Miracle-dz/UniFAR-FTUs huggingface dataset:
Assessing Variation in US Soybean Seed Composition (Protein and Oil)

Soybean [Glycine max (L.) Merr. ] seed composition and yield are a function of genetics (G), environment (E), and management (M) practices, but contribution of each factor to seed composition and yield are not well understood. The goal of this synthesis-analysis was to identify the main effects of G, E, and M factors on seed composition (protein and oil concentration) and yield. The entire dataset (13,574 data points) consisted of 21 studies conducted across the United States (US) between 2002 and 2017 with varying treatments and all reporting seed yield and composition. Environment (E), defined as site-year, was the dominant factor accounting for more than 70% of the variation for both seed composition and yield. Of the crop management factors: (i) delayed planting date decreased oil concentration by 0.007 to 0.06% per delayed week (R2∼0.70) and a 0.01 to 0.04 Mg ha-1 decline in seed yield per week, mainly in northern latitudes (40–45 N); (ii) crop rotation (corn-soybean) resulted in an overall positive impact for both seed composition and yield (1.60 Mg ha-1 positive yield difference relative to continuous soybean); and (iii) other management practices such as no-till, seed treatment, foliar nutrient application, and fungicide showed mixed results. Fertilizer N application in lower quantities (10–50 kg N ha-1) increased both oil and protein concentration, but seed yield was improved with rates above 100 kg N ha-1. At southern latitudes (30–35 N), trends of reduction in oil and increases in protein concentrations with later maturity groups (MG, from 3 to 7) was found. Continuing coordinated research is critical to advance our understanding of G × E × M interactions.
Class I KNOX transcription factors promote differentiation of cambial derivatives into xylem fibers in the Arabidopsis hypocotyl

The class I KNOX transcription factors SHOOT MERISTEMLESS (STM) and KNAT1 are important regulators of meristem maintenance in shoot apices, with a dual role of promoting cell proliferation and inhibiting differentiation. We examined whether they control stem cell maintenance in the cambium of Arabidopsis hypocotyls, a wood-forming lateral meristem, in a similar fashion as in the shoot apical meristem. Weak loss-of-function alleles of KNAT1 and STM led to reduced formation of xylem fibers – highly differentiated cambial derivatives – whereas cell proliferation in the cambium was only mildly affected. In a knat1;stm double mutant, xylem fiber differentiation was completely abolished, but residual cambial activity was maintained. Expression of early and late markers of xylary cell differentiation was globally reduced in the knat1;stm double mutant. KNAT1 and STM were found to act through transcriptional repression of the meristem boundary genes BLADE-ON-PETIOLE 1 (BOP1) and BOP2 on xylem fiber differentiation. Together, these data indicate that, in the cambium, KNAT1 and STM, contrary to their function in the shoot apical meristem, promote cell differentiation through repression of BOP genes.
Oxytocin Enhances the Neural Efficiency of Social Perception

Face perception is a highly conserved process that directs our attention from infancy and is supported by specialized neural circuitry. Oxytocin (OT) can increase accuracy and detection of emotional faces, but these effects are mediated by valence, individual differences, and context. We investigated the temporal dynamics of OT’s influence on the neural substrates of face perception using event related potentials (ERPs). In a double blind, placebo controlled within-subject design, 21 healthy male adults inhaled OT or placebo and underwent ERP imaging during two face processing tasks. Experiment 1 investigated effects of OT on neural correlates of fearful vs. neutral facial expressions, and Experiment 2 manipulated point-of-gaze to neutral faces. In Experiment 1, we found that OT reduced N170 latency to fearful faces. In Experiment 2, N170 latency was decreased when participant gaze was directed to the eyes of neutral faces; however, there were no OT-associated effects in response to different facial features. Findings suggest OT modulates early stages of social perception for socially complex information such as emotional faces relative to neutral. These results are consistent with models suggesting OT impacts the salience of socially informative cues during processing, which leads to downstream effects in behavior. Future work should examine how OT affects neural processes underlying basic components of social behavior (such as, face perception) while varying emotional expression of stimuli or comparing different characteristics of participants (e.g., gender, personality traits).
Disparity of the Chinese elderly’s health-related quality of life between urban and rural areas: a mediation analysis

Objectives This study aimed to examine the urban–rural disparity in health-related quality of life (HRQoL) of the Chinese elderly and to explore the mediating roles of socioeconomic status (SES) and frequency of contact with children in the relationship between urban/rural areas and HRQoL. Methods This cross-sectional study used data from China Health and Retirement Longitudinal Study for 2015–2016, involving 12 369 Chinese aged 45 years and over. HRQoL of respondents was measured by three-level EuroQol five dimensions (EQ-5D-3L). SES, based on principal components analysis, was combined by the individual possessions of durable consumer goods and houses. Frequency of contact with children was derived from the responses to whether they live with children and how often they contact with them. Mediation analyses were performed to examine the mediating effects of SES and frequency of contact in the relationship between urban/rural areas and HRQoL. Results Urban respondents had higher scores of HRQoL than rural respondents (p<0.05). As SES and frequency of contact with children increased, the scores of HRQoL of the elderly went up as well. Mediation analyses proved the possible mediating effects of SES and frequency of contact in the relationship between urban/rural areas and HRQoL (0.0713 and 0.0064). The indirect effects induced by SES and frequency of contact were 65.45% and 5.90%, respectively. Conclusions There was a significant difference in HRQoL between urban and rural middle-aged and elderly participants, which was partially mediated by urban–rural disparities in SES and frequency of contact with children. Higher SES and frequency of contact with children contributed to higher health status in the Chinese elderly.
Three Leptospira Strains From Western Indian Ocean Wildlife Show Highly Distinct Virulence Phenotypes Through Hamster Experimental Infection

Leptospirosis is one of the most widespread zoonoses worldwide, with highest incidence reported on tropical islands. Recent investigations carried out in a One-Health framework have revealed a wide diversity of pathogenic Leptospira lineages on the different islands of Western Indian Ocean carried out by a large diversity of mammal reservoirs, including domestic and wild fauna. Using golden Syrian hamsters as a model of acute infection, we studied the virulence of Leptospira interrogans, L. mayottensis, and L. borgpetersenii isolates obtained from rats, tenrecs, and bats, respectively. Hamsters were inoculated with 2.108 bacterial cells and monitored for 1 month. The L. interrogans isolate proved to be the most pathogenic while L. mayottensis and L. borgpetersenii isolates induced no clinical symptoms in the infected hamsters. High leptospiral DNA amounts were also detected in the urine and organs of hamsters infected with the L. interrogans isolate while L. mayottensis and L. borgpetersenii isolates mostly failed to disseminate into the organism. In addition, histological damage was more pronounced in the kidneys and lungs of hamsters infected with the L. interrogans isolate. Altogether, these data support that Leptospira strains shed by mammals endemic to this insular ecosystem (L. mayottensis and L. borgpetersenii isolates) are less pathogenic than the L. interrogans rat-borne isolate. These results may provide a relevant framework for understanding the contrasting epidemiology of human leptospirosis observed among Western Indian Ocean islands.
Effectiveness of a Novel Nutraceutical Compound Containing Red Yeast Rice, Polymethoxyflavones and Antioxidants in the Modulation of Cholesterol Levels in Subjects With Hypercholesterolemia and Low-Moderate Cardiovascular Risk: The NIRVANA Study

Background: Red yeast rice supplements are broadly accepted as treatment for dyslipidaemia in subjects without high cardiovascular (CV) risk. Their effect on lipid profile is well known, but few data are available on their effect on endothelial function. Objectives: To study the effect of a novel nutraceutical compound (NC) containing low monacolin K dose, polymethoxyflavones and antioxidants on lipid profile, endothelial function and oxidative stress. Methods: Fifty-two subjects with low-moderate CV risk and dyslipidaemia (according to European guidelines) were enrolled and treated for 8 weeks with the NC. Blood samples were collected at baseline and at the end of treatment to assess changes in lipid profile, endothelial function and oxidative stress. The primary endpoint was the reduction of low density lipoprotein (LDL) cholesterol. Endothelial function was assessed through measurement of rate of apoptosis and nitric oxide (NO) production in human umbilical vein endothelial cells (HUVECs) treated with subject’s serum. High-sensitivity C-reactive protein, 4-hydroxynonenal (HNE) and oxidized LDL (oxLDL) were markers of oxidative stress. Results: Fifty subjects completed the study. The treatment caused a significant decrease in LDL (−15.6%, p < 0.001), oxLDL (−21.5%, p < 0.001), total cholesterol (TC), triglycerides, and ApoB. Apoptosis rate of HUVECs significantly decreased (−15.9%, p < 0.001). No changes were noted for NO levels and 4-HNE protein adducts. The reduction of the apoptosis rate was correlated to the reduction of oxLDL. Conclusion: An 8-week treatment based on a novel NC containing low manocolin K dose, polymethoxyflavones and antioxidants improved lipid profile in subjects with dyslipidaemia and low-moderate CV risk. Secondarily, we observed an improvement in surrogate markers of endothelial function that may result from the reduction of oxLDL (Registered at www.clinicaltrials.gov, NCT03216811).
Novel Mouse Tauopathy Model for Repetitive Mild Traumatic Brain Injury: Evaluation of Long-Term Effects on Cognition and Biomarker Levels After Therapeutic Inhibition of Tau Phosphorylation

Traumatic brain injury (TBI) is a risk factor for a group of neurodegenerative diseases termed tauopathies, which includes Alzheimer's disease and chronic traumatic encephalopathy (CTE). Although TBI is stratified by impact severity as either mild (m), moderate or severe, mTBI is the most common and the most difficult to diagnose. Tauopathies are pathologically related by the accumulation of hyperphosphorylated tau (P-tau) and increased total tau (T-tau). Here we describe: (i) a novel human tau-expressing transgenic mouse model, TghTau/PS1, to study repetitive mild closed head injury (rmCHI), (ii) quantitative comparison of T-tau and P-tau from brain and plasma in TghTau/PS1 mice over a 12 month period following rmCHI (and sham), (iii) the usefulness of P-tau as an early- and late-stage blood-based biochemical biomarker for rmCHI, (iii) the influence of kinase-targeted therapeutic intervention on rmCHI-associated cognitive deficits using a combination of lithium chloride (LiCl) and R-roscovitine (ros), and (iv) correlation of behavioral and cognitive changes with concentrations of the brain and blood-based T-tau and P-tau. Compared to sham-treated mice, behavior changes and cognitive deficits of rmCHI-treated TghTau/PS1 mice correlated with increases in both cortex and plasma T-tau and P-tau levels over 12 months. In addition, T-tau, but more predominantly P-tau, levels were significantly reduced in the cortex and plasma by LiCl + ros approaching the biomarker levels in sham and drug-treated sham mice (the drugs had only modest effects on the T-tau and P-tau levels in sham mice) throughout the 12 month study period. Furthermore, although we also observed a reversal of the abnormal behavior and cognitive deficits in the drug-treated rmCHI mice (compared to the untreated rmCHI mice) throughout the time course, these drug-treated effects were most pronounced up until 10 and 12 months where the abnormal behavior and cognition deficits began to gradually increase. These studies describe: (a) a translational relevant animal model for TBI-linked tauopathies, and (b) utilization of T-tau and P-tau as rmCHI biomarkers in plasma to monitor novel therapeutic strategies and treatment regimens for these neurodegenerative diseases.
Depression and anxiety in pet owners after a diagnosis of cancer in their pets: a cross-sectional study in Japan

Objective To determine the presence and predictors of depression and anxiety in pet owners after a diagnosis of cancer in their pets. Design Cross-sectional study. Setting A veterinary medical centre specialised in oncology for dogs and cats and two primary veterinary clinics in Japan. Participants The participants for analysis were 99 owners of a pet with cancer diagnosis received in the past 1–3 weeks and 94 owners of a healthy pet. Main outcome measures Self-reported questionnaires were used to assess depression and anxiety. Depression was assessed using the Center of Epidemiologic Studies Depression Scale, and anxiety was measured by using the State–Trait Anxiety Inventory-Form JYZ. Results Depression scores were significantly higher in owners of a pet with cancer than owners of a healthy pet, even after adjustment for potential confounders (p<0.001). Within the owners of a pet with cancer, depression was significantly more common in those who were employed than those who were unemployed (p=0.048). State anxiety scores were significantly higher in owners of a pet with cancer than owners of a healthy pet, even after adjustment for potential confounders, including trait–anxiety scores (p<0.001). Furthermore, in owners of a pet with cancer, state anxiety was higher in owners with high trait anxiety (p<0.001) and in owners whose pets had a poor prognosis (p=0.027). Conclusion The results indicate that some owners tended to become depressed and anxious after their pets had received a diagnosis of cancer. Employment may be a predictor of depression. High trait anxiety and a pet with a poor prognosis may increase owners’ state anxiety. Including the pet in a family genogram and attention to the pet’s health condition may be important considerations for family practice.
Influence of Low Protein Diet-Induced Fetal Growth Restriction on the Neuroplacental Corticosterone Axis in the Rat

Objectives: Placental steroid metabolism is linked to the fetal hypothalamus-pituitary-adrenal axis. Intrauterine growth restriction (IUGR) might alter this cross-talk and lead to maternal stress, in turn contributing to the pathogenesis of anxiety-related disorders of the offspring, which might be mediated by fetal overexposure to, or a reduced local enzymatic protection against maternal glucocorticoids. So far, direct evidence of altered levels of circulating/local glucocorticoids is scarce. Liquid chromatography tandem-mass spectrometry (LC-MS/MS) allows quantitative endocrine assessment of blood and tissue. Using a rat model of maternal protein restriction (low protein [LP] vs. normal protein [NP]) to induce IUGR, we analyzed fetal and maternal steroid levels via LC-MS/MS along with the local expression of 11beta-hydroxysteroid-dehydrogenase (Hsd11b). Methods: Pregnant Wistar dams were fed a low protein (8%, LP; IUGR) or an isocaloric normal protein diet (17%, NP; controls). At E18.5, the expression of Hsd11b1 and 2 was determined by RT-PCR in fetal placenta and brain. Steroid profiling of maternal and fetal whole blood, fetal brain, and placenta was performed via LC-MS/MS. Results: In animals with LP-induced reduced body (p < 0.001) and placental weights (p < 0.05) we did not observe any difference in the expressional Hsd11b1/2-ratio in brain or placenta. Moreover, LP diet did not alter corticosterone (Cort) or 11-dehydrocorticosterone (DH-Cort) levels in dams, while fetal whole blood levels of Cort were significantly lower in the LP group (p < 0.001) and concomitantly in LP brain (p = 0.003) and LP placenta (p = 0.002). Maternal and fetal progesterone levels (whole blood and tissue) were not influenced by LP diet. Conclusion: Various rat models of intrauterine stress show profound alterations in placental Hsd11b2 gatekeeper function and fetal overexposure to corticosterone. In contrast, LP diet in our model induced IUGR without altering maternal steroid levels or placental enzymatic glucocorticoid barrier function. In fact, IUGR offspring showed significantly reduced levels of circulating and local corticosterone. Thus, our LP model might not represent a genuine model of intrauterine stress. Hypothetically, the observed changes might reflect a fetal attempt to maintain anabolic conditions in the light of protein restriction to sustain regular brain development. This may contribute to fetal origins of later neurodevelopmental sequelae.
Acute generalized exanthematous pustulosis associated with polysensitivity to paracetamol and bromhexine: the diagnostic role of in vitro interferon‐γ release test

We report a patient with acute generalized exanthematous pustulosis (AGEP), which occurred 3 days after ingesting paracetamol and bromhexine. Both were immediately stopped and the rash resolved rapidly. To determine the offending drug responsible for AGEP, an in vitro drug‐induced interferon (IFN)‐γ release test was performed using an ELISA technique. Increased IFN‐γ release was observed following in vitro challenge of the patient's lymphocytes with paracetamol or bromhexine (110% and 157% increase, respectively). In vitro challenge with paracetamol or bromhexine in a control patient, treated with paracetamol and bromhexine, did not induce an increase in IFN‐γ. These findings suggest that the patient with AGEP may have polysensitivity to both drugs. The ELISA assessment also demonstrates the relevance of in vitro cytokine release tests in the investigation of such dermatoses.
How long did it take to fix bugs?

The number of bugs (or fixes) is a common factor used to measure the quality of software and assist bug related analysis. For example, if software files have many bugs, they may be unstable. In comparison, the bug-fix time--the time to fix a bug after the bug was introduced--is neglected. We believe that the bug-fix time is an important factor for bug related analysis, such as measuring software quality. For example, if bugs in a file take a relatively long time to be fixed, the file may have some structural problems that make it difficult to make changes. In this report, we compute the bug-fix time of files in ArgoUML and PostgreSQL by identifying when bugs are introduced and when the bugs are fixed. This report includes bug-fix time statistics such as average bug-fix time, and distributions of bug-fix time. We also list the top 20 bug-fix time files of two projects.
Bibliometric impact measures leveraging topic analysis

Measurements of the impact and history of research literature provide a useful complement to scientific digital library collections. Bibliometric indicators have been extensively studied, mostly in the context of journals. However, journal-based metrics poorly capture topical distinctions in fast-moving fields, and are increasingly problematic with the rise of open-access publishing. Recent developments in latent topic models have produced promising results for automatic sub-field discovery. The fine-grained, faceted topics produced by such models provide a clearer view of the topical divisions of a body of research literature and the interactions between those divisions. We demonstrate the usefulness of topic models in measuring impact by applying a new phrase-based topic discovery model to a collection of 300,000 computer science publications, collected by the Rexa automatic citation indexing system
Cavefish eye loss in response to an early block in retinal differentiation progression

The troglomorphic phenotype shared by diverse cave-dwelling animals is regarded as a classical example of convergent evolution. One unresolved question is whether the characteristic eye loss in diverse cave species is based on interference with the same genetic program. Phreatichthys andruzzii, a Somalian cavefish, has evolved under constant conditions in complete darkness and shows severe troglomorphic characteristics, such as complete loss of eyes, pigments and scales. During early embryonic development, a complete eye is formed but is subsequently lost. In Astyanax mexicanus, another blind cavefish, eye loss has been attributed to interference during eye field patterning. To address whether similar pathways have been targeted by evolution independently, we investigated the retinal development of P. andruzzii, studying the expression of marker genes involved in eye patterning, morphogenesis, differentiation and maintenance. In contrast to Astyanax, patterning of the eye field and evagination of the optic vesicles proceeds without obvious deviation. However, the subsequent differentiation of retinal cell types is arrested during generation of the first-born cell type, retinal ganglion cells, which also fail to project correctly to the optic tectum. Eye degeneration in both species is driven by progressive apoptosis. However, it is retinal apoptosis in Phreatichthys that progresses in a wave-like manner and eliminates progenitor cells that fail to differentiate, in contrast to Astyanax, where lens apoptosis appears to serve as a driving force. Thus, evolution has targeted late retinal differentiation events, indicating that there are several ways to discontinue the development and maintenance of an eye. Summary: The characteristic eye loss seen in cavefish species occurs via different mechanisms, indicating that there are several ways to arrest the development and maintenance of an eye.
The history tablecloth: illuminating domestic activity

The History Tablecloth is a flexible substrate screen-printed with electroluminescent material forming a grid of lace-like elements. When objects are left on the table, cells beneath them light to form a halo that grows over a period of hours, highlighting the flow of objects in the home. The Tablecloth explores an approach to design that emphasises engaging, open-ended situations over defined utilitarian purposes. Long-term deployment of the History Tablecloth in a volunteer household revealed complex ways that people experienced and interacted with the Tablecloth. Beyond evoking reflection on the flow of objects over a particular table, the Tablecloth served as a ground for interpretative reflection about technology, an asset for social interaction, and an aesthetic object. Even behaviours we saw as system errors were interpreted by the users as interactively rich. Their experience highlights the subtlety of domestic ubiquitous computing, illustrating alternatives to traditional views of technology's domestic role.
Designing exploratory design games: a framework for participation in Participatory Design?

The dogma of Participatory Design is the direct involvement of people in the shaping of future artefacts. Thus central for designers within this field are the staging of a design process involving participation of people. Organising collaboration between people having various competencies and interests is challenging and therefore designers need frameworks, which can accommodate this work. This paper discusses the use of exploratory design games to organise participation in participatory design projects. Examples of different exploratory design games as sources of inspiration are presented. Through a comparison of different exploratory design games the paper sheds light on the repertoire of possibilities for designers to be aware of when creating their own exploratory design games.