Miracle-dz/UniFAR-FTUs huggingface dataset:
Function of the HYDROXYCINNAMOYL-CoA:SHIKIMATE HYDROXYCINNAMOYL TRANSFERASE is evolutionarily conserved in embryophytes

The plant phenylpropanoid pathway generates a major class of specialized metabolites and precursors of essential extracellular polymers that initially appeared upon plant terrestrialization. Despite its evolutionary significance, little is known about the complexity and function of this major metabolic pathway in extant bryophytes, the ancestors of which were the first land plants. Here, we report that the HYDROXYCINNAMOYL-CoA:SHIKIMATE HYDROXYCINNAMOYL TRANSFERASE (HCT) gene, which plays a critical function in the phenylpropanoid pathway during seed plant development, is functionally conserved in Physcomitrium (Physcomitrella) patens, in the moss lineage of bryophytes. Phylogenetic analysis indicates that bona fide HCT function emerged in the progenitor of embryophytes. In vitro enzyme assays, moss phenolic pathway reconstitution in yeast and in planta gene inactivation coupled to targeted metabolic profiling collectively indicate that P. patens HCT (PpHCT), similar to tracheophyte HCT orthologs, uses shikimate as a native acyl acceptor to produce a p-coumaroyl-5-O-shikimate intermediate. Phenotypic and metabolic analyses of loss-of-function mutants show that PpHCT is necessary for the production of caffeate derivatives, including previously reported caffeoyl-threonate esters, and for the formation of an intact cuticle. Deep conservation of HCT function in embryophytes is further suggested by the ability of HCT genes from P. patens and the liverwort Marchantia polymorpha to complement an Arabidopsis thaliana CRISPR/Cas9 hct mutant, and by the presence of phenolic esters of shikimate in representative species of the three major bryophyte lineages. One sentence summary Multidisciplinary study of the HYDROXYCINNAMOYL-CoA:SHIKIMATE HYDROXYCINNAMOYL TRANSFERASE (HCT) gene in Physcomitrium (Physcomitrella) patens points to its functional conservation in embryophytes.
Breadth and function of antibody response to acute SARS-CoV-2 infection in humans

Serological and plasmablast responses and plasmablast-derived IgG monoclonal antibodies (MAbs) have been analysed in three COVID-19 patients with different clinical severities. Potent humoral responses were detected within 3 weeks of onset of illness in all patients and the serological titre was elicited soon after or concomitantly with peripheral plasmablast response. An average of 13.7% and 3.5% of plasmablast-derived MAbs were reactive with virus spike glycoprotein or nucleocapsid, respectively. A subset of anti-spike (10 of 32) antibodies cross-reacted with other betacoronaviruses tested and harboured extensive somatic mutations, indicative of an expansion of memory B cells upon SARS-CoV-2 infection. Fourteen of 32 anti-spike MAbs, including five anti-receptor-binding domain (RBD), three anti-non-RBD S1 and six anti-S2, neutralised wild-type SARS-CoV-2 in independent assays. Anti-RBD MAbs were further grouped into four cross-inhibiting clusters, of which six antibodies from three separate clusters blocked the binding of RBD to ACE2 and five were neutralising. All ACE2-blocking anti-RBD antibodies were isolated from two recovered patients with prolonged fever, which is compatible with substantial ACE2-blocking response in their sera. Finally, the identification of non-competing pairs of neutralising antibodies would offer potential templates for the development of prophylactic and therapeutic agents against SARS-CoV-2.
Functional outcomes of patients with stroke treated with thrombectomy by aspiration

ABSTRACT Purpose: To determine the time of procedure, the value of modified Thrombolysis in Cerebral Infarction and National Institute Health of Stroke Scale as predictors of the functional results of patients with stroke treated with mechanical thrombectomy by aspiration. Methods: Observational, analytical, and retrospective case series analysis of consecutive patients with internal carotid and cerebral media branch occlusions. Clinical outcome was measured with the modified Rankin Scale at 90 days after stroke. To analyze the differences between groups, the Chi2 test was used for the qualitative variables. Results: The sample size was 58 patients treated with thrombectomy by aspiration. We observed that the thrombectomy time determines the recanalization results; meanwhile, modified Thrombolysis in Cerebral Infarction is a predictor of modified Rankin Scale at discharge but not after 3 months. National Institute Health of Stroke Scale was determinant for modified Rankin Scale result. Conclusions: Mechanical thrombectomy by aspiration proves to be an effective treatment of acute stroke, improving the patient’s vital and functional prognosis. The thrombectomy time is a predictor of the result in relation to the degree of recanalization determined by the modified Thrombolysis in Cerebral Ischemia. Also, the degree of recanalization predicts functional outcome at discharge but not at 3 months.
Forebrain Acetylcholine Modulates Isoflurane and Ketamine Anesthesia in Adult Mice

Background: Cholinergic drugs are known to modulate general anesthesia, but anesthesia responses in acetylcholine-deficient mice have not been studied. It was hypothesized that mice with genetic deficiency of forebrain acetylcholine show increased anesthetic sensitivity to isoflurane and ketamine and decreased gamma-frequency brain activity. Methods: Male adult mice with heterozygous knockdown of vesicular acetylcholine transporter in the brain or homozygous knockout of the transporter in the basal forebrain were compared with wild-type mice. Hippocampal and frontal cortical electrographic activity and righting reflex were studied in response to isoflurane and ketamine doses. Results: The loss-of-righting-reflex dose for isoflurane was lower in knockout (mean ± SD, 0.76 ± 0.08%, n = 18, P = 0.005) but not knockdown (0.78 ± 0.07%, n = 24, P = 0.021), as compared to wild-type mice (0.83 ± 0.07%, n = 23), using a significance criterion of P = 0.017 for three planned comparisons. Loss-of-righting-reflex dose for ketamine was lower in knockout (144 ± 39 mg/kg, n = 14, P = 0.006) but not knockdown (162 ± 32 mg/kg, n = 20, P = 0.602) as compared to wild-type mice (168 ± 24 mg/kg, n = 21). Hippocampal high-gamma (63 to 100 Hz) power after isoflurane was significantly lower in knockout and knockdown mice compared to wild-type mice (isoflurane-dose and mouse-group interaction effect, F[8,56] = 2.87, P = 0.010; n = 5 to 6 mice per group). Hippocampal high-gamma power after ketamine was significantly lower in both knockout and knockdown mice when compared to wild-type mice (interaction effect F[2,13] = 6.06, P = 0.014). The change in frontal cortical gamma power with isoflurane or ketamine was not statistically different among knockout, knockdown, and wild-type mice. Conclusions: These findings suggest that forebrain cholinergic neurons modulate behavioral sensitivity and hippocampal gamma activity during isoflurane and ketamine anesthesia. In genetically modified mice lacking the vesicular acetylcholine transporter in the forebrain, lower doses of isoflurane and ketamine were necessary to induce the loss of the righting reflex, a surrogate for loss of consciousness, when compared to wild-type counterparts. Hippocampal gamma power was lower in genetically modified mice lacking forebrain acetylcholine than in the wild-type mice during both isoflurane and ketamine anesthesia. These observations suggest that forebrain cholinergic neurons modulate anesthetic sensitivity during isoflurane and ketamine anesthesia. Supplemental Digital Content is available in the text.
Impact of ivabradine on the cardiac function of chronic heart failure reduced ejection fraction: Meta‐analysis of randomized controlled trials

Elevated resting heart rate in chronic heart failure (HF) patients has been associated with higher mortality and poor prognosis. Ivabradine is a new pure bradycardic agent that has been used to treat angina or heart failure reduced ejection fraction (HFrEF) with sinus heart rate above 70 beats per minute. However, the effect of ivabradine for chronic HF patients on rehospitalization and cardiac function is still inconsistent. Thus, this meta‐analysis aimed to elucidate the effect of Ivabradine in chronic HFrEF patients. We systematically searched PubMed, Medline, Clinical Trials.gov, and The Cochrane Central Register of Controlled Trials for randomized controlled trials (RCTs) of ivabradine with search terms Ivabradine (MeSH Terms), chronic heart failure and beta‐blocker. The primary endpoints of the study include the impact of Ivabradine on heart rate, left ventricle ejection fraction (LVEF), left ventricular remodeling, exercise capacity, and quality of life (QoL) in patients with chronic HFrEF. Secondary endpoints were safety analysis of Ivabradine including cardiovascular mortality, worsening HF readmission, visual disturbances, and asymptomatic bradycardia. The analysis was done by Review Manager 5.4 Analyzer, to analyze the mean differences (MD) for continuous data and risks ratio (RR) for dichotomous data. A total of six RCTs and one subgroup analysis showed add of Ivabradine to standard HF therapy was associated with greater resting heart rate reduction (MD = −9.57; 95% CI ‐11.15, −8.00), improved LVEF (MD = 3.89; 95% CI 2.61, 5.17), left ventricular reverse remodeling improvement (MD = −3.73; 95% CI ‐4.25, −3.21, LVESV; MD = −17.00, 95%CI ‐29.65, −4.35, LVEDD; MD = −1.43, 95%CI ‐2.78, −0.08, LVEDV; MD = −14.75, 95%CI ‐34.36, 4.87), increased exercise capacity (exercise duration; MD = 8.52; 95%CI 0.09, 16.94), and significant reduction on rehospitalization due to worsening HF (RR = 0.76, 95%CI 0.69, 0.84). However, Ivabradine has no significant effect on the quality of life (MD = 0.65; 95%CI ‐10.52, 11.82), and cardiovascular mortality (RR = 0.92; 95%CI 0.82, 1.03). Moreover, there were some events of visual disturbances and asymptomatic bradycardia observed in the Ivabradine group compared to the placebo group (RR = 4.76; 95%CI 3.03, 7.48; RR = 3.78; 95%CI 2.77, 5.15, respectively). Addition of Ivabradine to standard HF therapy is associated with cardiac function improvement, reduction on worsening HF readmission, greater HR reduction, and better exercise capacity in chronic HFrEF patients, although it cannot reduce cardiovascular mortality or improve the quality of life.
A nonlinear mixed model approach to predict energy expenditure from heart rate

Objective. Heart rate (HR) monitoring provides a convenient and inexpensive way to predict energy expenditure (EE) during physical activity. However, there is a lot of variation among individuals in the EE-HR relationship, which should be taken into account in predictions. The objective is to develop a model that allows the prediction of EE based on HR as accurately as possible and allows an improvement of the prediction using calibration measurements from the target individual. Approach. We propose a nonlinear (logistic) mixed model for EE and HR measurements and an approach to calibrate the model for a new person who does not belong to the dataset used to estimate the model. The calibration utilizes the estimated model parameters and calibration measurements of HR and EE from the person in question. We compare the results of the logistic mixed model with a simpler linear mixed model for which the calibration is easier to perform. Main results. We show that the calibration is beneficial already with only one pair of measurements on HR and EE. This is an important benefit over an individual-level model fitting, which requires a larger number of measurements. Moreover, we present an algorithm for calculating the confidence and prediction intervals of the calibrated predictions. The analysis was based on up to 11 pairs of EE and HR measurements from each of 54 individuals of a heterogeneous group of people, who performed a maximal treadmill test. Significance. The proposed method allows accurate energy expenditure predictions based on only a few calibration measurements from a new individual without access to the original dataset, thus making the approach viable for example on wearable computers.
Ratio of Oxygen Saturation Index to Guide Management of COVID-19 Pneumonia

1 Scaravilli V, Grasselli G, Castagna L, Zanella A, Isgr o S, Lucchini A, et al. Prone positioning improves oxygenation in spontaneously breathing nonintubated patients with hypoxemic acute respiratory failure: a retrospective study. J Crit Care 2015;30:1390–1394. 2 Ding L, Wang L, Ma W, He H. Efficacy and safety of early prone positioning combined with HFNC or NIV in moderate to severe ARDS: a multi-center prospective cohort study. Crit Care 2020;24:28. 3 P erez-NietoOR,Guerrero-Guti errezMA,Deloya-TomasE, ~ Namendys-Silva SA. Prone positioning combined with high-flow nasal cannula in severe noninfectious ARDS. Crit Care 2020;24:114. 4 Valter C, Christensen AM, Tollund C, Schønemann NK. Response to the prone position in spontaneously breathing patients with hypoxemic respiratory failure. Acta Anaesthesiol Scand 2003;47:416–418. 5 Ng Z, Tay WC, Ho CHB. Awake prone positioning for non-intubated oxygen dependent COVID-19 pneumonia patients. Eur Respir J 2020;56: 2001198. 6 Despres C, Brunin Y, Berthier F, Pili-Floury S, Besch G. Prone positioning combined with high-flow nasal or conventional oxygen therapy in severe Covid-19 patients. Crit Care 2020;24:256. 7 Bentley SK, Iavicoli L, Cherkas D, Lane R, Wang E, Atienza M, et al. Guidance and patient instructions for proning and repositioning of awake, nonintubated COVID-19 patients. Acad Emerg Med 2020;27:787–791. 8 Brown SM, Grissom CK, Moss M, Rice TW, Schoenfeld D, Hou PC, et al.; NIH/NHLBI PETAL Network Collaborators. Nonlinear imputation of PaO2/ FiO2 from SpO2/FiO2 among patients with acute respiratory distress syndrome. Chest 2016;150:307–313. 9 Hallifax RJ, Porter BM, Elder PJ, Evans SB, Turnbull CD, Hynes G, et al.; Oxford Respiratory Group. Successful awake proning is associated with improved clinical outcomes in patients with COVID-19: single-centre highdependency unit experience. BMJ Open Respir Res 2020;7:e000678.
Crop diversity enriches arbuscular mycorrhizal fungal communities in an intensive agricultural landscape

Summary Arbuscular mycorrhizal fungi (AMF) are keystone symbionts of agricultural soils but agricultural intensification has negatively impacted AMF communities. Increasing crop diversity could ameliorate some of these impacts by positively affecting AMF. However, the underlying relationship between plant diversity and AMF community composition has not been fully resolved. We examined how greater crop diversity affected AMF across farms in an intensive agricultural landscape, defined by high nutrient input, low crop diversity and high tillage frequency. We assessed AMF communities across 31 field sites that were either monocultures or polycultures (growing > 20 different crop types) in three ways: richness, diversity and composition. We also determined root colonization across these sites. We found that polycultures drive the available AMF community into richer and more diverse communities while soil properties structure AMF community composition. AMF root colonization did not vary by farm management (monocultures vs polycultures), but did vary by crop host. We demonstrate that crop diversity enriches AMF communities, counteracting the negative effects of agricultural intensification on AMF, providing the potential to increase agroecosystem functioning and sustainability.
Interaural Place-of-Stimulation Mismatch Estimates Using CT Scans and Binaural Perception, But Not Pitch, Are Consistent in Cochlear-Implant Users

Bilateral cochlear implants (BI-CIs) or a CI for single-sided deafness (SSD-CI; one normally functioning acoustic ear) can partially restore spatial-hearing abilities, including sound localization and speech understanding in noise. For these populations, however, interaural place-of-stimulation mismatch can occur and thus diminish binaural sensitivity that relies on interaurally frequency-matched neurons. This study examined whether plasticity—reorganization of central neural pathways over time—can compensate for peripheral interaural place mismatch. We hypothesized differential plasticity across two systems: none for binaural processing but adaptation for pitch perception toward frequencies delivered by the specific electrodes. Interaural place mismatch was evaluated in 19 BI-CI and 23 SSD-CI human subjects (both sexes) using binaural processing (interaural-time-difference discrimination with simultaneous bilateral stimulation), pitch perception (pitch ranking for single electrodes or acoustic tones with sequential bilateral stimulation), and physical electrode-location estimates from computed-tomography (CT) scans. On average, CT scans revealed relatively little BI-CI interaural place mismatch (26° insertion-angle mismatch) but a relatively large SSD-CI mismatch, particularly at low frequencies (166° for an electrode tuned to 300 Hz, decreasing to 14° at 7000 Hz). For BI-CI subjects, the three metrics were in agreement because there was little mismatch. For SSD-CI subjects, binaural and CT measurements were in agreement, suggesting little binaural-system plasticity induced by mismatch. The pitch measurements disagreed with binaural and CT measurements, suggesting place-pitch plasticity or a procedural bias. These results suggest that reducing interaural place mismatch and potentially improving binaural processing by reprogramming the CI frequency allocation would be better done using CT-scan than pitch information. SIGNIFICANCE STATEMENT Electrode-array placement for cochlear implants (bionic prostheses that partially restore hearing) does not explicitly align neural representations of frequency information. The resulting interaural place-of-stimulation mismatch can diminish spatial-hearing abilities. In this study, adults with two cochlear implants showed reasonable interaural alignment, whereas those with one cochlear implant but normal hearing in the other ear often showed mismatch. In cases of mismatch, binaural sensitivity was best when the same cochlear locations were stimulated in both ears, suggesting that binaural brainstem pathways do not experience plasticity to compensate for mismatch. In contrast, interaurally pitch-matched electrodes deviated from cochlear-location estimates and did not optimize binaural sensitivity. Clinical correction of interaural place mismatch using binaural or computed-tomography (but not pitch) information may improve spatial-hearing benefits.
Investigating the Influence of Ads on User Search Performance, Behaviour, and Experience during Information Seeking

The phenomenon of banner blindness explains that users can mentally ignore online advertisements (ads). However, eye-tracking studies have shown that users still fixate on ads, and even without direct gaze, ads still fall within a user's peripheral vision, which may negatively overload cognition. It is therefore unknown how blind, banner blindness, truly is, and what other effect ads may have on user's information seeking. To address this gap, a within-subjects design experiment was conducted with 37 participants who performed search tasks from the TREC 2017 Common Core News Collection, where 3 search tasks contained various types of ads, and one search task had no ads. Although our results showed that on average, participants retrieved similar amounts of relevant documents regardless of whether ads were present or absent, participants took significantly longer achieving this performance when ads were present. Furthermore, when ads were absent, participants reported less frustration, and not only believed they learned more, but a post-task recall test showed that participants actually did learn up to 38% more. Consequently, our findings suggest that banner blindness is more costly than just mere annoyance, and that the influence of ads on user's information retrieval recall may extend current theories of visual crowding.
Children's Perspective on How Emojis Help Them to Recognise Relevant Results: Do Actions Speak Louder Than Words?

We discuss the exploratory study we conducted to better understand children's ability to recognise relevant results when searching in the classroom. Teachers in two European schools sharing the same language assigned their students (ages 10 and 11) an online information discovery exercise about a history topic covered in class. For this, children used a classic search interface and two novel ones enriched with emojis associated to relevant vs. irrelevant results. At the end of the exercise, children filled out a post-task questionnaire meant to elicit their perception on usability of the interfaces. Guided by four lenses, we analyse our findings and discuss whether (i) emoji-enriched interfaces lead to better performance for children using a search engine in the classroom and (ii) "actions speak louder than words'' when looking at children's search experience. We learned various lessons from our examination of children's search behaviour that will guide the design of future interfaces, including the fact that emoji-enriched interfaces result in significant improvement in terms of children identifying relevant resources.
The Effect of Nudges and Boosts on Browsing Privacy in a Naturalistic Environment

During everyday web browsing and search users reveal many pieces of private information to third parties. Even though people report being concerned about their privacy online, they often do not take steps to protect it. This is known as the 'privacy paradox' in the literature. In this work we study two well-known strategies based on theories from the behavioral sciences, nudging and boosting, which encourage users to browse in a way that their private data are less exposed. First, an online survey (N=127) tested the comprehensibility and efficacy of various facts (boosts), before the most effective of these were evaluated against 'nudge' interventions previously shown to be efficacious in lab-studies. A three week naturalistic study (N=68) using a browser extension revealed that both nudges and boosts improve browsing privacy, as approximated by different measures. Boosts are also shown to improve user knowledge about privacy in the short term, but the benefit weakens over time.
Rethinking Interest in Studies of Interactive Information Retrieval

Interest characterizes a cognitive-emotional relationship between people and information and is a key construct in human information interaction. As a motivational variable, interest has been widely studied in psychology and education, but has received less consistent and theory-driven attention in the field of interactive information retrieval (IIR). In this perspective paper we examine the role of interest and review how it has been studied and operationalized in IIR research. We draw upon a survey of 58 research studies that have manipulated, controlled or measured searcher interest in some way. The intent of the paper is to raise the profile of interest as a user-centred variable in IIR and to advocate for more conceptual and methodological consistency in future studies to better evaluate the impact of interest in information search.