Miracle-dz/UniFAR-FTUs huggingface dataset:
Effectiveness of “rescue saccades” on the accuracy of tracking multiple moving targets: An eye-tracking study on the effects of target occlusions

Occlusion is one of the main challenges in tracking multiple moving objects. In almost all real-world scenarios, a moving object or a stationary obstacle occludes targets partially or completely for a short or long time during their movement. A previous study (Zelinsky & Todor, 2010) reported that subjects make timely saccades toward the object in danger of being occluded. Observers make these so-called “rescue saccades” to prevent target swapping. In this study, we examined whether these saccades are helpful. To this aim, we used as the stimuli recorded videos from natural movement of zebrafish larvae swimming freely in a circular container. We considered two main types of occlusion: object-object occlusions that naturally exist in the videos, and object-occluder occlusions created by adding a stationary doughnut-shape occluder in some videos. Four different scenarios were studied: (1) no occlusions, (2) only object-object occlusions, (3) only object-occluder occlusion, or (4) both object-object and object-occluder occlusions. For each condition, two set sizes (two and four) were applied. Participants’ eye movements were recorded during tracking, and rescue saccades were extracted afterward. The results showed that rescue saccades are helpful in handling object-object occlusions but had no reliable effect on tracking through object-occluder occlusions. The presence of occlusions generally increased visual sampling of the scenes; nevertheless, tracking accuracy declined due to occlusion.
USGS44, a new high‐purity calcium carbonate reference material for δ 13C measurements

Rationale The stable carbon isotopic (δ 13C) reference material (RM) LSVEC Li2CO3 has been found to be unsuitable for δ 13C standardization work because its δ 13C value increases with exposure to atmospheric CO2. A new CaCO3 RM, USGS44, has been prepared to alleviate this situation. Methods USGS44 was prepared from 8 kg of Merck high‐purity CaCO3. Two sets of δ 13C values of USGS44 were determined. The first set of values was determined by online combustion, continuous‐flow (CF) isotope‐ratio mass spectrometry (IRMS) of NBS 19 CaCO3 (δ 13CVPDB = +1.95 milliurey (mUr) exactly, where mUr = 0.001 = 1‰), and LSVEC Li2CO3 (δ 13CVPDB = −46.6 mUr exactly), and normalized to the two‐anchor δ 13CVPDB‐LSVEC isotope‐delta scale. The second set of values was obtained by dual‐inlet (DI)‐IRMS of CO2 evolved by reaction of H3PO4 with carbonates, corrected for cross contamination, and normalized to the single‐anchor δ 13CVPDB scale. Results USGS44 is stable and isotopically homogeneous to within 0.02 mUr in 100‐μg amounts. It has a δ 13CVPDB‐LSVEC value of −42.21 ± 0.05 mUr. Single‐anchor δ 13CVPDB values of −42.08 ± 0.01 and −41.99 ± 0.02 mUr were determined by DI‐IRMS with corrections for cross contamination. Conclusions The new high‐purity, well‐homogenized calcium carbonate isotopic reference material USGS44 is stable and has a δ 13CVPDB‐LSVEC value of −42.21 ± 0.05 mUr for both EA/IRMS and DI‐IRMS measurements. As a carbonate relatively depleted in 13C, it is intended for daily use as a secondary isotopic reference material to normalize stable carbon isotope delta measurements to the δ 13CVPDB‐LSVEC scale. It is useful in quantifying drift with time, determining mass‐dependent isotopic fractionation (linearity correction), and adjusting isotope‐ratio‐scale contraction. Due to its fine grain size (smaller than 63 μm), it is not suitable as a δ 18O reference material. A δ 13CVPDB‐LSVEC value of −29.99 ± 0.05 mUr was determined for NBS 22 oil.
MARGRA Lamb Eating Quality and Human Health-Promoting Omega-3 Long-Chain Polyunsaturated Fatty Acid Profiles of Tattykeel Australian White Sheep: Linebreeding and Gender Effects

Health-conscious consumers increasingly demand healthier, tastier, and more nutritious meat, hence the continuous need to meet market specifications and demand for high-quality lamb. We evaluated the longissimus dorsi muscle of 147 Tattykeel Australian White (TAW) sheep fed on antioxidant-rich ryegrass pastures exclusive to MAGRA lamb brand for meat eating quality parameters of intramuscular fat (IMF) content, fat melting point (FMP) and omega-3 long-chain polyunsaturated fatty acids (n-3 LC-PUFA). The aim was to assess the impact of linebreeding and gender on pasture-fed lamb eating quality and to test the hypothesis that variation in healthy lamb eating quality is a function of lamb gender and not its antioxidant status or inbreeding coefficient (IC). After solid-phase extraction and purification, phenolics and antioxidant enzyme activities were analysed by high-performance liquid chromatography and mass spectrometry. IMF and fatty acid composition were determined using solvent extraction and gas chromatography, respectively. IC was classified into low (0–5%), medium (6–10%) and high (>10%) and ranged from 0–15.6%. FMP and IMF ranged from 28 to 39 °C and 3.4% to 8.2%, with overall means of 34.6 ± 2.3 °C and 4.4 ± 0.2%, respectively, and n-3 LC-PUFA ranged from “source” to “good source” levels of 33–69 mg/100 g. Ewes had significantly (P ˂ 0.0001) higher IMF, C22:5n-3 (DPA), C22:6n-3 (DHA), C18:3n-6, C20:3, C22:4n-6, C22:5n-6, total monounsaturated (MUFA), PUFA and Σn-3 fatty acids and lower total saturated fatty acids (SFA) and FMP, than rams. As IC increased, there were no differences in FMP and IMF. Folin–Ciocalteu total phenolics, ferric reducing antioxidant power and antioxidant activities of glutathione peroxidase, catalase and superoxide dismutase enzymes did not differ by either gender or IC. This study provides evidence that IC is inconsequential in affecting antioxidant status, IMF, FMP and n-3 LC-PUFA in linebred and pasture-fed TAW sheep because the observed variation in individual fatty acids was mainly driven by gender differences between ewes and rams, hence the need to accept the tested hypothesis. This finding reinforces the consistent healthy eating quality of MARGRA lamb brand from TAW sheep regardless of its linebred origin.
Functional tests associated with sarcopenia in moderate chronic obstructive pulmonary disease

ABSTRACT Objectives: To evaluate the association of physical and functional measures with sarcopenia in moderate chronic obstructive pulmonary disease (COPD) and to establish cutoff points for sarcopenia screening. Methods: The study included COPD with and without sarcopenia, of both sexes who were over 50 years old. Participants were assessed for lung function, body composition, grip strength, Short Physical Performance Battery (SPPB), 5-repetition, 10-repetition and 30-s sit-to-stand tests (5STS, 10STS, and 30STS, respectively). In addition, 6-min walking test, respiratory muscular strength, and physical activity level were tested. Results: The study had 35 participants, 24 men (68.6%) and moderate COPD (51.4%). COPD-sarcopenia showed lower values in lean mass, body fat and body mass alongside lower performance in 10 and 30 STS tests, SPPB and gait speed compared to non-sarcopenic group. The cutoff points with better sensitivity and specificity to identify sarcopenia were 10.88 and 34.14 s, 15 repetitions, and 10 points in the 5STS, 10STS, 30STS, and SPPB, respectively. The comparison of the receiver operating curves evidenced no differences between the functional tests. Only 30STS and SPPB showed acceptable discriminatory power. Conclusion: Functional tests, especially 30STS and SPPB, are simple and affordable tools for screening sarcopenia in COPD with moderate obstruction.
National inter-rater agreement of standardised simulated-patient-based assessments

Abstract Purpose The forthcoming UK Medical Licensing Assessment will require all medical schools in the UK to ensure that their students pass an appropriately designed Clinical and Professional Skills Assessment (CPSA) prior to graduation and registration with a licence to practice medicine. The requirements for the CPSA will be set by the General Medical Council, but individual medical schools will be responsible for implementing their own assessments. It is therefore important that assessors from different medical schools across the UK agree on what standard of performance constitutes a fail, pass or good grade. Methods We used an experimental video-based, single-blinded, randomised, internet-based design. We created videos of simulated student performances of a clinical examination at four scripted standards: clear fail (CF), borderline (BD), clear pass (CPX) and good (GD). Assessors from ten regions across the UK were randomly assigned to watch five videos in 12 different combinations and asked to give competence domain scores and an overall global grade for each simulated candidate. The inter-rater agreement as measured by the intraclass correlation coefficient (ICC) based on a two-way random-effects model for absolute agreement was calculated for the total domain scores. Results 120 assessors enrolled in the study, with 98 eligible for analysis. The ICC was 0.93 (95% CI 0.81–0.99). The mean percentage agreement with the scripted global grade was 74.4% (range 40.8–96.9%). Conclusions The inter-rater agreement amongst assessors across the UK when rating simulated candidates performing at scripted levels is excellent. The level of agreement for the overall global performance level for simulated candidates is also high. These findings suggest that assessors from across the UK viewing the same simulated performances show high levels of agreement of the standards expected of students at a ‘clear fail,’ ‘borderline,’ ‘clear pass’ and ‘good’ level.
Characterization of sheep spermatogenesis through single‐cell RNA sequencing

Spermatogenesis is an important biological process in male reproduction. The interaction between male germ cells and somatic cells during spermatogenesis, is necessary for male reproductive activities. This cellular heterogeneity has made it difficult to profile distinct cell types at different stages of development. Here, we present the first comprehensive, unbiased single‐cell transcriptomic study of sheep spermatogenesis using 10× genomics single cell sequencing (scRNA‐seq). We collected scRNA‐seq data from 11 772 cells from the adult sheep testis and identified all known germ cells (including early primary spermatocytes, late primary spermatocytes, round spermatids, elongated spermatids, and sperm), and somatic cells (Sertoli cells and Leydig cells), as well as one somatic cell that unexpectedly contained leukocytes. The functional enrichment analysis indicated that several pathways of cell cycle, gamete generation, protein processing, and mRNA surveillance pathways were significantly enriched in testicular germ cell types, and ribosome pathway was significantly enriched in testicular somatic cell types. Further analysis identified several stage‐specific marker genes of sheep germ cells, such as EZH2, SOX18, SCP2, PCNA, and PRKCD. Our research explored for the first time of the changes in the transcription level of various cell types during the process of sheep spermatogenesis, providing new insights for sheep spermatogenesis and spermatogenic cell development.
Myths and methodologies: Reliability of non‐invasive estimates of cardiac autonomic modulation during whole‐body passive heating

Observed individual variability in cardiac baroreflex sensitivity (cBRS) and heart rate variability (HRV) is extensive, especially during exposure to stressors such as heat. A large part of the observed variation may be related to the reliability (consistency) of the measurement. We therefore examined the test–retest reliability of cBRS and HRV measurements on three separate occasions in 14 young men (age: 24 (SD 5) years), at rest and during whole‐body heating (water‐perfused suit) to raise and clamp oesophageal temperature 0.6°C, 1.2°C and 1.8°C above baseline. Beat‐to‐beat measurements of RR interval and systolic blood pressure (BP) were obtained for deriving HRV (from RR), and cBRS calculated via (i) the spontaneous method, α coefficients and transfer function analysis at each level of heat strain, and (ii) during forced oscillations via squat–stand manoeuvres (0.1 Hz) before and after heating. Absolute values and changes in all cBRS estimates were variable but generally consistent with reductions in parasympathetic activity. cBRS estimates demonstrated poor absolute reliability (coefficient of variation ≥25%), but relative reliability (intraclass correlation coefficient; ICC) of some frequency estimates was acceptable (ICC ≥0.70) during low‐heat strain (ICC: 0.56–0.74). After heating, forced oscillations in BP demonstrated more favourable responses than spontaneous oscillations (better reliability, lower minimum detectable change). Absolute reliability of HRV estimates were poor, but relative reliability estimates were often acceptable (≥0.70). Our findings illustrate how measurement consistency of cardiac autonomic modulation estimates are altered during heat stress, and we demonstrate the possible implications on research design and data interpretation.
A Biochemical Platform to Define the Relative Specific Activity of IDUA Variants Identified by Newborn Screening

The lysosomal storage disorder, mucopolysaccharidosis I (MPSI), results from mutations in IDUA, the gene that encodes the glycosaminoglycan-degrading enzyme α-L-iduronidase. Newborn screening efforts for MPSI have greatly increased the number of novel IDUA variants identified, but with insufficient experimental evidence regarding their pathogenicity, many of these variants remain classified as variants of uncertain significance (VUS). Defining pathogenicity for novel IDUA variants is critical for decisions regarding medical management and early intervention. Here, we describe a biochemical platform for the characterization of IDUA variants that relies on viral delivery of IDUA DNA into IDUA-deficient HAP1 cells and isolation of single cell expression clones. The relative specific activity of wild-type and variant α-iduronidase was determined using a combination of Western blot analysis and α-iduronidase activity assays. The specific activity of each variant enzyme was consistent across different single cell clones despite variable IDUA expression and could be accurately determined down to 0.05–0.01% of WT α-iduronidase activity. With this strategy we compared the specific activities of known pseudodeficiency variants (p.His82Gln, p.Ala79Thr, p.Val322Glu, p.Asp223Asn) or pathogenic variants (p.Ser633Leu, p.His240Arg) with variants of uncertain significance (p.Ser586Phe, p.Ile272Leu). The p.Ser633Leu and p.His240Arg variants both show very low activities consistent with their association with Scheie syndrome. In our experiments, however, p.His240Arg exhibited a specific activity five times higher than p.Ser633Leu in contrast to other reports showing equivalent activity. Cell clones expressing the p.Ser586Phe and p.Ile272Leu variants had specific activities in the range of other pseudodeficiency variants tested. Our findings show that pseudodeficiency and pathogenic variants can be distinguished from each other with regard to specific activity, and confirms that all the pseudodeficiency variants variably reduce α-iduronidase activity. We envision this platform will be a valuable resource for the rigorous assessment of the novel IDUA variants emerging from the expansion of newborn screening efforts.
Setting the Stage: Genes Controlling Mechanosensation and Ca2+ Signaling in Escherichia coli

Although mechanistic understanding of calcium signaling in bacteria remains inchoate, current evidence clearly links Ca2+ signaling with membrane potential and mechanosensation. Adopting a radically new approach, Luder et al. scanned the Keio collection of Escherichia coli gene knockouts (R. ABSTRACT Although mechanistic understanding of calcium signaling in bacteria remains inchoate, current evidence clearly links Ca2+ signaling with membrane potential and mechanosensation. Adopting a radically new approach, Luder et al. scanned the Keio collection of Escherichia coli gene knockouts (R. Luder, G. N. Bruni, and J. M. Kralj, J Bacteriol 203:e00509-20, 2021, https://doi.org/10.1128/JB.00509-20) to identify mutations that cause changes in Ca2+ transients. They identify genes associating Ca2+ signaling with outer membrane biogenesis, proton motive force, and, surprisingly, long-term DNA damage. Their work has major implications for electrophysiological communication between bacteria and their environment.
Five-year long-term outcomes of intrastromal corneal ring segment implantation using the manual technique for keratoconus management

This retrospective study of 124 eyes concluded that ICRS implantation was a stable, safe, and effective procedure for keratoconus management over a 5-year follow-up period. Purpose: To evaluate the long-term effectiveness, safety, and stability of Ferrara-type intrastromal corneal ring segments (ICRS) by manual surgery implantation in patients with keratoconus. Setting: Ophthalmology Department, Hospital de Braga, Braga, Portugal. Design: Retrospective cohort study. Methods: This study included 124 eyes that had ICRS implantation using the manual technique with a follow-up of 5 years. Uncorrected distance visual acuity (UDVA) and corrected distance visual acuity (CDVA), subjective refraction, keratometry, aberrometry, and pachymetry maps were evaluated preoperatively and at 6 months, 1 year, and 5 years postoperatively. A secondary analysis of all variables was performed comparing 2 subgroups of patients: a group younger than 30 years and a group of 30 years or older. Results: At 5 years, both mean UDVA and CDVA improved significantly (P < .0001) from a preoperative value of 0.91 ± 0.36 to 0.46 ± 0.32 logMAR and 0.40 ± 0.27 to 0.22 ± 0.20 logMAR, respectively. Spherical equivalent, refractive cylinder, and all topography values significantly decreased postoperatively (P < .0001). No regression was observed in any visual or topographic parameter during the entire follow-up. Regarding the subgroup analysis, both younger and older patients demonstrated similar and stable results from the preoperative to the 5-year visit, except for minimum pachymetry value change over time. Conclusions: Ferrara-type ICRS implantation significantly improved visual acuity, refractive error, and topographic values; the improvement was stable throughout a 5-year follow-up period. This study confirms that ICRS implantation surgery for keratoconus is a stable procedure in a long-term follow-up, regardless of the preoperative patient's age.
Position Identification for Robust Myoelectric Control Against Electrode Shift

The vulnerability to the electrode shift was one of the key barriers to the wide application of pattern recognition-based (PR-based) myoelectric control systems outside the controlled laboratory conditions. To overcome this challenge, a novel framework named position identification (PI) was proposed. In the PI framework, an anchor gesture performed by the user was first analyzed to identify the current electrode position from a pool of potential electrode shift positions. Next, the classifier calibrated by the data of the identified position would be selected for following myoelectric control tasks. The results of the amputee and able-bodied participants both demonstrated that the differential filter combined with majority voting improved the PI accuracy. With only one second contraction of the chosen anchor gesture (hand close), the subsequent PR-based myoelectric control performance was fully restored from eight different electrode shift scenarios, with 1 cm in either or both perpendicular and parallel directions. The classification accuracies with PI framework were not significant before and after the shift ( ${p}< $ 0.001). The advantage of restoring performance fully in just one second made it a practical solution to improve the robustness of PR-based myoelectric control systems in a wide range of real-world applications.
Prognostic factors and predictors of outcome in patients with COVID-19 and related pneumonia: a retrospective cohort study

Abstract The aim of the present study was to simultaneously assess several potential predictors of outcome (co-morbidity, previous and in-hospital treatment, radiologic Brixia score) in patients with COVID-19. This retrospective cohort study included 258 consecutive patients with confirmed COVID-19 admitted to a medical ward at Montichiari Hospital, Brescia, Italy from February 28th to April 30rd, 2020. Patients had SARS-CoV-2 related pneumonia with respiratory failure, and were treated with hydroxychloroquine and lopinavir plus ritonavir. In some patients, additional treatment with tocilizumab, dexamethasone and enoxaparin was adopted. Outcomes (death or recovery) were assessed at the end of the discharge period or at the end of the follow-up (August 2020). During hospitalization, 59 patients died, while 6 died after discharge. The following variables were demonstrated to be associated with a worse prognosis: Radiologic Brixia score higher than 8, presence at baseline of hypertension, diabetes, chronic obstructive pulmonary disease, heart disease, cancer, previous treatment with ACE-inhibitors or anti-platelet drugs. Anticoagulant treatment during hospital admission with enoxaparin at a dose higher than 4000 U once daily was associated with a better prognosis. In conclusion, our study demonstrates that some co-morbidities and cardiovascular risk factors may affect prognosis. The radiologic Brixia score may be a useful tool to stratify the risk of death at baseline. Anticoagulant treatment with enoxaparin might be associated to a clinical benefit in terms of survival in patients with COVID-19.
The KH domain facilitates the substrate specificity and unwinding processivity of DDX43 helicase

The K-homology (KH) domain is a nucleic acid–binding domain present in many proteins. Recently, we found that the DEAD-box helicase DDX43 contains a KH domain in its N-terminus; however, its function remains unknown. Here, we purified recombinant DDX43 KH domain protein and found that it prefers binding ssDNA and ssRNA. Electrophoretic mobility shift assay and NMR revealed that the KH domain favors pyrimidines over purines. Mutational analysis showed that the GXXG loop in the KH domain is involved in pyrimidine binding. Moreover, we found that an alanine residue adjacent to the GXXG loop is critical for binding. Systematic evolution of ligands by exponential enrichment, chromatin immunoprecipitation–seq, and cross-linking immunoprecipitation–seq showed that the KH domain binds C-/T-rich DNA and U-rich RNA. Bioinformatics analysis suggested that the KH domain prefers to bind promoters. Using 15N-heteronuclear single quantum coherence NMR, the optimal binding sequence was identified as TTGT. Finally, we found that the full-length DDX43 helicase prefers DNA or RNA substrates with TTGT or UUGU single-stranded tails and that the KH domain is critically important for sequence specificity and unwinding processivity. Collectively, our results demonstrated that the KH domain facilitates the substrate specificity and processivity of the DDX43 helicase.