Find research datasets worth reusing

FIG. 12 in Horses in the suburbs of a medieval city - a case study from Brno (Czech Republic)

FIG. 12.— Modřice: horses M_802, M_803.

FIG. 4 in Horses in the suburbs of a medieval city - a case study from Brno (Czech Republic)

FIG. 4. — Trnitá Street, Brno: horse T_1490. Courtesy of Archaia Brno.

FIG. 6 in Horses in the suburbs of a medieval city - a case study from Brno (Czech Republic)

FIG. 6. — Trnitá Street, Brno: horses T_3256, T_3257, T_3258. Courtesy of Archaia Brno.

TABLE 9 in Horses in the suburbs of a medieval city - a case study from Brno (Czech Republic)

TABLE 9. — Strontium radiogenic isotopic composition of 10 studied horses from Brno region. Abbreviations and symbols: d, duplicate; 2 s.e., two standard error; ±1 σ, standard deviation between two enamel samples from same horse; *, fragments of mandible not included in zooarchaeological analysis.<table><tbody><tr><th></th><th>Lab N</th><th>Sample</th><th>ID</th><th>Tooth</th><th>87 Sr/ 86 Sr</th><th>2 s.e.</th><th>±1 σ</th></tr><tr><th>Brno, Trnitá</th></tr></tbody><tbody><tr><th>1</th><td>4859</td><td>1-B-Tr</td><td>T_1490 M1</td><td>0.709355</td><td>±17</td><td>0.00001</td></tr><tr><th></th><td>4859d –</td><td>–</td><td>–</td><td>0.709361</td><td>±12</td><td>–</td></tr><tr><th></th><td>4860</td><td>2-B-Tr</td><td>–</td><td>I</td><td>0.709375</td><td>±19</td><td>–</td></tr><tr><th>2</th><td>4861</td><td>3-B-Tr</td><td>T_3256 M1</td><td>0.715298</td><td>±11</td><td>–</td></tr><tr><th></th><td>4861d</td><td>–</td><td>–</td><td>–</td><td>0.715262</td><td>±10</td><td>–</td></tr><tr><th></th><td>4862</td><td>4-B-Tr</td><td>–</td><td>I3</td><td>0.711503</td><td>±18</td><td>–</td></tr><tr><th></th><td>4862d –</td><td>–</td><td>–</td><td>0.711506</td><td>±20</td><td>–</td></tr><tr><th></th><td>5026</td><td>–</td><td>–</td><td>3rd</td><td>0.712181</td><td>±07</td><td>–</td></tr><tr><th>phalanx</th></tr><tr><th>articular</th></tr><tr><th>surface</th></tr><tr><th>3</th><td>4863</td><td>5-B-Tr</td><td>T_3257 I3</td><td>0.711265</td><td>±11</td><td>0.00052</td></tr><tr><th></th><td>4864</td><td>6-B-Tr</td><td>–</td><td>M1</td><td>0.710531</td><td>±16</td><td>–</td></tr><tr><th>4</th><td>4866</td><td>8-B-Tr</td><td>T_3258 M1</td><td>0.710525</td><td>±10</td><td>0.00052</td></tr><tr><th></th><td>4867</td><td>9-B-Tr</td><td>–</td><td>I3</td><td>0.709787</td><td>±13</td><td>–</td></tr><tr><th>5</th><td>4868</td><td>10-B-Tr</td><td>T_420</td><td>M1</td><td>0.712012</td><td>±08</td><td>0.00017</td></tr><tr><th></th><td>4869</td><td>11-B-Tr</td><td>–</td><td>P</td><td>0.711772</td><td>±07</td><td>–</td></tr><tr><th>Brno, K&rcaron;ídlovická</th></tr><tr><th>6</th><td>4870</td><td>12-B-K&rcaron;</td><td>K_801</td><td>Dp</td><td>0.710733</td><td>±09</td><td>–</td></tr><tr><th></th><td>4871</td><td>13-B-K&rcaron;</td><td>K_802</td><td>M1</td><td>0.710135</td><td>±17</td><td>0.0001</td></tr><tr><th>7</th><td>4872</td><td>14-B-K&rcaron;</td><td>–</td><td>I3</td><td>0.709992</td><td>±16</td><td>–</td></tr><tr><th>8*</th><td>4873</td><td>15-B-K&rcaron;</td><td>K_803*</td><td>M1 or</td><td>0.709758</td><td>±13</td><td>0.00008</td></tr><tr><th></th><td></td><td></td><td></td><td>M2</td><td></td><td></td><td></td></tr><tr><th></th><td>4874</td><td>16-B-K&rcaron;</td><td>–</td><td>I2</td><td>0.709874</td><td>±14</td><td>–</td></tr><tr><th>Mod&rcaron;ice</th></tr><tr><th>9</th><td>4875</td><td>17-Mod M_803</td><td>I2, foal</td><td>0.711005</td><td>±14</td><td>0.00011</td></tr><tr><th>10</th><td>4876</td><td>18-Mod M_802</td><td>P</td><td>0.711333</td><td>±09</td><td>0.000001</td></tr><tr><th></th><td>4877</td><td>19-Mod</td><td>–</td><td>I3</td><td>0.711334</td><td>±13</td><td>–</td></tr></tbody></table>

TABLE 6 in Horses in the suburbs of a medieval city - a case study from Brno (Czech Republic)

TABLE 6. — Comparison of the wither’s height of horses from Brno with the Czech Medieval and Modern archaeological sites.Estimated withers height is given for each element together with mean withers heigh and standard deviation (±1σ). Abbreviations: F, femur; H, humerus; MC, metacarpus; MT, metatarsus; R, radius; T, tibia.<table><tbody><tr><th></th><th></th><th></th><th></th><th></th><th></th><th></th><th>Number of</th><th></th><th></th></tr><tr><th>ID</th><th>Period</th><th>H</th><th>F</th><th>R</th><th>T</th><th>MC</th><th>MT</th><th>Measurements Mean</th><th>±1 σ</th></tr></tbody><tbody><tr><th>T_1490</th><td>Late Medieval –</td><td>142 144.2-145.3</td><td>144.7-145.1</td><td>146</td><td>145.2</td><td>–</td><td>8</td><td>144.7</td><td>1.2</td></tr><tr><td>Early Modern</td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr><th>T_3256</th><td>Late Medieval – 136.9-137.3</td><td>137.6</td><td>136.1-136.5</td><td>137.7-138.5</td><td>136.1</td><td>138.3-139.4</td><td>11</td><td>137.3</td><td>1.1</td></tr><tr><td>Early Modern</td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr><th>T_3257</th><td>Late Medieval –</td><td>–</td><td>142.5</td><td>–</td><td>–</td><td>–</td><td>–</td><td>1</td><td>142.5</td><td>–</td></tr><tr><td>Early Modern</td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr><th>T_3258</th><td>Late Medieval –</td><td>147-148</td><td>153</td><td>146.8-147.2</td><td>150</td><td>142.2</td><td>145.1-146.2</td><td>11</td><td>147</td><td>3.2</td></tr><tr><td>Early Modern</td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr><th>T_3164</th><td>Late Medieval –</td><td>138.7 143.9-144.6</td><td>142-143.9</td><td>147.2</td><td>147.1</td><td>149.8-150.4</td><td>10</td><td>145.5</td><td>3.5</td></tr><tr><td>Early Modern</td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr><th>M_802</th><td>Late Medieval – 136.4-136.9</td><td>140</td><td>141.8</td><td>141.7-142.1</td><td>142.8-143.4</td><td>147.2</td><td>10</td><td>141.9</td><td>3.6</td></tr><tr><th>Early Modern</th></tr><tr><th>K_801</th><td>Early Modern</td><td>–</td><td>–</td><td>139.4</td><td>141.7</td><td>144-144.6</td><td>146.2</td><td>6</td><td>143.7</td><td>2.7</td></tr><tr><th>K_802</th><td>Early Modern</td><td>141-142</td><td>146.3 c. 144.7-145.5</td><td>145.6</td><td>148.3-148.9</td><td>149.8-150.4</td><td>8 (10)</td><td>146.5</td><td>3.5</td></tr><tr><td>Modern 136.4-145.7</td><td>138-148.8</td><td>135.3-166.5</td><td>153.9-156.3</td><td>131.8-156.2</td><td>146.7-149.3</td><td>25</td><td>146.6</td><td>8</td></tr><tr><td>Late Medieval – 136.4-148 137.6-153</td><td>136.1-147.2</td><td>137.7-150</td><td>136.1-148.9</td><td>138.3-150.4</td><td>65</td><td>143.6</td><td>4.3</td></tr><tr><td>Early Modern</td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr><td>Early Medieval 130.4-138.3 131.9-142.9</td><td>122-149</td><td>129.5-148.6</td><td>123.3-149.5</td><td>120.9-146.4</td><td>226</td><td>136.5</td><td>5.8</td></tr><tr><td>Migration 128.5-134.6</td><td>127.4</td><td>135.2-138.1</td><td>131.4-139.3</td><td>132.4-137.9</td><td>135.7-144.1</td><td>25</td><td>135.4</td><td>3.6</td></tr></tbody></table>

TABLE 5 in Horses in the suburbs of a medieval city - a case study from Brno (Czech Republic)

TABLE 5. — Summary table providing information on dating,mean withers height,robusticity ratios, sex, and age of the horses from Brno.Abbreviations: Bd, greatest breadth of the distal epiphysis; GL, greatest length; MC, metacarpal; MT, metatarsal; SD, smallest width of the diaphysis; WH, withers height.<table><tbody><tr><th></th><th></th><th>Number of</th><th></th><th></th><th></th><th></th><th></th><th></th><th></th><th></th></tr><tr><th></th><th></th><th>measured WH mean</th><th>MC SD/GL x</th><th>MT SD/GL x</th><th>MC Bd/GL x</th><th>MT Bd/GL x</th><th>Age</th></tr><tr><th>ID Site</th><th>Century long bones</th><th>(cm) WH (SD)</th><th>100</th><th>100</th><th>100</th><th>100</th><th>Sex (years)</th></tr></tbody><tbody><tr><th>T_1490 Brno-Trnitá</th><td>15-16</td><td>10</td><td>144.7</td><td>1.2</td><td>14.8</td><td>–</td><td>21.6</td><td>–</td><td>M</td><td>10-13</td></tr><tr><th>T_3256 Brno-Trnitá</th><td>15-16</td><td>15</td><td>137.3</td><td>1.1</td><td>16.2</td><td>12.8</td><td>22.1</td><td>18.2</td><td>M</td><td>10-11</td></tr><tr><th>T_3257 Brno-Trnitá</th><td>15-16</td><td>1</td><td>142.5</td><td>–</td><td>–</td><td>–</td><td>–</td><td>–</td><td>M</td><td>7-8</td></tr><tr><th>T_3258 Brno-Trnitá</th><td>15-16</td><td>15</td><td>147</td><td>3.2</td><td>14.5</td><td>11.9</td><td>22.7</td><td>17.6</td><td>F</td><td>9-11</td></tr><tr><th>T_3164 Brno-Trnitá</th><td>15-16</td><td>14</td><td>145.5</td><td>3.5</td><td>14.4</td><td>11.6</td><td>21.8</td><td>18.6</td><td>M</td><td>> 5</td></tr><tr><th>M_802 Brno-Mod&rcaron;ice</th><td>15-16</td><td>14</td><td>141.9</td><td>3.6</td><td>14.2</td><td>11.4</td><td>21.4</td><td>17.6</td><td>M</td><td>12-14</td></tr><tr><th>M_803 Brno-Mod&rcaron;ice</th><td>15-16</td><td>0</td><td>–</td><td>–</td><td>–</td><td>–</td><td>–</td><td>–</td><td>? newborn</td></tr><tr><th>K_800 Brno-K&rcaron;ídlovická 17-18</th><td>0</td><td>–</td><td>–</td><td>–</td><td>–</td><td>–</td><td>–</td><td>? <3-3.5</td></tr><tr><th>K_801 Brno-K&rcaron;ídlovická 16-17</th><td>9</td><td>143.7</td><td>2.7</td><td>14</td><td>10.9</td><td>20.7</td><td>17.1</td><td>?</td><td>3-4</td></tr><tr><th>K_802 Brno-K&rcaron;ídlovická 16-17</th><td>12 (14)</td><td>146.5</td><td>3.5</td><td>13.6</td><td>11.5</td><td>20.9</td><td>17.8</td><td>M</td><td>9-11</td></tr><tr><th>K_803 Brno-K&rcaron;ídlovická 16-17</th><td>0</td><td>–</td><td>–</td><td>–</td><td>–</td><td>–</td><td>–</td><td>?</td><td>9-12</td></tr></tbody></table>

TABLE 7 in Horses in the suburbs of a medieval city - a case study from Brno (Czech Republic)

TABLE 7. — Measurements of enamel dentine exposure and recorded presence/ absence of occlusal bevel. Abbreviations: LDH, height of enamel/dentine exposure; LDW, Enamel dentine exposure at widest point.<table><tbody><tr><th></th><th>LDH (Left)</th><th>LDW (Left)</th><th>LDH (Right)</th><th>LDW (Right)</th><th>Profile (bevel)</th></tr><tr><th>ID</th></tr></tbody><tbody><tr><th>T_1490</th><td>1.93</td><td>3.01</td><td>No</td><td>No</td><td>Yes</td></tr><tr><th>T_3256</th><td>3.64</td><td>1.82</td><td>12.16</td><td>3.62</td><td>No</td></tr><tr><th>T_3257</th><td>13.27</td><td>5.8</td><td>15.11</td><td>5.54</td><td>No</td></tr><tr><th>T_3258</th><td>9.29</td><td>3.58</td><td>10.81</td><td>6.22</td><td>No</td></tr><tr><th>T_3164</th><td>–</td><td>–</td><td>–</td><td>–</td><td>–</td></tr><tr><th>K_800</th><td>–</td><td>–</td><td>–</td><td>–</td><td>–</td></tr><tr><th>K_801</th><td>–</td><td>–</td><td>–</td><td>–</td><td>–</td></tr><tr><th>K_802</th><td>13.13</td><td>6.16</td><td>10.27</td><td>7.1</td><td>No</td></tr><tr><th>M_802</th><td>–</td><td>–</td><td>–</td><td>–</td><td>–</td></tr></tbody></table>

TABLE 1 in Horses in the suburbs of a medieval city - a case study from Brno (Czech Republic)

TABLE 1. — Brno, Trnitá: list of horse burials<table><tbody><tr><th></th><th>Pit description</th><th></th></tr><tr><th>Skeleton</th><th>(shape, size</th><th></th></tr><tr><th>numberPreservation</th><th>in m, fill)</th><th>Dating</th><th>Figure</th></tr></tbody><tbody><tr><th>T_1490</th><td>Fragmentary</td><td>Irregular,</td><td>Second half</td><td>4</td></tr><tr><th></th><td>cranium.</td><td>approximately</td><td>of the 15th</td><td></td></tr><tr><th>Lower</th><td>oval pit,</td><td>and first</td></tr><tr><th>hindlimbs</th><td>> 2 x 1.5 x 0.5 m.</td><td>half of the</td></tr><tr><th></th><td>were not</td><td>Grey sandy silt</td><td>16th century.</td><td></td></tr><tr><th></th><td>retrieved.</td><td>with a random</td><td></td><td></td></tr><tr><th></th><td></td><td>appearance</td><td></td><td></td></tr><tr><th></th><td></td><td>of charcoal,</td><td></td><td></td></tr><tr><th></th><td>pebbles, and</td><td></td></tr><tr><th></th><td>other angular</td><td></td></tr><tr><th></th><td></td><td>stones.</td><td></td><td></td></tr><tr><th>T_3164</th><td>Complete</td><td>Almost rectangular</td><td>Second half</td><td>5</td></tr><tr><th></th><td>postcranial</td><td>or oval pit.</td><td>of the 15th</td><td></td></tr><tr><th>skeleton.</th><td>> 1.4 x 0.9 x 0.4 m.</td><td>to the first</td></tr><tr><th></th><td></td><td>Gravel mixed of</td><td>half of the</td><td></td></tr><tr><th></th><td></td><td>cobbles, pebbles</td><td>16th century.</td><td></td></tr><tr><th></th><td></td><td>and coarse sand.</td><td></td><td></td></tr><tr><th>T_3256</th><td>Fragmentary</td><td>Unknown shape</td><td>Second half</td><td>6</td></tr><tr><th></th><td>cranium.</td><td>of the pit.</td><td>of the 15th</td><td></td></tr><tr><th>Anterior</th><td>Depth = 0.5.</td><td>and first</td></tr><tr><th>middle</th><td>Grey sandy silt</td><td>half of the</td></tr><tr><th></th><td>and distal</td><td>with a random</td><td>16th century.</td><td></td></tr><tr><th></th><td>phalanges</td><td>appearance</td><td></td><td></td></tr><tr><th></th><td>were not</td><td>of charcoal,</td><td></td><td></td></tr><tr><th></th><td>retrieved.</td><td>cobbles, pebbles</td><td></td><td></td></tr><tr><th></th><td></td><td>and brick</td><td></td><td></td></tr><tr><th></th><td></td><td>fragments.</td><td></td><td></td></tr><tr><th>T_3257</th><td>Fragmentary</td><td>Unknown</td><td>Second half</td><td>6</td></tr><tr><th></th><td>cranium</td><td>pit shape.</td><td>of the 15th</td><td></td></tr><tr><th>and axial</th><td>Depth = 0.4-0.6.</td><td>and first</td></tr><tr><th>skeleton.</th><td>Grey sandy silt</td><td>half of the</td></tr><tr><th></th><td>Limb bones</td><td>with frequent</td><td>16th century.</td><td></td></tr><tr><th></th><td>except</td><td>lamps of</td><td>Object</td><td></td></tr><tr><th>for one</th><td>yellowish clay</td><td>disrupted</td></tr><tr><th>femur and</th><td>and random</td><td>by the pit</td></tr><tr><th>fragments of</th><td>appearance</td><td>containing</td></tr><tr><th>scapula were</th><td>of charcoal,</td><td>individual</td></tr><tr><th></th><td>not retrieved.</td><td>cobbles, pebbles</td><td>3258.</td><td></td></tr><tr><th></th><td></td><td>and brick</td><td></td><td></td></tr><tr><th></th><td></td><td>fragments.</td><td></td><td></td></tr><tr><th>T_3258</th><td>Fragmentary</td><td>Unknown</td><td>Second half</td><td>6</td></tr><tr><th></th><td>cranium.</td><td>pit shape.</td><td>of the 15th</td><td></td></tr><tr><th>Cervical</th><td>Depth = 0.8. Grey</td><td>to the first</td></tr><tr><th>vertebrae 3-7</th><td>sandy silt with</td><td>half of the</td></tr><tr><th></th><td>and thoracic</td><td>frequent lamps</td><td>16th century.</td><td></td></tr><tr><th></th><td>vertebrae</td><td>of yellowish clay</td><td>The context</td><td></td></tr><tr><th>3-18 were not</th><td>and random</td><td>disturbing</td></tr><tr><th></th><td>retrieved.</td><td>appearance</td><td>3257.</td><td></td></tr><tr><th></th><td></td><td>of charcoal,</td><td></td><td></td></tr><tr><th></th><td></td><td>cobbles, pebbles</td><td></td><td></td></tr><tr><th></th><td></td><td>and brick</td><td></td><td></td></tr><tr><th></th><td></td><td>fragments.</td><td></td><td></td></tr></tbody></table>

TABLE 2 in Horses in the suburbs of a medieval city - a case study from Brno (Czech Republic)

TABLE 2. — Brno, K&rcaron;ídlovická street: list of horse burials.<table><tbody><tr><th>Skeleton number Preservation</th><th>Pit description (shape, size in m, fill)</th><th>Dating Figure</th></tr></tbody><tbody><tr><th>K_800</th><td>Poorly preserved fragments of scapula,</td><td>Pit shape is unidentified. Grey sandy silt Second half of the 17th</td><td>8</td></tr><tr><th></th><td>humerus, thoracic vertebrae and ribs.</td><td>covering the skeleton.</td><td>and first half of the</td><td></td></tr><tr><th></th><td></td><td></td><td>18th century.</td><td></td></tr><tr><th>K_801</th><td>Fragmentary cranium, complete</td><td>Rectangular, NE-SW,> 1.4 x 0.95 x 0.6.</td><td>16th-17th century.</td><td>9</td></tr><tr><th></th><td>appendicular skeleton.</td><td>Brown-grey soil rarely contains small</td><td></td><td></td></tr><tr><th></th><td>Three horseshoes in situ.</td><td>ceramic fragments.</td><td></td><td></td></tr><tr><th>K_802</th><td>Complete postcranial skeleton and</td><td>Rectangular pit, E-W, 1.93 x 0.8 x 0.45.</td><td>16th century-first half of the</td><td>10</td></tr><tr><th></th><td>fragmentary cranium. Four horse shoes Grey-brown sandy silt is occasionally</td><td>17th century.</td><td></td></tr><tr><th></th><td>in situ.</td><td>mixed with ceramic sherds.</td><td></td><td></td></tr><tr><th>K_803</th><td>Fragments of mandible. Postcranial</td><td>Found together with K_802 (intrusion).</td><td>16th century-first half of the</td><td>–</td></tr><tr><th></th><td>skeleton not preserved.</td><td></td><td>17th century.</td><td></td></tr></tbody></table>

opencc-zeroDec 2018View details →

dryad36/100

Data from: Genomics overrules mitochondrial DNA, siding with morphology on a controversial case of species delimitation

Species delimitation is a major quest in biology and is essential for adequate management of the organismal diversity. A challenging example comprises the fish species of red snappers in the Western Atlantic. Red snappers have been traditionally recognized as two separate species based on morphology: Lutjanus campechanus (northern red snapper) and L. purpureus (southern red snappers). Recent genetic studies using mitochondrial markers, however, failed to delineate these nominal species, leading to the current lumping of the northern and southern populations into a single species (L. campechanus). This decision carries broad implications for conservation and management as red snappers have been commercially over-exploited across the Western Atlantic and are currently listed as vulnerable. To address this conflict, we examine genome-wide data collected throughout the range of the two species. Population genomics, phylogenetic and coalescent analyses favor the existence of two independent evolutionary lineages, a result that confirms the morphology-based delimitation scenario in agreement with conventional taxonomy. While we find evidence of introgression in geographically neighboring populations in northern South America, the genetic differences strongly support isolation and differentiation of these species, suggesting that the northern and southern red snappers should be treated as distinct taxonomic entities.

dryad36/100

Data from: How "simple" methodological decisions affect interpretation of population structure based on reduced representation library DNA sequencing: a case study using the lake whitefish

Reduced representation (RRL) sequencing approaches (e.g., RADSeq, genotyping by sequencing) require decisions about how much to invest in genome coverage and sequencing depth (library quality), as well as choices of values for adjustable bioinformatics parameters. To empirically explore the importance of these "simple" decisions, we generated two independent sequencing libraries for the same 142 individual lake whitefish (Coregonus clupeaformis) using a nextRAD RRL approach: (1) A small number of loci and low sequencing depth (library A); and (2) more loci and higher sequencing depth (library B). The fish were selected from populations with different levels of expected genetic subdivision. Each library was analyzed using the STACKS pipeline followed by three types of population structure assessment (FST, DAPC and ADMIXTURE) with iterative increases in the stringency of sequencing depth and missing data requirements, as well as more specific a priori population maps. Library B was always able to resolve strong population differentiation in all three types of assessment regardless of the selected parameters. In contrast, library A produced more variable results; increasing the minimum sequencing depth threshold (-m) resulted in a reduced number of retained loci, and therefore lost resolution at high -m values for FST and ADMIXTURE, but not DAPC. FST and DAPC were robust to varying the population map and increasing the stringency of missing data requirements. In contrast, ADMIXTURE was unable to resolve strong population differentiation when increasing these same parameters in library A. Similarly, when examining fine scale population subdivision, library B was robust to changing parameters but library A lost resolution depending on the parameter set. We used library B to examine actual subdivision in our study populations. All three types of analysis found complete subdivision among populations in Lake Huron, ON and Dore Lake, SK, Canada using 10,640 SNP loci. Weak population subdivision was detected in Lake Huron with fish from sites in the north-west, Search Bay, North Point and Hammond Bay, showing slight differentiation. Overall, we show that apparently simple decisions about library quality and bioinformatics parameters can have potentially important impacts on the interpretation of population subdivision. Although costly, the early investment in a high-quality library and more conservative stringency settings on STACKS parameters lead to a final dataset that was more consistent and robust when examining both weak and strong population differentiation.

opencc-zeroMar 2020View details →

opencc-by-4.0Mar 2021View details →

Figure 3 in The strange case of Colophotia miranda Olivier, 1886 (Coleoptera: Lampyridae: Luciolinae)

Figure 3. Genitalia of Colophotia miranda male. A–C) Aedeagal

opencc-by-sa-4.0Jun 2021View details →

Automatic translation and multilingual cultural heritage retrieval: a case study with transcriptions in Europeana (dataset)

The dataset contains all the data required to reproduce the experiments done in the paper "Automatic translation and multilingual cultural heritage retrieval: a case study with transcriptions in Europeana", published in the 25th International Conference on Theory and Practice of Digital Libraries (<a href="http://www.tpdl.eu/tpdl2021/">TPDL'21</a>). In that work we run an experiment using the Europeana CH digital library as a use case, and we evaluated the effectiveness of a multilingual information retrieval strategy using machine translations to English as pivot language. We used the CEF translation service (eTranslation) for the translation of queries and content to English (<a href="https://ec.europa.eu/cefdigital/wiki/display/CEFDIGITAL/eTranslation">https://ec.europa.eu/cefdigital/wiki/display/CEFDIGITAL/eTranslation</a>). The dataset is also available at <a href="https://rnd-2.eanadev.org/share/crosslingual-search/">https://rnd-2.eanadev.org/share/crosslingual-search/</a>, and it is organized in four main folders: <ul> <li>queries: sample of 68 queries and their translations to English. The queries were issued in languages other than English from the Europeana Portal, using the Europeana’s 1914-1918 thematic collection, between January and August 2019.</li> <li>transcriptions: sample of 18,257 handwriting transcriptions  and its translations to English. The transcriptions are taken  from the Europeana 1914-1918 thematic collection, and obtained from the Transcribathon crowdsourcing platform (https://europeana.transcribathon.eu/).</li> <li>solr_configuration: Apache Solr search engine configuration used in the experiments (which replicates the one used in Europeana).</li> <li>results: manual evaluation of the query translations, and automatic evaluation of the multilingual retrieval.</li> </ul>

Supplementary data for "Enhancing Resource-based Test Case Generation For RESTful APIs with SQL Handling"

Supplement to: Enhancing Resource-based Test Case Generation For RESTful APIs with SQL Handling In this repository, we provide tests and their coverage reports (conducted by Intellij coverage reports) that are used in the Discussion section of the paper.

opencc-by-4.0Jun 2021View details →

Worker Cooperatives' Potential for Migrant Women's Self-Empowerment. Insights from a Case Study in New York City

Many migrant women in New York City face structural discrimination and administrative hurdles that complicate their access to safe and well-paid labor. Worker cooperatives have been shown to reduce the precarity and economic exclusion of marginalized groups. However, although much is known about worker cooperatives’ economic potential for improving workers’ lives, other social effects remain far less well explored. The present research contributes to exploring this gap by examining how joining a worker cooperative empowers migrant women in their everyday lives. We apply the concept of self-empowerment to several spheres of the everyday lives of migrant women. At an empirical level, the study focuses on migrant women who are members of nine cleaning- or care-worker cooperatives in New York City. The data were gathered using a participatory research approach and consist of interviews, participant observations, and a quantitative survey. The findings are that worker cooperatives have empowering effects on migrant women beyond the sphere of paid work. Although the additional unpaid workload as co-owners of cooperatives represents an extra burden for many migrant women, they now have better wages, more flexibility, and safer workplaces. Furthermore, they acquire a range of leadership skills, enlarge their social network beyond their ethnic communities, and earn increased esteem as co-owners of businesses. Through worker-ownership, migrant women thus increase their economic, cultural, social, and symbolic capital, which enables them to exercise more agency not only in their paid work but also in their families and leisure time.

dryad36/100

Understanding the local drivers of beta-diversity patterns under climate change: The case of seaweed communities in Galicia, North West of the Iberian Peninsula

Aim: To understand spatial-temporal changes (beta-diversity) in coastal communities and their drivers in the context of climate change. Coastal ecosystems are extremely exposed and dynamic, where changes in seaweed assemblages have been associated with changing water temperatures. However, at the local scale, the effects of changes in the upwelling events and related stressors seek further exploration. Location: Galicia rías, North West of the Iberian Peninsula Methods: Using data collected in 42 sampling localities in Galicia rias and over two time periods (1998 and 2014), we analyzed changes in the seaweed community's composition through time and space. We calculated the temporal beta diversity index and spatial beta diversity as the pairwise composition differences between sampling localities. We use generalized dissimilarity models, to identify local environmental drivers of spatial and temporal beta-diversity. Results: We found a significant change in seaweed communities of Galicia rias, between 1998 and 2014 (temporal beta-diversity). They were mostly related to species loss rather than to species replacement. The dissimilarity among localities (spatial beta diversity) was significantly higher in 2014 than 1998. Nitrate concentration was consistently predicted as the main driver of both temporal and spatial beta-diversity patterns. Main conclusions: Unlike other studies in marine ecosystems, our results suggest that observed changes in the structure of perennial seaweed assemblages in Galicia Rias might lead to a local biotic heterogenization, indirectly linked to climate change through changes in nutrients availability and the upwelling intensity. Changes in Galicia seaweed communities call scientific attention to the importance of local stressors in climate change studies.

opencc-zeroJul 2021View details →

opencc-by-4.0Jun 2021View details →

Looking in the medicine cabinet: methods for using real-world data to assess the impact of measles, mumps and rubella (MMR) and recombinant adjuvanted varicella-zoster vaccines on coronavirus disease 2019 (COVID-19) prevention and case fatality

Supplementary File S1.  20210712_vx_off_target_pubdraft_S1 (Tables, Graphs and scripts associated with publication) Data file 1. Basic_Analysis.R (descriptive analysis script in R, for use with cleaned data files 3, 4 and 6) Data file 2. Cleaning (Script demonstrating how Cerner data was cleaned upon download) Data file 3. COVID_all_cleaned (CSV file with all COVID+ subjects in Cerner institutions) Data file 4. COVID_mmr_data_cleaned (CSV file with COVID+ patients between 25-64 years old, including institution id, age category, gender, whether patient is in emergency department or inpatient, flu vaccine history, MMR vaccine history and mortality outcomes) Data file 5. COVID_mmr_data_matched (CSV file matching MMR vaccine-exposed cases to controls based on propensity scores) Data file 6. COVID_zoster_data_cleaned (CSV file with COVID+ patients above 50 years old, including institution id, age category, gender, whether patient is in emergency department or inpatient, flu vaccine history, zoster vaccine history and mortality outcomes) Data file 7. COVID_zoster_data_matched (CSV file matching zoster vaccine-exposed cases to controls based on propensity scores) Data file 8. General_25_64_data_cleaned (CSV file, all patients in Cerner institutions between 25 – 64 years old, including institution id, age category, gender, whether patient is in emergency department or inpatient, flu vaccine history, MMR vaccine history, SARS-CoV-2 infection and COVID-19 mortality outcomes ). Data file 9. General_over50_data_cleaned (CSV file, all patients in Cerner institutions above 50 years old, including institution id, age category, gender, whether patient is in emergency department or inpatient, flu vaccine history, zoster vaccine history, SARS-CoV-2 infection and COVID-19 mortality outcomes). Data file 10. Included_tenants (CSV file, institution IDs whose contributed cases comprise at least 0.5% of the aggregate sample size). Data file 11. MMR_ps (R script to run for MMR-related files analysis) Data file 12. Zoster_ps (R script to run for zoster-related files analysis)

CSV-format data for: Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7

This is a supplementary upload to <a href="https://zenodo.org/record/4579857">https://zenodo.org/record/4579857</a>. This upload provides the same anonymised individual-level SARS-CoV-2 testing data for England as that earlier upload provided, but provides it in CSV format (comma-separated values) instead of in the previous QS format. The QS format requires specialised software (e.g. the qs package for R) to read, so I am providing the data in CSV format to facilitate access to and re-use of the data. Please see the original data upload, <a href="https://zenodo.org/record/4579857">https://zenodo.org/record/4579857</a>, the associated journal article, <a href="https://www.nature.com/articles/s41586-021-03426-1">Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7</a>, and the project's Github repository, <a href="https://github.com/nicholasdavies/cfrvoc">https://github.com/nicholasdavies/cfrvoc</a>, for full details.

A case study on automatic summarization for gray literature

Replication package for a case study on using PositionRank to automatic summarize blog posts based on the Spicy implementation of the algorithm

Fault test cases for series compensated transmission line with capacitor at line terminal

This data set contains time series data of different simulated fault cases in high voltage series compensated transmission lines. The simulation is done in PSCAD using the Python automation library. The capacitor is located at one of the line terminals with CT and VT. The modelled line is 500 kV and 200 km long. The simulation is run for 1 second with 10 kHz sampling rate.  Each file contains 7 data in the following order,  <ol> <li>Time</li> <li>Voltage phase A</li> <li>Voltage phase B</li> <li>Voltage phase C</li> <li>Current phase A</li> <li>Current phase B</li> <li>Current phase C</li> </ol> The variables used to study different test cases are shown below, <ul> <li>Fault inception angle (phase A): 0 and 90 degree</li> <li>Source impedance ratio: 0.20 and 0.35</li> <li>Capacitor level: 94 µF(50%), 78 µF(60%), 67 µF(70%)</li> <li>Fault resistance: 0.10, 10, 20, 30 ohm</li> <li>Fault location: 10 km reverse, 10 km, 50 km, 100 km, 125 km, 150 km, 155 km, 160 km. 165 km, 170 km, 180 km, 190 km</li> <li>Fault type: No-fault, AG, BG, CG, ABG, CAG, BCG, ABCG, AB, CA, BC, ABC</li> </ul> All these factors lead to 6912 test cases in total. The test cases are organized in four (4) zipped folders each containing 1728 test cases. The PSCAD model file and an example python script that can be used to automate the simulations are also included herewith for anyone interested to replicate the results.  The name of the folder contains the information regarding fault inception angle and source impedance ratio for all test cases inside that folder, for example, the folder name Outputs_0_0.20 can be decoded as, 0: Fault inception angle (phase A) 0.20: Source impedance ration The files names inside the folders include information about the other variables used in generating the test case. For example, the name test_f_10_0_67_0.01 can be interpreted as, test_f: f for forward fault, r for reverse fault 10: fault location, 10 km 0: Fault type 67: Compensation level 0.01: Fault resistance Fault types are interpreted as in PSCAD. 0 = No-Fault, 1 = Phase A to Ground 2 = Phase B to Ground 3 = Phase C to Ground 4 = Phase AB to Ground 5 = Phase AC to Ground 6 = Phase BC to Ground 7 = Phase ABC to Ground 8 = Phase AB 9 = Phase AC 10 = Phase BC 11 = Phase ABC The different line parameters used in the PSCAD model is as below, Conductor Type: Chukar Geometric mean radius: 20.345 mm DC resistance: 0.0318Ω/km Strands: 84 Strand radius: 1.8491 mm Relative permeability: 1.0 Sag: 12 m Height: 22 m Sub-conductor: 2 Sub-conductor spacing: 0.4572 m Ground wire number: 2 Radius: 5.5245 mm DC resistance: 2.8645Ω/km Relative permeability: 1.0 Sag: 10 m Height: 10 m Impedance Positive sequence0.018 +j0.339 Ω/km Zero sequence0.266 +j1.017 Ω/km   These simulations were run for assessing time-domain protections. Therefore, the parallel CB protection across the series capacitor is disabled, as one can safely assume even with the highest current levels, the CB will take at least 20 ms to operate. This is higher than the time limits for time-domain protection.