Dublin City University participation in the VTT track at TRECVid 2017

Dublin City University participated in the video-to-text caption generation task in TRECVid and this paper describes the three approaches we took for our 4 submitted runs. The first approach is based on extracting regularly-spaced keyframes from a video, generating a text caption for each keyframe and then combining the keyframe captions into a single caption. The second approach is based on detecting image crops from those keyframes using saliency map to include as much of the attractive part of the image as possible, generating a caption for each crop in each keyframe, and combining the captions into one. The third approach is an end-to-end system, a true deep learning submission based on MS-COCO, an externally available set of training captions. The paper presents a description and the official results of each of the approaches

DNA barcoding of marine fish species in the waters surrounding Hainan Island, northern South China Sea

IntroductionHainan Island is encompassed within the shallow waters of the tropical continental shelf in China, which is recognized as a significant hotspot for fish biodiversity. Despite extensive research conducted on marine fish taxonomy surrounding Hainan Island, there remains a substantial gap between our current understanding and the actual fish diversity within this oceanic area.MethodsIn this study, we employed DNA barcoding and molecular identification approaches to explore the species diversity and distribution pattern of marine fish in both the northern and southern sea areas of Hainan Island in the northern South China Sea.ResultsA total of 186 sequences were obtained from the collected marine fish samples in the two sea areas surrounding Hainan Island. Through DNA identification, it was confirmed that all 186 sequences corresponded to typical fish species found in the northern South China Sea, all sequences represented a total of 56 species, 47 genera, 34 families, and 17 orders. The average Kimura 2-parameter (K2P) distances within species, genus, family, order and class were 0.15%, 6.53%, 13.17%, 16.95% and 24.81%, respectively.DiscussionOur investigation in the northern sea areas of Hainan Islands identified a total of 33 distinct species, while the southern sea areas exhibited 29 distinct species, with only 5 species found to be shared between both regions. These findings clearly indicate a significant disparity in the species composition of fish communities between the northern and southern sea regions

Effects of antibiotic resistance, drug target attainment, bacterial pathogenicity and virulence, and antibiotic access and affordability on outcomes in neonatal sepsis: an international microbiology and drug evaluation prospective substudy (BARNARDS)

Background Sepsis is a major contributor to neonatal mortality, particularly in low-income and middle-income countries (LMICs). WHO advocates ampicillin–gentamicin as first-line therapy for the management of neonatal sepsis. In the BARNARDS observational cohort study of neonatal sepsis and antimicrobial resistance in LMICs, common sepsis pathogens were characterised via whole genome sequencing (WGS) and antimicrobial resistance profiles. In this substudy of BARNARDS, we aimed to assess the use and efficacy of empirical antibiotic therapies commonly used in LMICs for neonatal sepsis. Methods In BARNARDS, consenting mother–neonates aged 0–60 days dyads were enrolled on delivery or neonatal presentation with suspected sepsis at 12 BARNARDS clinical sites in Bangladesh, Ethiopia, India, Pakistan, Nigeria, Rwanda, and South Africa. Stillborn babies were excluded from the study. Blood samples were collected from neonates presenting with clinical signs of sepsis, and WGS and minimum inhibitory concentrations for antibiotic treatment were determined for bacterial isolates from culture-confirmed sepsis. Neonatal outcome data were collected following enrolment until 60 days of life. Antibiotic usage and neonatal outcome data were assessed. Survival analyses were adjusted to take into account potential clinical confounding variables related to the birth and pathogen. Additionally, resistance profiles, pharmacokinetic–pharmacodynamic probability of target attainment, and frequency of resistance (ie, resistance defined by in-vitro growth of isolates when challenged by antibiotics) were assessed. Questionnaires on health structures and antibiotic costs evaluated accessibility and affordability. Findings Between Nov 12, 2015, and Feb 1, 2018, 36 285 neonates were enrolled into the main BARNARDS study, of whom 9874 had clinically diagnosed sepsis and 5749 had available antibiotic data. The four most commonly prescribed antibiotic combinations given to 4451 neonates (77·42%) of 5749 were ampicillin–gentamicin, ceftazidime–amikacin, piperacillin–tazobactam–amikacin, and amoxicillin clavulanate–amikacin. This dataset assessed 476 prescriptions for 442 neonates treated with one of these antibiotic combinations with WGS data (all BARNARDS countries were represented in this subset except India). Multiple pathogens were isolated, totalling 457 isolates. Reported mortality was lower for neonates treated with ceftazidime–amikacin than for neonates treated with ampicillin–gentamicin (hazard ratio [adjusted for clinical variables considered potential confounders to outcomes] 0·32, 95% CI 0·14–0·72; p=0·0060). Of 390 Gram-negative isolates, 379 (97·2%) were resistant to ampicillin and 274 (70·3%) were resistant to gentamicin. Susceptibility of Gram-negative isolates to at least one antibiotic in a treatment combination was noted in 111 (28·5%) to ampicillin–gentamicin; 286 (73·3%) to amoxicillin clavulanate–amikacin; 301 (77·2%) to ceftazidime–amikacin; and 312 (80·0%) to piperacillin–tazobactam–amikacin. A probability of target attainment of 80% or more was noted in 26 neonates (33·7% [SD 0·59]) of 78 with ampicillin–gentamicin; 15 (68·0% [3·84]) of 27 with amoxicillin clavulanate–amikacin; 93 (92·7% [0·24]) of 109 with ceftazidime–amikacin; and 70 (85·3% [0·47]) of 76 with piperacillin–tazobactam–amikacin. However, antibiotic and country effects could not be distinguished. Frequency of resistance was recorded most frequently with fosfomycin (in 78 isolates [68·4%] of 114), followed by colistin (55 isolates [57·3%] of 96), and gentamicin (62 isolates [53·0%] of 117). Sites in six of the seven countries (excluding South Africa) stated that the cost of antibiotics would influence treatment of neonatal sepsis

The complete mitochondrial genome of bullet tuna (Auxis rochei) from South China Sea

Auxis rochei is one of genus Auxis and widely distributed in tropical and subtropical waters. In this study, we described the complete mitochondrial genome of A. rochei. The genome is 16505 bp in length, encoding the standard set of 13 protein-coding genes, 21 transfer RNA genes, two ribosomal RNA genes, and a non-coding D-loop, with circular organization. The overall base composition of the whole mitochondrial genome was A (27.92%), T (25.01%), G (17.09%), and C (29.98%) with an AT bias of 52.94%. The longest protein-coding genes of these species was ND5, whereas the shortest ATP8

The complete mitochondrial genome of frigate tuna (Auxis thazard) from South China Sea

Auxis thazard is one of genus Auxis and widely distributed in tropical and subtropical waters. In this study, we described the complete mitochondrial genome of Auxis thazard. The genome is 16,506 bp in length, encoding the standard set of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and a non-coding D-loop, with a circular organization. The overall base composition of the whole mitochondrial genome was A (27.86%), T (24.88%), G (17.16%), and C (30.10%) with an AT bias of 52.94%. The longest protein-coding genes of these species was ND5, whereas the shortest ATP8

The complete mitochondrial genome of oceanic puffer (Lagocephalus lagocephalus) from South China Sea

Lagocephalus lagocephalus is one of genus Lagocephalus and widely distributed in tropical and temperate oceans. In this study, we described the complete mitochondrial genome of L. lagocephalus. The genome is 166,443 bp in length, encoding the standard set of 13 protein-coding genes (PCGs), 22 transfer RNA genes, 2 ribosomal RNA genes, and a non-coding D-loop, with circular organization. The overall base composition of the whole mitochondrial genome was A (27.95%), T (25.07%), G (16.14%), and C (30.83%) with an AT bias of 53.03%. The longest PCG of these species was ND5, whereas the shortest ATP8

The complete mitochondrial genome of loliginid squid (Uroteuthis chinensis) from Minnan–Taiwan bank fishing ground

The squid Uroteuthis chinensis is commercially important fishery species in many coastal regions of Asia. In this study, we described the complete mitochondrial genome of U. chinensis. The genome is 17,353 bp in length, encoding the standard set of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, with circular organization. The overall base composition of the whole mitochondrial genome was A (39.56%), T (31.71%), G (9.05%) and C (19.68%) with an AT bias of 71.27%. The longest protein-coding genes of these species was ND5, whereas the shortest ATP8

Trophic connectivity between intertidal and offshore food webs in Mirs Bay, China

Summary: Trophic interactions are common worldwide, both within and between ecosystems. This study elucidated the trophic connectivity between intertidal and offshore zone, in Mirs Bay, China. The contributions of offshore suspended particulate organic matter (SPOM), intertidal macroalgae and epiphytes to consumer biomass were assessed, and the trophic pathways were identified through the use of stable isotope ratios of carbon (δ13C) and nitrogen (δ15N) of basal sources and consumers. Mean δ13C values of basal sources had a wide range (−19.6‰ to −11.8‰) and were generally well separated in Mirs Bay. The average δ13C of consumers in Mirs Bay ranged from −19.2‰ to −11.8‰, reflecting a carbon source integrated from different primary producer signals. IsoSource model solutions indicated consumers assimilated organic carbon from a mixture of basal sources. Offshore SPOM carbon was the primary carbon source supporting most consumers in both intertidal and offshore zones. Intertidal macroalgae and epiphytes also accounted for a large fraction for some consumers. δ15N data indicated 5 trophic levels in Mirs Bay. Intertidal consumers, except for Capitulum mitella, had a TP (trophic position) between 2 and 3, and mainly included filter-feeders and grazers. In contrast, almost all offshore consumers had a TP of between 3 and 4 except for filter-feeders (zooplankton), planktivores (Clupanodon punctatus and Sardinella aurita) and piscivores (Gymnura japonica). The basal sources fueled consumers through two trophic pathways, each of which involved organisms of both intertidal and offshore zones, implying trophic connectivity between them in the Mirs Bay ecosystem. Keywords: Food webs, Trophic connectivity, Carbon pathways, Stable isotopes, Mirs Ba

Abacus Training Modulates the Neural Correlates of Exact and Approximate Calculations in Chinese Children: An fMRI Study

Exact (EX) and approximate (AP) calculations rely on distinct neural circuits. However, the training effect on the neural correlates of EX and AP calculations is largely unknown, especially for the AP calculation. Abacus-based mental calculation (AMC) is a particular arithmetic skill that can be acquired by long-term abacus training. The present study investigated whether and how the abacus training modulates the neural correlates of EX and AP calculations by functional magnetic resonance imaging (fMRI). Neural activations were measured in 20 abacus-trained and 19 nontrained Chinese children during AP and EX calculation tasks. Our results demonstrated that: (1) in nontrained children, similar neural regions were activated in both tasks, while the size of activated regions was larger in AP than those in the EX; (2) in abacus-trained children, no significant difference was found between these two tasks; (3) more visuospatial areas were activated in abacus-trained children under the EX task compared to the nontrained. These results suggested that more visuospatial strategies were used by the nontrained children in the AP task compared to the EX; abacus-trained children adopted a similar strategy in both tasks; after long-term abacus training, children were more inclined to apply a visuospatial strategy during processing EX calculations