Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparison of widefield swept-source optical coherence tomography angiography with ultra-widefield colour fundus photography and fluorescein angiography for detection of lesions in diabetic retinopathy

Aims To compare widefield swept-source optical coherence tomography angiography (WF SS-OCTA) with ultra-widefield colour fundus photography (UWF CFP) and fluorescein angiography (UWF FA) for detecting diabetic retinopathy (DR) lesions. Methods This prospective, observational study was conducted at Massachusetts Eye and Ear from December 2018 to October 2019. Proliferative DR, non-proliferative DR and diabetic patients with no DR were included. All patients were imaged with a WF SS-OCTA using a Montage 15×15 mm scan. UWF CFP and UWF FA were taken by a 200°, single capture retinal imaging system. Images were independently evaluated for the presence or absence of DR lesions including microaneurysms (MAs), intraretinal microvascular abnormalities (IRMAs), neovascularisation elsewhere (NVE), neovascularisation of the optic disc (NVD) and non-perfusion areas (NPAs). All statistical analyses were performed using SPSS V.25. 0. Results One hundred and fifty-two eyes of 101 participants were included in the study. When compared with UWF CFP, WF SS-OCTA was found to be superior in detecting IRMAs (p<0.001) and NVE/NVD (p=0.007). The detection rates of MAs, IRMAs, NVE/NVD and NPAs in WF SS-OCTA were comparable with UWF FA images (p>0.05). Furthermore, when we compared WF SS-OCTA plus UWF CFP with UWF FA, the detection rates of MAs, IRMAs, NVE/NVD and NPAs were identical (p>0.005). Agreement (κ=0.916) between OCTA and FA in classifying DR was excellent. Conclusion WF SS-OCTA is useful for identification of DR lesions. WF SS-OCTA plus UWF CFP may offer a less invasive alternative to FA for DR diagnosis.
Caregiver anxiety and the association with acute postoperative pain in children undergoing elective ambulatory surgery in a lower‐middle‐income country setting

Moderate to severe postoperative pain complicates surgeries performed on children in upper‐income countries. The successful management of postoperative pain in children requires a biopsychosocial approach. Situational anxiety and anxiety disorders among caregivers influence a child's perioperative experience. This study aims to determine whether there is an association between caregiver's preoperative anxiety and children's postoperative pain in a lower‐middle‐income country (LMIC) setting.
KEY TO ADULT MALES OF CONIFER-FEEDING SPECIES OF CHORISTONEURA LEDERER (LEPIDOPTERA: TORTRICIDAE) IN CANADA AND ALASKA

Abstract A key, based on morphological characters of adult males, separating six traditionally recognized conifer-feeding Choristoneura species, C. pinus Freeman, C. lambertiana (Busck), C. fumiferana (Clemens), C. occidentalis Freeman, C. biennis Freeman, and C. orae Freeman occurring in Canada and Alaska is provided and illustrated. The newly discovered morphological features, the aedeagus of C. fumiferana and C. pinus with a short apical spine and with many microscopic spicules on the distal half, are used to separate these two species from their western allies C. occidentalis, C. biennis and.C. orae. Résumé L'auteur fournit une clef de détermination illustrée basée sur les caractères morphologiques des adultes mâles pour séparer les six espèces du genre Choristoneura traditionnellement reconnues comme des ravageurs des conifères du Canada et de l'Alaska, C. pinus Freeman, C. lambertiana (Busck), C. fumiferana (Clemens), C. occidentalis Freeman, C. biennis Freeman et C. orae Freeman. Les nouveaux caractères morphologiques, soit l'édéage du C. fumiferana et du C. pinus avec une épine apicale courte et la présence de spicules microscopiques sur la moitié distale de l'édéage, permettent de séparer ces deux espèces des C. occidentalis, C. biennis et C. orae.
AMP‐activated protein kinase activator AICAR attenuates hypoxia‐induced murine fetal growth restriction in part by improving uterine artery blood flow

Pregnancy at high altitude is associated with a greater incidence of fetal growth restriction due, in part, to lesser uterine artery blood flow. AMP‐activated protein kinase (AMPK) activation vasodilates arteries and may increase uterine artery blood flow. In this study, pharmacological activation of AMPK by the drug AICAR improved fetal growth and elevated uterine artery blood flow. These results suggest that AMPK activation is a potential strategy for improving fetal growth and raising uterine artery blood flow in pregnancy, which may be important in pregnancy disorders characterized by uteroplacental ischaemia and/or fetal hypoxia.
Molecular Phylogeny and Infrageneric Classification of Actinidia (Actinidiaceae)

Abstract Nuclear ribosomal DNA internal transcribed spacers (ITS) and chloroplast matK gene were sequenced for 23 species of Actinidia, the genus of kiwifruit. Neither ITS nor matK phylogeny supports monophyly of any of the four sections of the genus. Species of section Leiocarpae form a paraphyletic group at the base of both gene trees. Species of sections Maculatae, Strigosae, and Stellatae plus A. rufa of section Leiocarpae form a monophyletic group, which is consistent with the morphological feature of presence of lenticels on fruit exocarps. Within this clade, however, each of the three sections is polyphyletic on both gene phylogenies. Polymorphic ITS sequences were cloned from 17 of 27 accessions sampled in this study. The polymorphic sequences that are distantly related on the phylogeny may have derived from hybridization or introgression. The infrageneric classification of Actinidia should be revised on the basis of a robust phylogenetic reconstruction inferred from additional molecular, morphological, and cytological data. Communicating Editor: Matt Lavin
Fiber-Specific Changes in White Matter Microstructure in Individuals With X-Linked Auditory Neuropathy.

OBJECTIVES Auditory neuropathy (AN) is the term used to describe a group of hearing disorders, in which the hearing impairment occurs as a result of abnormal auditory nerve function. While our understanding of this condition has advanced significantly over recent years, the ability to determine the site of lesion and the extent of dysfunction in affected individuals remains a challenge. To this end, we investigated potential axonal degeneration in the white matter tracts of the brainstem in individuals with X-linked AN. We hypothesized that individuals with X-linked AN would show focal degeneration within the VIII nerve and/or auditory brainstem tracts, and the degree of degeneration would correlate with the extent of auditory perceptual impairment. DESIGN This was achieved using a higher-order diffusion magnetic resonance imaging (dMRI)-based quantitative measure called apparent fiber density as obtained from a technique called single-shell 3-tissue constrained spherical deconvolution and analyzed with the fixel-based analysis framework. Eleven subjects with genetically confirmed X-linked AN and 11 controls with normal hearing were assessed using behavioral and objective auditory measures. dMRI data were also collected for each participant. RESULTS Fixel-based analysis of the brainstem region showed that subjects with X-linked AN had significantly lower apparent fiber density in the VIII nerve compared with controls, consistent with axonal degeneration in this region. Subsequent analysis of the auditory brainstem tracts specifically showed that degeneration was also significant in these structures overall. The apparent fiber density findings were supported by objective measures of auditory function, such as auditory brainstem responses, electrocochleography, and otoacoustic emissions, which showed VIII nerve activity was severely disrupted in X-linked AN subjects while cochlear sensory hair cell function was relatively unaffected. Moreover, apparent fiber density results were significantly correlated with temporal processing ability (gap detection task) in affected subjects, suggesting that the degree of VIII nerve degeneration may impact the ability to resolve temporal aspects of an acoustic signal. Auditory assessments of sound detection, speech perception, and the processing of binaural cues were also significantly poorer in the X-linked AN group compared with the controls with normal hearing. CONCLUSIONS The results of this study suggest that the dMRI-based measure of apparent fiber density may provide a useful adjunct to existing auditory assessments in the characterization of the site of lesion and extent of dysfunction in individuals with AN. Additionally, the ability to determine the degree of degeneration has the potential to guide rehabilitation strategies in the future.
How Data ScientistsWork Together With Domain Experts in Scientific Collaborations

In recent years there has been an increasing trend in which data scientists and domain experts work together to tackle complex scientific questions. However, such collaborations often face challenges. In this paper, we aim to decipher this collaboration complexity through a semi-structured interview study with 22 interviewees from teams of bio-medical scientists collaborating with data scientists. In the analysis, we adopt the Olsons' four-dimensions framework proposed in Distance Matters to code interview transcripts. Our findings suggest that besides the glitches in the collaboration readiness, technology readiness, and coupling of work dimensions, the tensions that exist in the common ground building process influence the collaboration outcomes, and then persist in the actual collaboration process. In contrast to prior works' general account of building a high level of common ground, the breakdowns of content common ground together with the strengthen of process common ground in this process is more beneficial for scientific discovery. We discuss why that is and what the design suggestions are, and conclude the paper with future directions and limitations.
Effect of eutrophication on air–sea CO2 fluxes in the coastal Southern North Sea: a model study of the past 50 years

The RIVERSTRAHLER model, an idealized biogeochemical model of the river system, has been coupled to MIRO‐CO2, a complex biogeochemical model describing diatom and Phaeocystis blooms and carbon and nutrient cycles in the marine domain, to assess the dual role of changing nutrient loads and increasing atmospheric CO2 as drivers of air–sea CO2 exchanges in the Southern North Sea with a focus on the Belgian coastal zone (BCZ). The whole area, submitted to the influence of two main rivers (Seine and Scheldt), is characterized by variable diatom and Phaeocystis colonies blooms which impact on the trophic status and air–sea CO2 fluxes of the coastal ecosystem. For this application, the MIRO‐CO2 model is implemented in a 0D multibox frame covering the eutrophied Eastern English Channel and Southern North Sea and receiving loads from the rivers Seine and Scheldt. Model simulations are performed for the period between 1951 and 1998 using real forcing fields for sea surface temperature, wind speed and atmospheric CO2 and RIVERSTRAHLER simulations for river carbon and nutrient loads. Model results suggest that the BCZ shifted from a source of CO2 before 1970 (low eutrophication) towards a sink during the 1970–1990 period when anthropogenic DIN and P loads increased, stimulating C fixation by autotrophs. In agreement, a shift from net annual heterotrophy towards autotrophy in BCZ is simulated from 1980. The period after 1990 is characterized by a progressive decrease of P loads concomitant with a decrease of primary production and of the CO2 sink in the BCZ. At the end of the simulation period, the BCZ ecosystem is again net heterotroph and acts as a source of CO2 to the atmosphere. R‐MIRO‐CO2 scenarios testing the relative impact of temperature, wind speed, atmospheric CO2 and river loads variability on the simulated air–sea CO2 fluxes suggest that the trend in air–sea CO2 fluxes simulated between 1951 and 1998 in the BCZ was mainly controlled by the magnitude and the ratio of inorganic nutrient river loads. Quantitative nutrient changes control the level of primary production while qualitative changes modulate the relative contribution of diatoms and Phaeocystis to this flux and hence the sequestration of atmospheric CO2.
Association of polymorphism of the alpha 1-antitrypsin gene with milk production traits in Chinese Holstein

Protein degradation in bovine milk affects the quality of dairy products. Alpha 1-antitrypsin (AAT) can protect vulnerable elastic tissues from degradation by neutrophil elastase. The aim of this study was to assess the association of polymorphisms in bovine AAT gene with milk yield and milk composition in Chinese Holstein. Traits analyzed were fat percentage, protein percentage, 305-day milk yield and somatic cell score (SCS). Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP), created restriction site-polymerase chain reaction (CRS-PCR) and allele specific-polymerase chain reaction (AS-PCR) methods were used to genotype five loci in coding regions of the sequence, including position 5504, 5609, 5624, 5747 and 8178 in Chinese Holstein. The five mutations were all silent mutation that caused no alteration in the amino acid sequence. In order to determine the relationship between the polymorphisms of the AAT gene and milk production traits and SCS, the General Linear Model (GLM) procedure from the Statistical Analysis Software was used. SNP5504 affected milk fat percentage, SNP8178 affected milk protein percentage and SNP5609 and SNP5624 affected 305-day milk yield. These results suggest that AAT is a candidate gene that influences milk production traits and it could be implemented in breeding programmes to improve the production performance of Chinese Holstein cattle. Keywords : Dairy cattle, α1-protease inhibitor, SNPs, milk traits, somatic cell score
Digital cementum luminance analysis (DCLA): a tool for the analysis of climatic and seasonal signals in dental cementum

Cementum banding patterns have been used by archaeozoologists and wildlife managers for a number of decades to assess the season and age at death of mammalian populations. However, the observation and measurement of the nature of cementum banding, especially that of the final band, has proved to be difficult except under conditions of excellent preservation and advanced microscopy. The research presented here details a method for extracting luminance data from the banding patterns of cementum in order to quantify the optical properties of cementum tissue. By doing so, analysis of the relationship between cementum deposition and environmental variables is achieved. We present the results of a digital cementum luminance analysis (DCLA) on a sample of first molars from two species, Ovis aries, Soay and Capra ibex. The results indicate that significant relationships occur between seasonal temperature changes and cementum histology. Furthermore, we show that luminance values can be used to assess the geographical range of genetically similar populations. Our results demonstrate that the study of luminance is a vital tool for the quantitative study of dental cementum for both archaeological and ecological studies. Copyright © 2007 John Wiley & Sons, Ltd.
Storage Protein Patterns in Somatic and Zygotic Embryos of Lentil (Lens culinaris Medik.)

In a program aimed at developing a reproducible transformation-capableregeneration system for lentil only somatic embryo-like bodies (SEB) were obtained. In order to find out whether SEBs are true somatic embryos, storage protein patterns in somatic and zygotic lentil embryos were compared by SDSPAGE and Western blot analysis. As control, proteins from lentil leaves as well as zygotic embryos were investigated. As no lentil-specific antibodies were available, four different polyclonal antibodies against each of the major storage protein families in pea (legumin, vicilin, phaseolin and glycinin) were applied. The storage protein patterns found in zygotic embryos were also found to occur in somatic embryos. No specific signals were observed in leaf extracts.
Effects of a local auxiliary protein on the two-dimensional affinity of a TCR–peptide MHC interaction

ABSTRACT The affinity of T-cell receptors (TCRs) for major histocompatibility complex molecules (MHCs) presenting cognate antigens likely determines whether T cells initiate immune responses, or not. There exist few measurements of two-dimensional (2D) TCR–MHC interactions, and the effect of auxiliary proteins on binding is unexplored. Here, Jurkat T-cells expressing the MHC molecule HLA-DQ8-glia-α1 and the ligand of an adhesion protein (rat CD2) were allowed to bind supported lipid bilayers (SLBs) presenting fluorescently labelled L3-12 TCR and rat CD2, allowing measurements of binding unconfounded by cell signaling effects or co-receptor binding. The 2D Kd for L3-12 TCR binding to HLA-DQ8-glia-α1, of 14±5 molecules/μm2 (mean±s.d.), was only marginally influenced by including CD2 up to ∼200 bound molecules/μm2 but higher CD2 densities reduced the affinity up to 1.9-fold. Cell–SLB contact size increased steadily with ligand density without affecting binding for contacts at up to ∼20% of total cell area, but beyond this lamellipodia appeared, giving an apparent increase in bound receptors of up to 50%. Our findings show how parameters other than the specific protein–protein interaction can influence binding behavior at cell–cell contacts. Summary: Two-dimensional affinity measurements of a T-cell receptor binding its agonistic peptide major histocompatibility complex molecule and the influence of cellular context.
Loss of Function of an RNA Polymerase III Subunit Leads to Impaired Maize Kernel Development1[OPEN]

ZmNRPC2 affects RNAPIII activity and regulates the expression of genes involved in cell proliferation and endoreduplication to control maize kernel development. Kernel size is an important factor determining grain yield. Although a number of genes affecting kernel development in maize (Zea mays) have been identified by analyzing kernel mutants, most of the corresponding mutants cannot be used in maize breeding programs due to low germination or incomplete seed development. Here, we characterized small kernel7, a recessive small-kernel mutant with a mutation in the gene encoding the second-largest subunit of RNA polymerase III (RNAPΙΙΙ; NRPC2). A frame shift in ZmNRPC2 leads to a premature stop codon, resulting in significantly reduced levels of transfer RNAs and 5S ribosomal RNA, which are transcribed by RNAPΙΙΙ. Loss-of-function nrpc2 mutants created by CRISPR/CAS9 showed significantly reduced kernel size due to altered endosperm cell size and number. ZmNRPC2 affects RNAPIII activity and the expression of genes involved in cell proliferation and endoreduplication to control kernel development via physically interacting with RNAPIII subunits RPC53 and AC40, transcription factor class C1 and Floury3. Notably, unlike the semidominant negative mutant floury3, which has defects in starchy endosperm, small kernel7 only affects kernel size but not the composition of kernel storage proteins. Our findings provide novel insights into the molecular network underlying maize kernel size, which could facilitate the genetic improvement of maize in the future.
Evaluation of a new cropping option using a participatory approach with on-farm monitoring and simulation: a case study of spring-sown mungbeans

In the northern Australian cropping region, mungbean is commonly sown as an opportunity crop, usually on low soil water after a winter cereal, and consequently has a reputation for being a low yielding, high risk crop. Yield prospects could be improved and risks reduced if it was sown on soils with a higher soil water content, for instance in spring after a winter fallow. However, there is a lack of experience and confidence in alternative roles for mungbean in the farming system. This paper describes a research approach involving researchers, farmers, advisers, and grain traders in which on-farm monitoring of spring-sown commercial crops and cropping systems simulation with APSIM were used to explore yield prospects for a spring-sown crop after a winter fallow. The key elements of the approach are: (1) identification of possible options through simulation of scenarios, (2) testing the new practice with innovative farmers, and (3) monitoring of the management and performance of commercial crops and comparing yields with benchmarks estimated with a model. In this case, after 2 years of on-farm testing, spring- sown mungbean has been shown to have a potential for high returns in the northern cropping systems.
Comparison of ingredient usage and formula costs in poultry feeds using different amino acid digestibility databases

SUMMARY This study showed how using different database values for digestible amino acid contents influences ingredient usage and feed costs for broiler, layer, and turkey diets with recent ingredient costs from the United States and Pakistan. A series of feeds were formulated to compare results from using 2 commercial ingredient composition databases: Ajinomoto Heartland (AH; rooster assay values) and Evonik Degussa (ED; chick assay values). The ingredient composition matrix was based on NRC (1994) tables, except for digestible amino acids and protein. Requirements were for a broiler starter (Ross), broiler finisher (Cobb), turkey starter (Nicholas), turkey finisher (British United Turkeys), and leghorn prelay (ISA) and peak (Hy-Line) diets. Costs were local market prices in Pakistan (June 2010) and average US prices (2009). Formula costs were higher using the ED digestible amino acid values, ranging from $1.00/ton for the turkey finisher diet to $8.40/ton for the turkey starter diet. The broiler starter and finisher diets were $6.20 and $2.60/ton higher using the ED digestible amino acid values. Differences in formulation costs were due to higher levels of supplemental amino acids and soybean meal when using the ED database. The shadow prices of distillers dried grains with solubles ranged from $199.50/ton in the turkey starter diet, with AH digestible amino acid values, to $266.20/ton in the leghorn prelay diet, with AH digestible amino acid values. Not knowing the digestible amino acid levels in feed ingredients or choosing inappropriate digestible amino acid values may result (at least) in inefficiencies averaging $3.00 to $4.00/ton of finished feed for broilers, layers, and turkeys (approximately $6.00 for starter feed and $3.00 for finisher feed). Comparative values are similar for dollars and rupees. Differences in feed costs from using the different digestibility values can give an estimate of potential savings (costs) from using one particular database vs. the other. The cost difference may be used to demonstrate the magnitude of research monies that should be dedicated to estimating amino acid digestibility values most accurately.