189,049 research outputs found
Alburnoides holciki Coad & Bogutskaya 2012
No full text<i>Alburnoides holciki</i> Coad & Bogutskaya, 2012 [N]—Spirlin <p> <b>Taxonomy.</b> Original description: <i>Alburnoides holciki</i> Coad & Bogutskaya, 2012: 44, figs. 1–2 [Hari River at Herat, 34°20’N, 62°12’E, Afghanistan; holotype: SNMB 6788].— Afghanistan synonyms: <i>Alburnoides parhami</i> Mousavi-Sabet, Vatandoust & Doadrio, 2015.—Revisions: None.—Illustration: Coad & Bogutskaya (2012: figs. 1–2).</p> <p> <b>Status in Afghanistan.</b> First identified from Afghanistan by Coad & Bogutskaya (2012); confirmed by Coad (2015: 227).—Afghanistan materials: None.</p> <p> <b>Distribution and habitat.</b> Distribution in Afghanistan: Hari River.—General distribution: Central Asia: Hari [= Tedzhen / Hariroud] River, Afghanistan, its western tributary in Iran, southern Turkmenistan, Uzbekistan and western Tajikistan.—Habitat: This species lives in all kinds of streams. Freshwater.</p> <p> <b>Economic importance.</b> No commercial importance.</p> <p> <b>Conservation.</b> Conservation status in Afghanistan: Unknown.—IUCN: NE (2023).—Threats: Unknown.— Moderate sensitivity to human activities.—Not considered as a keystone species.—Decline status: Unknown.— Low priority for conservation action.</p>Published as part of <i>Çiçek, Erdoğan, Fricke, Ronald, Eagderi, Soheil, Sungur, Sevil, Coad, Brian W & Hamdard, Mohammad Hamid, 2023, Fishes of Afghanistan; a revised and updated annotated checklist, pp. 1-69 in Zootaxa 5305 (1)</i> on page 34, DOI: 10.11646/zootaxa.5305.1.1, <a href="http://zenodo.org/record/8048564">http://zenodo.org/record/8048564</a>
Prognostic nomogram of TCGA-COAD patients.
No full text(A) Nomogram for predicting the 1-, 3-, and 5-year overall survival of TCGA-COAD patients. (B) The calibration curve of 1- and 3-year overall survival of TCGA-COAD patients.</p
COAD paired sample isoform level read counts
No full text<p>TCGA COAD paired sample isoform level read counts from Level 3 RNASeq-v2 data.</p
FABP4 expression correlated with infiltration immune cells in COAD patients.
No full text(A) The mRNA expression levels of FABP4 in TCGA-COAD samples and normal samples, *** p <0.001. (B) The protein level of FABP4 in COAD tissues and adjacent noncancerous colon tissues (magnified, X100 and X200). (C) Correlation analysis of FABP4 expression and immune infiltration cells based on TIMER database.</p
Alburnoides holciki Coad & Bogutskaya, 2012, new species
No full textAlburnoides holciki, new species (Figs. 1, 2) Holotype (Fig. 1). SNM 6788, female, 101.8 mm TL, 80.0 mm SL, AFGHANISTAN, Hari River at Herat (Herat is at 34 ° 20 ’N, 62 ° 12 ’E), 9 August 1974, coll. L. Jedlička. Paratypes. SNM 6788, 18 specimens, 49.6–92.6 mm SL, 8 males 49.6–70.2 mm SL and 10 females 56.4–92.6 mm SL, same data as holotype. Non-type material (Fig. 2). BMNH 1914.1.1: 30 -31, 2, 82.4–92.7 mm SL, IRAN, Kashaf River, Mashhad (Mashhad is at 36 ° 18 ’N, 59 ° 36 ’E), coll. P. Sykes (material dried at some point so not measurable in comparison with type series). Diagnosis. The species is distinguished by a combination of characters which includes a well-defined, sharp, scaleless or only slightly scaled, ventral keel; a short, slightly pointed snout; a terminal mouth with the tip of the mouth cleft on a level with the upper half of the pupil; a large eye (orbit width about equal to interorbital width), (46) 47–51 (55) lateral-line scales to posterior margin of hypurals (47–57 total lateral-line scales); 2.5–4.2 pharyngeal teeth; usually 8 ½ branched dorsal-fin rays; usually 13–16 ½ branched anal-fin rays; 40–42, usually 41, total vertebrae; caudal vertebral region longer than abdominal region (most frequent vertebral formulae 20 +21, 20+ 22 and 19 + 21); and usually 13 or 14 predorsal vertebrae. Description. Holotype. A ventral keel between the pelvics and the anal-fin is well-developed, sharp and scaleless. There is a pelvic axillary scale and scales extend over the proximal bases of the anal-fin. The lateral line is decurved and only the last few scales are elevated and on the mid-caudal peduncle. Lateral-line scales to posterior margin of hypurals number 47 (49 total), scales above lateral line to dorsal-fin origin are 11, scales below lateral line to anal-fin origin are 4, scales below lateral line to pelvic-fin origin are 5, predorsal scales are 23, and circumpeduncle scales are 17. Dorsal-fin rays are 3 unbranched and 8 ½ branched, anal-fin rays are 3 unbranched and 13 ½ branched, branched pectoral-fin rays are 13, pelvic-fin branched rays are 7. The anal-fin origin is under the 7 th branched ray of the dorsal-fin. There are 6 gill rakers on the entire first gill arch and the longest raker reaches the raker below when appressed. Pharyngeal teeth are – 4.2 on the right 5 th ceratobranchial. Total vertebrae are 41 (including 4 Weberian vertebrae and last complex centrum), abdominal vertebrae (including intermediate ones; precaudal vertebrae auctorum) are 20, caudal vertebrae are 21, and predorsal abdominal vertebrae (anterior to the first dorsal-fin pterygiophore) are 14. General topography of cephalic sensory canals and numbers of pores are typical of most Alburnoides, as described by Bogutskaya (1988). The supraorbital canal is not lengthened in its posterior section and has 10 (left) / 9 (right) pores, the infraorbital canal has 16 / 13 pores; the preopercular-mandibular canal is complete, with 15 / 15 pores, and the supratemporal canal is also complete, with 5 pores. The upper body profile is rounded while the lower profile is slightly more convex. The snout is short, slightly pointed, not stout. The mouth is upturned and terminal, the mouth cleft is straight, and its tip is on a level with the upper half of the pupil. Neither lower jaw nor upper jaw protrudes relative to each other. The caudal-fin lobes are pointed, the fin is clearly forked. Morphometrics are summarised in Table 1. The holotype in preservative is decoloured and discernible pigment is a light brown. Pigmentation consists of a darker back fading to a cream belly, pre- and post-dorsal-fin stripes on the back, small spots on the upper operculum and adjacently behind the eye that look like the remains of a dark lateral stripe, three rows of spots above the lateral line anteriorly before the pelvic-fin level, a dark line delimiting the hypaxial and epaxial muscle masses overlain by a diffuse stripe from the head to the tail, expanded on the tail base, a lateral line demarcated by pigment above and below it (the typical "stitched" pattern in many Alburnoides species), fins are mostly hyaline, faint pigment along the anterior dorsal-fin rays, a line of pigment along the proximal edge of the unbranched pectoral-fin ray and weak pigmentation on the first branched ray, and faint pigmentation on the caudal-fin centre branching distally to follow the inner margins of the fin fork. Paratypes. The ventral keel between the pelvics and anal-fin is a well-developed, sharp and protruding scaleless keel in 15 fish, with one scale behind the pelvic-fins (scaled along 1 / 4 of its length) in two fish, and with three scales (scaled along 1 / 3 of its length) in one fish. A pelvic axillary scale is present and the anal-fin base is proximally overlain by flank scales. Scales below the dorsal-fin on the upper flank are a vertical oval with rounded posterior, dorsal and ventral margins, and a wavy anterior margin. Scale radii are restricted to the posterior field encroaching laterally, circuli are fine and eccentric and the focus is anteriorly located. The lateral line is complete; it is decurved and only the last few scales are elevated and on the mid-caudal peduncle. Meristic characters showed no significant differences (p> 0.5) between males and females and the data were combined with the exception of the predorsal scale count. Lateral-line scales to posterior margin of hypurals 46 (1), 47 (4), 48 (6), 49 (2), 50 (1), 51 (3) or 55 (1) (48.8, 2.16); total lateral-line scales 47–53 (57 in one paratype); scales above lateral line to dorsal-fin origin 9 (2), 10 (14) or 11 (2) (10.0, 0.49), scales below lateral line to pelvic-fin origin 4 (3), 5 (14) or 6 (1) (4.9, 0.47), scales below lateral line to anal-fin origin 4 (7) or 5 (11) (4.6, 0.50), predorsal scales 20 (1), 21 (5) and 22 (2) for males (21.1,0.64) and 20 (1), 21 (1), 22 (2), 23 (3), 24 (1), 25 (1) or 26 (1) for females (22.9, 1.79 (p = 0.02), and circumpeduncular scales 16 (2) or 17 (16) (16.9, 0.32). Dorsal-fin unbranched rays 3 (in 12 paratypes) or 4 (in 6 paratypes), dorsal-fin branched rays 8 ½(15) or 9 ½(3) (mean 8.2, standard deviation 0.38), anal-fin unbranched rays 3, anal-fin branched rays 10 ½(1), 14 ½(6), 15 ½(8) or 16 ½(3) (14.6, 1.34) (14.8 and 0.73 if the abnormal number, 10 ½, is excluded), branched pectoral-fin rays 13 (8), 14 (9) or 15 (1) (13.6, 0.61), and pelvic-fin branched rays 7 (18). The dorsal-fin outer margin is truncate to slightly rounded and the anal-fin outer margin is slightly concave. The anal-fin origin is under the 5–7 th branched ray of the dorsal-fin. Pharyngeal tooth counts are 2.5–4.2 in 6 fish, and in other 13 fish only the right 5 th ceratobranchial was examined where – 4.2 were found in 12 specimens and – 5.2 in one. Teeth are hooked at the tip and not serrated below it. The gut shape is a simple “S” with larger fish having a slight loop to the left anteriorly. Total gill rakers in the outer row on first left arch number 5 (1), 6 (4), 7 (5), 8 (7) or 9 (1) (7.2, 1.04); gill rakers are not long and are widely spaced, touching the adjacent raker when appressed, often small and weakly developed. The total vertebrae are 40 (2), 41 (13) or 42 (3). Abdominal vertebrae are 19 (3), 20 (14) or 21 (1); predorsal abdominal vertebrae are 12 (1), 13 (13) or 14 (4); intermediate vertebrae are 2 (3), 3 (14) or 4 (1). Caudal vertebrae are 20 (1), 21 (13) or 22 (4). The vertebral formulae are 20 + 21 (11), 20 + 22 (3), 19 + 21 (3), 19 + 22 (1) or 21 + 20 (1). Thus, the caudal vertebral region most commonly (in all specimens but one) is longer then the abdominal region, the difference between abdominal and caudal counts being – 1 (11), – 2 (6), – 3 (1) or 1 (1). A postcleithrum in the pectoral-fin skeleton is small and maybe absent on one or both sides. Canal pores counts were examined in 13 paratypes on both sides. The supraorbital canal has 8 (11), 9 (13) or 10 (2) pores, the infraorbital canal has 12 (1), 13 (2), 14 (9), 15 (9), 16 (1), 17 (2), 18 (1) or 20 (1) pores, the preopercular-mandibular canal has 14 (11), 15 (12), 16 (1) or 17 (2) pores, and the supratemporal canal (unpaired) has 5 (3), 6 (5), or 7 (5) pores. The body is markedly compressed. The upper body profile is moderately rounded while the lower profile is more convex or both profiles are about equally convex. The eye is large, orbit width about equal to interorbital width. The snout is short, slightly pointed, not stout. The mouth is terminal, with the tip of the mouth cleft on a level with the upper half of the pupil. Neither lower jaw nor upper jaw protrudes relative to each other, so no ‘chin’ is formed by the symphysis of the lower jaws. The mouth cleft is always turned upward, never horizontal, and the junction of the lower jaw and the quadrate is on about a vertical through the anterior eye margin. In those paratypes with an unbroken caudal-fin its lobes are pointed, the fin is clearly forked. Morphometrics are summarised in Table 1. The majority of morphometric characters are not significantly different between males and females as shown by values in Table 1. Exceptions are pectoral-fin and dorsal-fin lengths are longer in males (pectoral-fin often reaching the pelvic-fin origin), and preanal and pelvic-fin to anal-fin distances are longer in females. Colouration. Pigmentation in preserved fish is as described for the holotype but there are 3–4 rows of spots anteriorly on the flank and these rows may extend to the end of the pelvic-fin level or just beyond it. Additionally, there may be 1–2 rows of spots below the anterior lateral line in front of the pelvic-fin level and above the pectoralfin. The peritoneum is white-grey to light brown overall, the latter from distinct but crowded pale brown spots. Some fish have a few, very small, black pigment dots. Description of non-type material. Two specimens from River Kashaf share with holotype and the paratypes most diagnostic features. Thus, they have a completely scaleless sharp ventral keel, – 4.2 teeth on the right 5 th ceratobranchial, an upturned mouth, 8 ½ branched dorsal-fin rays, 13 ½ and 14 ½ anal-fin branched rays, 41 (20 + 21) total vertebrae and 13 predorsal abdominal vertebrae (Fig. 2) Etymology. The new species is named for the late Juraj Holcík, Bratislava, colleague and friend, in recognition of his many contributions to the science of ichthyology. Distribution and habitat. The new species is only known from historical collections in the Hari (= Tedzhen) River of Afghanistan and its western tributary from Iran, the Kashaf River (Fig. 3). The Hari River or Harirud is known as the Tedzhen River in Turkmenistan where it is lost in the sands of the Kara Kum desert. The Hari River in Afghanistan dried up completely in 2000 (Payvand News at www.payvand.com/news/ 01/jan/ 1011.html) and is usually dry from August to November as water is diverted for irrigation and precipitation is low. The city of Mashhad on the Kashaf River in Iran has a population of about 2.5 million people with a concomitant draw on water resources. Water quality in the Kashaf River at Mashhad is degraded (Najafpoor et al., 2007). These shallow rivers with little riparian vegetation in a desert climate have habitats that are stressful for fishes. Comparative remarks. Alburnoides holciki clearly differs from Iranian species A. petrubanarescui Bogutskaya & Coad, 2009, A. namaki Bogutskaya & Coad, 2009, A. nicolausi Bogutskaya & Coad, 2009 and A. idignensis Bogutskaya & Coad, 2009 distributed in the south of the Caspian Sea basin by having a short, slightly pointed snout (vs. stout and rounded), a terminal mouth with the tip of the mouth cleft on a level with the upper half of the pupil (vs. almost or completely subterminal with a tip of the mouth on a level with the lower margin of the pupil to below the lower margin of the eye), a clearly forked caudal-fin with pointed lobes (vs. shallowly forked with rounded lobes), and 13–16 ½, usually 14–15 ½, branched anal-fin rays (vs. 8–13 ½, usually 9–12 ½), and orbit width about equal to interorbital width (vs. smaller). The new species is further easily distinguishable from A. petrubanarescui in having a sharp, usually scaleless ventral keel (vs. smooth and completely scaled) and a caudal vertebral region longer than an abdominal region: most frequent vertebral formulae 20 +21, 20+ 22 and 19 + 21 (vs. shorter, usually 21 + 19 and 21 + 20), from A. nicolausi – in having usually 8 ½ branched anal-fin rays (vs. usually 7 ½), and from both A. nicolausi and A. idignensis – in having 40–42, usually 41, total vertebrae and 13 or 14 predorsal vertebrae (vs. 37–40, usually 39, and 11–13, usually 12, respectively). Alburnoides holciki and A. namaki are similar in having a sharp scaleless ventral keel but A. holciki is clearly different from the latter species in having a pointed snout and a terminal mouth with the tip of the mouth cleft on a level with the upper half of the pupil (vs. a stout markedly rounded snout, a subterminal mouth with the tip of the mouth cleft on a level below the lower margin of the eye), 40–42, usually 41, total vertebrae (vs. 39–41, usually 40), 13 or 14 predorsal vertebrae (vs. usually 12), and 13–16 ½, usually 14–15 ½, branched anal-fin rays (vs. 10–13 ½, usually 11–12 ½). The new species resembles Alburnoides qanati Coad & Bogutskaya, 2009 in having a terminal upturned mouth but in the latter species the mouth cleft is even more vertical and the tip of the mouth cleft is on about a level with the upper margin of the pupil. Alburnoides holciki differs from A. qanati in having a sharp scaleless ventral keel (vs. smooth and scaled), 13–16 ½ branched anal-fin rays (vs. 10–12 ½). Alburnoides from the Caspian and Aral basins (including presently endorheic drainages such as Murghab, Hari and rivers of the Kopetdag Mountains) contain at least two species described up to now (the third one is being described in this paper), A. eichwaldii (De Filippi, 1863) and A. varentsovi Bogutskaya & Coad, 2009. Alburnoides eichwaldii was originally described from the "Kur presso Tiflis" (= Kura River near Tbilisi, now Georgia), so an Alburnoides from Kura River drainage is a bearer of the name; there is another nominal subspecies in the Aras River (a tributary of the Kura) system of Armenia, Alburnoides bipunctatus armeniensis Dadikyan, 1972, from the rivers Arpa, Vorotan, Vedi, Marmarik, Kasakh and their tributaries, now regarded as a synonym of eichwaldii (Bogutskaya & Coad 2009). Bogutskaya & Coad (2009) made an assumption that riffle minnows from the Safid River drainage and the Amu Darya drainage may represent two distinct species. These issues are outside the goal of this paper; for comparisons that confirm the species status of A. holciki we subdivided the examined samples besides those of A. holciki into seven groups: 1. A. eichwaldii from Kura-Aras and Lenkoran (in the north from the Talysh Mountains), 2. Alburnoides cf. eichwaldii from rivers in the south from the Talysh Mountains and west from the Safid, 3. Alburnoides cf. eichwaldii from the Safid River drainage, 4. Alburnoides sp. from the Tajan River (in the east of the Safid), 5. Alburnoides sp. from the Atrek River drainage, 6. A. varentsovi from rivers of the northern slope of Kopetdag, 7. Alburnoides sp. from the Amu Darya drainage (Tables 2–4, Fig. 3). A UPGMA dendrogram using Kullback-Leibler divergences (Fig. 4) show the grouping of these units based on six meristic characters (the number of branched anal-fin rays and five vertebral counts). Alburnoides holciki is most similar to Alburnoides sp. from the Amu Darya drainage (Fig. 5) by the vertebral counts (Tables 3, 4), the presence of a sharp, scaleless ventral keel, 6–8 gill rakers, and 4 pharyngeal teeth in the long row on the 5 th ceratobranchial, but differs from it in having 13–16 ½, usually 14–15 ½, branched anal-fin rays (vs. 12–14 ½, usually 13 ½), and 46–51 (55) lateral-line scales to posterior margin of hypurals (vs. 43–47 in examined Amu Darya samples). Alburnoides holciki is also similar to the Atrek riffle minnow in having a sharp, scaleless keel, an upturned, terminal mouth (Fig. 6), and 46–51 (55) lateral-line scales to posterior margin of hypurals (45–51 in the Atrek samples). However, the new species differs from the Atrek fish in usually having 4 pharyngeal teeth in the long row on the 5 th ceratobranchial (vs. 5); 14–15 ½ branched anal-fin rays (vs. a mode of 13 ½); 6–8 gill rakers (vs. 9–10); 40–42, usually 41, total vertebrae (vs. 40); (12) 13–14 predorsal vertebrae (vs. 12–13 with a mode of 12); a longer caudal vertebral region, containing (20) 21–22 vertebrae (vs. 20–21 with a mode of 20); and 20 + 21 most usual vertebral formula (vs. 20 + 20). Alburnoides sp. from the Atrek drainage is morphologically very close to the riffle minnow from the Tajan River by anal-fin and vertebral counts (Fig. 4, Tables 2–4), the number of lateral-line scales to posterior margin of hypurals (45–51 in the Atrek samples and 46–53 in the Tajan sample), but differs by the shape of the mouth which is upturned with a pointed snout and a tip of the mouth cleft on a level with the upper half of the pupil (Fig. 6) (vs. a more horizontal, slightly curved mouth with a rounded snout and a tip of the mouth on a level with the lower margin of the pupil, Fig. 7), a sharp and commonly scaleless ventral keel (vs. sharp but variably scaled), and 5 pharyngeal teeth in the long row on the 5 th ceratobranchial (vs. usually 4). This is why we do not consider these samples as conspecific though the Tajan and the Atrek are geographically very close flowing into the south-eastern Caspian Sea. The new species is morphologically close to another geographically close species, A. varentsovi Bogutskaya & Coad, 2009, in having a large eye (the orbit diameter larger than the snout length and about equal to the interorbital width), a triangular-shaped head, and a clearly forked caudal-fin with moderately pointed lobes. But A. holciki is distinguishable from the latter species in having neither lower jaw nor upper jaw protruding relative to each other (vs. a lower jaw slightly protruding over the upper jaw), a sharp scaleless ventral keel (vs. smooth and partly scaleless), most often 2.5–4.2 pharyngeal teeth (vs. commonly 2.5–5.2), 13–16 ½, usually 14–15 ½, branched anal-fin rays (vs. 10–14 ½, usually 12–13 ½), 40–42, usually 41, total vertebrae (vs. 39–41 (42) with a mode of 40), 12–14, with a mode of 13, predorsal vertebrae (vs. 11–13, with a mode of 12), and a caudal vertebral region longer than the abdominal region, most frequent vertebral formulae 20 +21, 20+ 22 and 19 + 21 (vs. usually equal, 20 + 20) (Table 2–4). Alburnoides holciki is distinguishable from A. eichwaldii and Alburnoides sp. from rivers in the south of the Talysh Mountains and the Safid River drainage (Fig. 8) in having an upturned mouth with a tip of the mouth cleft on a level with the upper half of the pupil (vs. a more horizontal, slightly curved or straight but never upturned mouth, with a tip of the mouth cleft on a level with the middle of the eye or below), a pointed snout with a straight upper profile (vs. slightly to markedly rounded), a sharp scaleless keel (vs. smooth and variably scaled, often completely scaled), and usually 14–15 ½ branched anal-fin rays (vs. usually 12 ½ or 13 ½) Vertebral counts are summarised in Tables 3–4.Published as part of Coad, Brian W. & Bogutskaya, Nina G., 2012, A new species of riffle minnow, Alburnoides holciki, from the Hari River basin in Afghanistan and Iran (Actinopterygii: Cyprinidae), pp. 43-55 in Zootaxa 3453 on pages 44-54, DOI: 10.5281/zenodo.21478
COAD-MS Model and Figure 3
No full text<p>COAD-MS Model created by Philip Staudigel.</p><p>Includes the scripts to generate all components of Figure 3. </p><p>Included as part of a manuscript submission.</p>
Comparison of the performance metrics of different classifiers for COAD.
No full textComparison of the performance metrics of different classifiers for COAD.</p
Concerns about the consequences of patenting on scientometric research
No full textOur concerns about the practice of patenting scientometric techniques began with an electronic notification alerting one of us to a patent entitled “Scientometric methods for identifying emerging technologies” (Abercrombie et al., 2015). This came to our attention after we had already embarked on a research program to apply scientometric methods for the identification of emerging technologies here at the JRC.JRC.B.3 - Territorial Developmen
COAD-MS Model and Figure 2,3
No full text<p>COAD-MS Model created by Philip Staudigel.</p>
<p>Includes the scripts to generate all components of Figure 2 and 3. </p>
<p>Science Advances 2024, adn0155</p>
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