum (22, ventral; 23, lateral; 24, posterior; 25, posterior, cleared). 26, Female dorsal habitus. 27, Male palp. 28–29, Male habitus (28, dorsal; 29, lateral). Voucher: 22–24, 26, (DZUB 9280); 25, (DZUB 5357); 27–29, (DZUB 9279). Scale bars: genitalia, 0.25 mm; other drawings, 1 mm.

opennotspecifiedJan 2022View details →

FIGURE 30 in Diagnostic notes on the spider orb-weaving genera Carepalxis and Ocrepeira (Araneae: Araneidae), with description of three new species from Central Brazil

FIGURE 30. Distribution of Carepalxis quasimodo n. sp., Carepalxis topazio n. sp. and Ocrepeira planalto n. sp.

openukcrownJan 2022View details →

Climate and air quality relevant output diagnostics from UKESM1 for the additional AerChemMIP simulation ssp370SSTpdEmis

This dataset contains model output data for radiative fluxes, emissions, aerosols and ozone produced from an additional AerChemMIP model experiment where anthropogenic precursor emissions and trace gas constituents were held fixed at 2014 values. This model experiments was conducted by UKESM1, a model contributing to CMIP6, and was run over the period 2015 to 2100 to investigate the effect of anthropogenic emissions on near-term climate forcers. The atmosphere only CMIP6 configuration of UKESM1 was used to run this experiment. Model simulations were conducted at a global resolution of 1.875° x 1.25°.

opencc-by-4.0Feb 2022View details →

Percussion test: description and diagnostic accuracy of a new manual test for bone marrow edema of the knee - RAW DATASET

Background Prompt diagnosis of bone marrow lesion (BML) is difficult but critical for correct treatment. Magnetic resonance imaging is the gold standard, although expensive and time consuming. Simple and reliable clinical test for BML detection is lacking. Aim of the study is to describe a new manual clinical test called Percussion Test (PT) and to statistically determine its diagnostic accuracy in BML, compared to MRI imaging. Methods After evaluation of the inclusion and exclusion criteria, 218 consecutive patients with unilateral knee pain and age comprised between 18 and 80 years old were enrolled in our observational prospective study. Informed consent was obtained for each patient. After medical history collection, PT was performed by a single operator as described. MRI was performed in the affected knee to detect the presence of BML. Coherence in PT and MRI assessment was evaluated in each quadrant of the knee via contingency tables, as sensitivity, specificity, NPV, PPV and diagnostic accuracy were calculated. Results No correlation with a positive PT was demonstrated for the covariables gender (p =&thinsp;0.156), age (p =&thinsp;0.272) and BMI (p =&thinsp;0.639). PT showed a sensitivity ranging from 60.6 (40.6–80.6) to 79.5 (63.0–96.0) and a specificity ranging from 85.7 (80.0–91.5) to 96.0 (93.1–98.9) depending on knee quadrant. Diagnostic accuracy ranged from 81.6 (75.9–86.6) to 89.4 (84.6–93.2), and p-value was < 0.00001 in a chi-squared analysis for all quadrants. Conclusions PT showed sensitivity and specificity values that are comparable with other clinical tests routinely adopted in clinical practice. In the absence of other reliable clinical test, PT has the potential to become a useful bedside tool in the diagnosis and management of BMLs.

opencc-by-4.0Dec 2022View details →

Dataset to "Analysing cerebrospinal fluid with explainable deep learning: From diagnostics to insights"

Accompanying dataset for our paper "Analysing cerebrospinal fluid with explainable deep learning: From diagnostics to insights", in Neuropathology and Applied Neurobiology.

opencc-by-4.0Aug 2022View details →

Large-scale human tissue analysis identifies Uroplakin 3B as a useful diagnostic marker for mesothelioma and normal meso-thelial cells

Supplement Figure 1: IHC validation by comparison of antibodies. Using MSVA-736M, an apical membranous Upk3b positivity is seen in mesothelial cells covering an appendix (A), amnion cells of a placenta (B), and umbrella cells of the renal pelvis urothelium (C), while staining is absent in adrenal gland (D). Using clone C362, a similar membranous staining is seen in mesothelial cells of the appendix (E), amnion cells (F), and urothelial umbrella cells (G) despite of a higher level of background staining. Clone C362 results in a significant nuclear staining of adrenocortical cells (H) which was not seen by MSVA-736M.

opencc-by-4.0Aug 2022View details →

Gene-level read counts from bulk RNA-seq data for 38 follicular lymphoma diagnostic biopsies

Conventional (bulk) RNA-sequencing was performed on unfractionated cell suspension or snap frozen whole tissue material. Total RNA was isolated with TRIzol reagent followed by purification over PureLink RNA Mini Kit columns (Invitrogen). RNA-seq was performed using a polyA-enriched strand-specific library construction protocol (doi: 10.1016/j.ccell.2016.02.009) and paired-end 75bp sequencing on an Illumina HiSeq 2500 instrument. Raw reads were aligned to the reference human genome assembly GRCh37 (hg19) using STAR (v2.5.2.a). To improve spliced alignment, STAR was provided with exon junction coordinates from the reference annotations (Gencode v19). We applied a modified version of a bioinformatics workflow for normalization of raw read counts and differential gene expression analysis (doi: 10.12688/f1000research.9005.3). Gene-level read counts were quantified using HTSEQ-count (v0.11.0; intersection-strict, reverse mode) (doi: 10.1093/bioinformatics/btu638). Genes showing low read counts (i.e., genes not showing counts per million (cpm) > 1.0 in at least 10% of samples) were removed from further analysis. Raw counts from expressed genes were then TMM-normalized and scaled to counts per million (CPM) using the edgeR (v3.22.2) package (doi: 10.1093/bioinformatics/btp616). Sample IDs correspond to those referenced in Wang X et al, Nature Communications (2022).

opencc-by-4.0Sep 2022View details →

Raw datasets and media accompanying the manuscript: Fused Raman spectroscopy analysis of blood and saliva delivers high accuracy for head and neck cancer diagnostics

Raw datasets and media accompanying the manuscript: Fused Raman spectroscopy analysis of blood and saliva delivers high accuracy for head and neck cancer diagnostics

dryad32/100

Data from: Haplotype sequence collection of ABO blood group alleles by long-read sequencing reveals putative A1-diagnostic variants

In the era of blood group genomics, reference collections of complete and fully-resolved blood group gene alleles have gained high importance. For most blood groups, however, such collections are currently lacking, as resolving full-length gene sequences as haplotypes (i.e. separated maternal/paternal origin) remains exceedingly difficult with both Sanger and short-read next-generation sequencing. Using the latest third-generation long-read sequencing, we generated a collection of fully-resolved sequences for all six main ABO allele groups: ABO*A1/A2/B/O.01.01/O.01.02/O.02. We selected 77 samples from an ABO genotype dataset (n=25,200) of serologically-typed Swiss blood donors. The entire ABO gene was amplified in two overlapping long-range PCRs (covering ~23.6 kb) and sequenced by long-read Oxford Nanopore sequencing. For quality validation, two samples per ABO group were re-sequenced using Illumina and PacBio technology. All 154 full-length ABO sequences were resolved as haplotypes. We observed novel, distinct sequence patterns for each ABO group. Most genetic diversity was found between, not within, ABO groups. Phylogenetic tree and haplotype network analyses highlighted distinct clades of each ABO group. Strikingly, our data uncovered four genetic variants putatively specific for ABO*A1, for which direct diagnostic targets are currently lacking. We validated A1-diagnostic potential using whole-genome data (n=4,872) of a multi-ethnic cohort. Overall, our sequencing strategy proved powerful for producing high-quality ABO haplotypes and holds promise for generating similar collections for other blood groups. The publicly available collection of 154 haplotypes will serve as a valuable resource for molecular analyses of ABO, as well as studies about the function and evolutionary history of ABO.

opencc-zeroOct 2022View details →

FIGURE 6 in Resolution of the types, diagnostic features, and distribution of two easily confused Sand Lizards, Pedioplanis laticeps (Smith, 1845) and P. burchelli (Duméril & Bibron, 1839) (Squamata: Lacertidae)

FIGURE 6. Life pictures of the two newly collected individuals of P. laticeps from Aussenkehr/Namibia: (A) adult female ZMB 82782, (B) adult male ZMB 82783.

FIGURE 5. Holotype BMNH 1946.8.7.82 in Resolution of the types, diagnostic features, and distribution of two easily confused Sand Lizards, Pedioplanis laticeps (Smith, 1845) and P. burchelli (Duméril & Bibron, 1839) (Squamata: Lacertidae)

FIGURE 5. Holotype BMNH 1946.8.7.82 (previously 65.5.4.39) of Eremias burchelli Duméril & Bibron, 1839: (A) original drawing of the whole individual modified from Plate 45: 1 (Smith 1845); (B) dorsal view of the museum voucher; (C) ventral view; (D) dorsal head; (E) original drawing of the dorsal head modified from Plate 48: 4 (Smith 1845); (F) ventral head; (G) lateral head left; (H) original drawing of the lateral head modified from Plate 48: 4a (Smith 1845); (I) lateral head right. Scale units 1 mm.

FIGURE 4. Holotype BMNH 1946.8.7.56 in Resolution of the types, diagnostic features, and distribution of two easily confused Sand Lizards, Pedioplanis laticeps (Smith, 1845) and P. burchelli (Duméril & Bibron, 1839) (Squamata: Lacertidae)

FIGURE 4. Holotype BMNH 1946.8.7.56 (previously 65.5.4.55) of Eremias laticeps Smith, 1845: (A) original drawing of the whole individual modified from Plate 46: 1 (Smith 1845); (B) dorsal view of the museum voucher; (C) ventral view; (D) dorsal head; (E) original drawing of the dorsal head modified from Plate 48: 3 (Smith 1845); (F) ventral head; (G) lateral head left; (H) original drawing of the lateral head modified from Plate 48: 3a (Smith 1845); (I) lateral head right. Scale units 1 mm.

FIGURE 2 in Resolution of the types, diagnostic features, and distribution of two easily confused Sand Lizards, Pedioplanis laticeps (Smith, 1845) and P. burchelli (Duméril & Bibron, 1839) (Squamata: Lacertidae)

FIGURE 2. Distribution of P. laticeps compiled from the museum collections of the Museum for Naturkunde Berlin, (Germany), Naturhistorisches Museum Wien (Austria), Ditsong National Museum of Natural History Pretoria, Port Elizabeth Museum, IZIKO South African Museum Cape Town (all South Africa), Natural History Museum London (Great Britain) and the National Museum of Namibia in Windhoek (black dots) including the new record from near Aussenkehr (star). Points are underlain with the altitude level (downloaded from www.worldclim.org) ascending from light grey (sea level) to dark grey (6000 m). The Namibian localities are numbered from 1 through 6 (1: Farm Tafelkop; 2: Farm Louwshoop 330; 3: Klein Karas; 4: Ortmansbaum; 5: Farm Lützelhöhe; 6: Warmbad), the? represents the doubtful record from Angra Pequena/Lüderitz. White spots represent the centre of quarter-degree grids as published by Bates et al. (2014).

FIGURE 3. Holotype BMNH 1946.8.7.86 in Resolution of the types, diagnostic features, and distribution of two easily confused Sand Lizards, Pedioplanis laticeps (Smith, 1845) and P. burchelli (Duméril & Bibron, 1839) (Squamata: Lacertidae)

FIGURE 3. Holotype BMNH 1946.8.7.86 (previously IV.42.a) of Lacerta capensis Smith, 1838: (A) original drawing of the whole individual modified from Plate 45: 2 (Smith 1845); (B) dorsal view of the museum voucher; (C) ventral view; (D) dorsal head; (E) original drawing of the dorsal head modified from Plate 48: 7 (Smith 1845); (F) ventral head; (G) lateral head left; (H) original drawing of the lateral head modified from Plate 48: 7a (Smith 1845); (I) lateral head right. Scale units 1 mm.

FIGURE 1 in Resolution of the types, diagnostic features, and distribution of two easily confused Sand Lizards, Pedioplanis laticeps (Smith, 1845) and P. burchelli (Duméril & Bibron, 1839) (Squamata: Lacertidae)

FIGURE 1. Example of the counting method for enlarged scales arranged in rows (labials, collar, chin shields, ventral scales) using the upper and lower labials. All labials marked with a black dot were counted while the ones marked with X were not. This means that 9 upper labials and 6 lower labials were counted on this specimen.

FIGURES 33–39 in Four new species of the spider genus Nesticella Lehtinen & Saaristo, 1980 from Laos, Thailand and Myanmar and the first description of the male of Nesticella yui Wunderlich & Song, 1995 with a proposed new diagnostic character for the family Nesticidae Simon, 1894 (Arachnida, Araneae)

FIGURES 33–39. Leg setae with pipette setae of tibia IV of Nesticella beccus n. sp. (33–34) and Nesticus eremita (35–39). 33, Sexual dimorphism of leg setae; arrows pointing to pipette setae. 34, Pipette setae and tactile setae. 35, Pipette setae. 36, Pipette seta (left), tactile seta (centre), trichobothrium (right). 37, Tactile setae (long) and pipette setae (short). 38–39, Pipette seta, details (34–39, showing males). Photo credits: 34, 37–39, Rainer Foelix, 35–36, Rainer Foelix and Bruno Erb.

FIGURES 14–17. Nesticella laotica new species. 14–15 in Four new species of the spider genus Nesticella Lehtinen & Saaristo, 1980 from Laos, Thailand and Myanmar and the first description of the male of Nesticella yui Wunderlich & Song, 1995 with a proposed new diagnostic character for the family Nesticidae Simon, 1894 (Arachnida, Araneae)

FIGURES 14–17. Nesticella laotica new species. 14–15, Male palp (14, ventral; 15, retrolateral). 16, Epigynum, ventral. 17, Vulva, dorsal.

FIGURES 24–32 in Four new species of the spider genus Nesticella Lehtinen & Saaristo, 1980 from Laos, Thailand and Myanmar and the first description of the male of Nesticella yui Wunderlich & Song, 1995 with a proposed new diagnostic character for the family Nesticidae Simon, 1894 (Arachnida, Araneae)

FIGURES 24–32. Nesticella new species, habitus, dorsal. 24–25, Nesticella yui; 26–27, Nesticella beccus n. sp.; 28, Nesticella foelixi n. sp.; 29–30, Nesticella laotica n. sp.; 31–32, Nesticella michaliki n. sp. (24, 26, 28, 29, 31 male, 25, 27, 30, 32 female).

FIGURES 1–5. Nesticella laotica new species. 1 in Four new species of the spider genus Nesticella Lehtinen & Saaristo, 1980 from Laos, Thailand and Myanmar and the first description of the male of Nesticella yui Wunderlich & Song, 1995 with a proposed new diagnostic character for the family Nesticidae Simon, 1894 (Arachnida, Araneae)

FIGURES 1–5. Nesticella laotica new species. 1 Vulva, ventral. Lines with numbers indicating position of particular µ-CT scans and the respective figure numbers; 2–5, virtual cross sections through internal duct system. AC, apical chamber of functional receptaculum; CD, copulatory duct; FD, fertilization duct; WD, wound ducts of functional receptaculum.