Miracle-dz/UniFAR-FTUs huggingface dataset:
Nutrient Addition and Drought Interact to Change the Structure and Decrease the Functional Diversity of a Mediterranean Grassland

Anthropogenic activities are increasing nutrient availability and altering precipitation regimes. This may lead to critical changes in grasslands functioning and resilience. This is particularly important for grasslands in the Mediterranean Basin that have evolved in nutrient poor soils, and where more frequent and prolonged droughts are projected to occur. However, there is limited knowledge regarding the interacting effects of multiple nutrient inputs and rainfall variability on Mediterranean grassland functional structure and diversity. We conducted a nutrient addition experiment during four contrasting precipitation years in a Mediterranean grassland. We established four treatments that varied in the number of added nutrients from no added nutrients (control), to one added nutrient (Nitrogen-N, Phosphorus-P or Potassium-K), two added nutrients, (NP, NK or PK) and three added nutrients (NPK). We assessed the effect of increasing nutrient addition in wet, normal, dry and very dry years on species functional traits at the community level. We determined the community functional structure (e.g. Community Weighted Mean, CWM) and functional diversity (e.g. Functional Dispersion, FDis) for eight key functional traits indicators of nutrient and water use strategies. We also assessed if CWM, FDis and species richness were related to the aggregate grassland functioning property, productivity. We found that CWM was affected by nutrient addition and precipitation and, for some traits, by their interaction. However, FDis of most traits was affected by precipitation. The very dry year had a negative effect on FDis of most traits (e.g. dispersal modes, nutrient uptake strategies) and interacted with three added nutrients to decrease FDis of growth-forms. Conversely, FDis of reproductive traits decreased during the wet year. Species richness and FDis were not related to grassland productivity, whereas CWM was the main determinant of grassland productivity supporting the importance of species functional traits in determining ecosystem functioning. Our results highlight drought as a critical factor determining a decrease in the functional diversity of Mediterranean grasslands. Moreover, drought can also interact with nutrient addition changing the dominance of many traits and further decreasing functional diversity. This will have important implications for ecosystem functioning and resilience in the context of global changes.
PADDIT: Probabilistic Augmentation of Data using Diffeomorphic Image Transformation

For proper generalization performance of convolutional neural networks (CNNs) in medical image segmentation, the learnt features should be invariant under particular non-linear shape variations of the input. To induce invariance in CNNs to such transformations, we propose Probabilistic Augmentation of Data using Diffeomorphic Image Transformation (PADDIT) – a systematic framework for generating realistic transformations that can be used to augment data for training CNNs. The main advantage of PADDIT is the ability to produce transformations that capture the morphological variability in the training data. To this end, PADDIT constructs a mean template which represents the main shape tendency of the training data. A Hamiltonian Monte Carlo(HMC) scheme is used to sample transformations which warp the training images to the generated mean template. Augmented images are created by warping the training images using the sampled transformations. We show that CNNs trained with PADDIT outperforms CNNs trained without augmentation and with generic augmentation (0.2 and 0.15 higher dice accuracy respectively) in segmenting white matter hyperintensities from T1 and FLAIR brain MRI scans.
Stress echocardiography in valvular heart disease

ABSTRACT Introduction: The management of patients with heart valve disease can be complex. Patients may have symptoms disproportionate to the severity or the severity may be unclear. In addition, the optimal timing of intervention in patients with severe disease may be controversial. Areas covered: This article examines the role of stress echocardiography for assessment of patients with low-flow, low-gradient aortic stenosis, asymptomatic severe valve disease and patients where symptoms are discordant to the resting severity of valve disease. Expert commentary: Stress echocardiography helps clinicians determine the true severity of valve disease and may identify the cause of symptoms in patients with only mild/moderate disease. The data provided by stress echocardiography will help determine the appropriate management strategy and the correct timing of intervention.
A Convergence Analysis of Gradient Descent for Deep Linear Neural Networks

We analyze speed of convergence to global optimum for gradient descent training a deep linear neural network (parameterized as $x \mapsto W_N W_{N-1} \cdots W_1 x$) by minimizing the $\ell_2$ loss over whitened data. Convergence at a linear rate is guaranteed when the following hold: (i) dimensions of hidden layers are at least the minimum of the input and output dimensions; (ii) weight matrices at initialization are approximately balanced; and (iii) the initial loss is smaller than the loss of any rank-deficient solution. The assumptions on initialization (conditions (ii) and (iii)) are necessary, in the sense that violating any one of them may lead to convergence failure. Moreover, in the important case of output dimension 1, i.e. scalar regression, they are met, and thus convergence to global optimum holds, with constant probability under a random initialization scheme. Our results significantly extend previous analyses, e.g., of deep linear residual networks (Bartlett et al., 2018).
Feedback optimizes neural coding and perception of natural stimuli

Growing evidence suggests that sensory neurons achieve optimal encoding by matching their tuning properties to the natural stimulus statistics. However, the underlying mechanisms remain unclear. Here we demonstrate that feedback pathways from higher brain areas mediate optimized encoding of naturalistic stimuli via temporal whitening in the weakly electric fish Apteronotus leptorhynchus. While one source of direct feedback uniformly enhances neural responses, a separate source of indirect feedback selectively attenuates responses to low frequencies, thus creating a high-pass neural tuning curve that opposes the decaying spectral power of natural stimuli. Additionally, we recorded from two populations of higher brain neurons responsible for the direct and indirect descending inputs. While one population displayed broadband tuning, the other displayed high-pass tuning and thus performed temporal whitening. Hence, our results demonstrate a novel function for descending input in optimizing neural responses to sensory input through temporal whitening that is likely to be conserved across systems and species.
Measuring costs and quality of life for venous leg ulcers

Venous leg ulcers (VLUs) result in substantial economic costs and reduced quality of life (QoL); however, there are few Australian cost estimates, especially using patient‐level data. We measured community‐setting VLU management costs and the impact on the QoL of affected individuals. VLU patients were recruited from a specialist wound clinic, an outpatient clinic, and two community care clinics in Queensland. Cost data were collected at the baseline visit. QoL (EQ‐5D‐5L) and wound status data were collected at baseline, 1, 3, and 6 months. Patients were classified into guideline‐based/optimal care and usual care groups. Average weekly costs per patient were statistically significantly different between the usual care and optimal care groups—$214.61 and $294.72, respectively (P = 0.04). Baseline average QoL score for an unhealed ulcer was significantly higher in the optimal care group compared with usual care (P = 0.025). Time to healing differed between the usual care group and the optimal care group (P = 0.04), with averages of 3.9 and 2.7 months, respectively. These findings increase the understanding of the costs, QoL, and healing outcomes of VLU care. Higher optimal care costs may be offset by faster time to healing. This study provides data to inform an economic evaluation of guideline‐based care for VLUs.
Microencapsulation of Lactic Acid Bacteria Improves the Gastrointestinal Delivery and in situ Expression of Recombinant Fluorescent Protein

The microencapsulation process of bacteria has been used for many years, mainly in the food industry and, among the different matrixes used, sodium alginate stands out. This matrix forms a protective wall around the encapsulated bacterial culture, increasing its viability and protecting against environmental adversities, such as low pH, for example. The aim of the present study was to evaluate both in vitro and in vivo, the capacity of the encapsulation process to maintain viable lactic acid bacteria (LAB) strains for a longer period of time and to verify if they are able to reach further regions of mouse intestine. For this purpose, a recombinant strain of LAB (L. lactis ssp. cremoris MG1363) carrying the pExu vector encoding the fluorescence protein mCherry [L. lactis MG1363 (pExu:mCherry)] was constructed. The pExu was designed by our group and acts as a vector for DNA vaccines, enabling the host cell to produce the protein of interest. The functionality of the pExu:mCherry vector, was demonstrated in vitro by fluorescence microscopy and flow cytometry after transfection of eukaryotic cells. After this confirmation, the recombinant strain was submitted to encapsulation protocol with sodium alginate (1%). Non-encapsulated, as well as encapsulated strains were orally administered to C57BL/6 mice and the expression of mCherry protein was evaluated at different times (0–168 h) in different bowel portions. Confocal microscopy showed that the expression of mCherry was higher in animals who received the encapsulated strain in all portions of intestine analyzed. These results were confirmed by qRT-PCR assay. Therefore, this is the first study comparing encapsulated and non-encapsulated L. lactis bacteria for mucosal DNA delivery applications. Our results showed that the microencapsulation process is an effective method to improve DNA delivery, ensuring a greater number of viable bacteria are able to reach different sections of the bowel.
The First-Time Homebuyer Education and Counseling Demonstration: Early Insights

Congress and many researchers and practitioners in the field of housing counseling have asked whether pre-purchase homeownership counseling for higher risk borrowers leads to better borrower outcomes and reduced lender risk relative to no counseling. Prior research has suggested there are benefits of pre-purchase homeownership counseling, but those benefits have been questioned for over 20 years by concerns that those who choose counseling may be different than those that who do not choose to get counseling (selection bias). HUD designed The First-Time Homebuyer Education and Counseling Demonstration as a rigorous, large-scale, randomized experiment to definitively answer the question about the relative efficacy of homebuyer education and counseling on higher risk borrowers. This Early Insights report demonstrates that HUD has successfully implemented the first large-scale national experiment of homebuyer education and counseling that promises to become a foundational source of evidence for policymakers, lenders, and housing counseling practitioners and advocates regarding the impacts of homebuyer education and counseling.
Effect of dietary polyunsaturated fatty acid and antioxidant supplementation on the transcriptional level of genes involved in lipid and energy metabolism in swine

Porcine fat traits depend mostly on the interaction between nutritional and genetic factors. However, the pathways and biological processes influenced by this interaction are still poorly known in pigs, although they can have a huge impact on meat quality traits. The present research provides new knowledge insight into the effect of four diets (D1 = standard diet; D2 = linseed supplementation; D3 = linseed, vitamin E and selenium supplementation; D4 = linseed and plant-derived polyphenols supplementation) on the expression of 24 candidate genes selected for their role in lipid and energy metabolism. The data indicated that 10 out of 24 genes were differentially expressed among diets, namely ACACA, ADIPOQ, ADIPOR1, CHREBP (MLXPL), ELOVL6, FASN, G6PD, PLIN2, RXRA and SCD. Results from the univariate analysis displayed an increased expression of ACACA, ADIPOQ, ADIPOR1, CHREBP, ELOVL6, FASN, PLIN2, RXRA and SCD in D4 compared to D2. Similarly, ACACA, ADIPOQ, ADIPOR1, ELOVL6 and SCD were highly expressed in D4 compared to D3, while no differences were observed in D2-D3 comparison. Moreover, an increased expression of G6PD and ELOVL6 genes in D4 compared to D1 was observed. Results from the multivariate analysis confirmed that D2 was not different from D3 and that ACACA, SCD and FASN expression made D4 different from D2 and D3. Comparing D4 and D1, the expression levels of ELOVL6 and ACACA were the most influenced. This research provides evidence that the addition of both n-3 PUFA and polyphenols, derived from linseed, grape-skin and oregano supplementation in the diets, stimulates the expression of genes involved in lipogenesis and in oxidative processes. Results evidenced a greater effect on gene expression of the diet added with both plant extracts and n-3 PUFA, resulting in an increased expression of genes coding for fatty acid synthesis, desaturation and elongation in pig Longissimus thoracis muscle.
Adolescent attachment insecurity and the influence of MBT

ABSTRACT The aim of this study in a high-risk adolescent sample with personality disorders receiving intensive mentalisation-based treatment (MBT), was first, to examine deviations in insecure attachment distribution of the normative pattern, and in borderline personality disorder and other personality disorders; second, to explore whether MBT alters attachment representations and whether these alterations are related to changes in psychological distress. A total of 60 adolescents were investigated pre-treatment for both categorical and continuous measures of the Adult Attachment Interview (AAI). Pre- and post-AAI (N = 33) data were compared with psychological distress measured by the Symptom Checklist-90. While the most disturbed category of insecure attachment, the “cannot classify“ category, was overrepresented (46.7%) at pre-treatment, no differences were observed by type of personality disorder. At post-treatment, 48.5% of the participants showed positive change in the attachment representation, and their psychological distress lowered significantly (p = .002). The whole sample demonstrated change towards increased secure attachment (z = −2.85, p = .004). Attachment insecurity was found in all adolescent personality disorders which MBT seemed to be able to alter. However, as we included no control group, we cannot conclude that changes are due to the treatment itself.
Relationship between intra-operative vein graft treatment with DuraGraft® or saline and clinical outcomes after coronary artery bypass grafting

ABSTRACT Background: Saphenous vein grafts (SVGs) remain the most often used conduits for coronary bypass grafting (CABG). Progressive intimal hyperplasia contributes to vein-graft disease and vein-graft failure (VGF). We compared the impact of intraoperative preservation of SVGs in a storage solution (DuraGraft®) versus heparinized saline on VGF-related outcomes after CABG. Methods: From 1996 to 2004, 2436 patients underwent isolated CABG with ≥ 1 SVG. SVGs were consecutively treated with DuraGraft in 1036 patients (2001−2004) and heparinized saline in 1400 patients (1996−1999). Short- (< 30 days) and long-term (≥ 1000 days) outcomes were assessed using repeat revascularization (primary end point), and major adverse cardiac events (MACE) consisting of the composite of death, nonfatal myocardial infarction, or repeat revascularization. Results: Mean follow-up in the DuraGraft group was 8.5 ± 4.2 years and 9.9 ± 5.6 years in controls. Short-term event rates were low and generally did not differ between groups. DuraGraft was associated with a 45% lower occurrence of nonfatal myocardial infarction after 1000 days (hazard ratio 0.55, 95% CI 0.41−0.74; P < 0.0001). There was 35% and 19% lower long-term risk for revascularization (HR 0.65, 95% CI 0.44−0.97; P = 0.037) and MACE (HR 0.81, 95% CI 0.70−0.94; P = 0.0051), respectively, after DuraGraft. Mortality was comparable between both groups at 1, 5, and 10 years. There was no statistically significant association between DuraGraft exposure and time to death starting at 30 or 1000 days (HR 0.91, 95% CI 0.76−1.09; P = 0.29). Conclusion: In this study, intraoperative treatment of SVGs with DuraGraft was associated with a lower risk of long-term adverse events suggesting that efficient intraoperative SVG treatment may reduce VGF-related complications post-CABG. These data warrant randomized clinical trials to validate these findings.
Caricaturing faces to improve identity recognition in low vision simulations: How effective is current-generation automatic assignment of landmark points?

Purpose Previous behavioural studies demonstrate that face caricaturing can provide an effective image enhancement method for improving poor face identity perception in low vision simulations (e.g., age-related macular degeneration, bionic eye). To translate caricaturing usefully to patients, assignment of the multiple face landmark points needed to produce the caricatures needs to be fully automatised. Recent development in computer science allows automatic face landmark detection of 68 points in real time and in multiple viewpoints. However, previous demonstrations of the behavioural effectiveness of caricaturing have used higher-precision caricatures with 147 landmark points per face, assigned by hand. Here, we test the effectiveness of the auto-assigned 68-point caricatures. We also compare this to the hand-assigned 147-point caricatures. Method We assessed human perception of how different in identity pairs of faces appear, when veridical (uncaricatured), caricatured with 68-points, and caricatured with 147-points. Across two experiments, we tested two types of low-vision images: a simulation of blur, as experienced in macular degeneration (testing two blur levels); and a simulation of the phosphenised images seen in prosthetic vision (at three resolutions). Results The 68-point caricatures produced significant improvements in identity discrimination relative to veridical. They were approximately 50% as effective as the 147-point caricatures. Conclusion Realistic translation to patients (e.g., via real time caricaturing with the enhanced signal sent to smart glasses or visual prosthetic) is approaching feasibility. For maximum effectiveness software needs to be able to assign landmark points tracing out all details of feature and face shape, to produce high-precision caricatures.
Genetic Characterization of Canine Parvovirus Type 2 Detected in Wild Raccoon Dogs (Nyctereutes procyonoides) in the Republic of Korea

Abstract: Canine parvovirus (CPV) was detected in three of 136 samples from dead raccoon dogs (Nyctereutes procyonoides) in the Republic of Korea (South Korea) during 2016–17. By sequence and phylogenetic analysis of the complete VP2 gene, the strain belonged to CPV-2 and would be distinct from the previous reported CPV-2a and CPV-2b strains from Korean domestic dogs (Canis lupus familiaris). The results indicated that the CPV strains from raccoon dogs and domestic dogs might be not circulated between wild and domestic carnivores in Korea.
Proxyeconomics, A theory of proxy based competition

In many areas of society we rely on competition to achieve abstract societal goals. Ideally, this motivates effort and efficiently allocates resources. However, competition generally depends on imperfect proxy measures in order to assess performance. Examples include: in science, the publication count of an author; in healthcare, the number of patients treated; or in business, the profit achieved. Importantly, some practices may optimize proxy performance but not the actual societal goal. In such cases, individual decisions and cultural practices may shift away from the societal goal and toward the proxy. To paraphrase what has become known as Goodhart's or Campbell's law: Any proxy measure in a competitive societal system becomes a target for the competing individuals (or groups), promoting corruption of the measure. However, we lack a coherent theory of such a process. Here, we construct an agent based model to explore and formalize the basic components and dynamics of proxy based competition. The model combines an effort incentivization mechanism from economic multitasking theory and contest theory with a slower process of cultural evolution. We find, that an individual level intrinsic motivation towards the societal goal can bound an evolution towards corrupt practices. Overall, the model provides the first sketch of a general theory of proxy based competition in complex societal systems.
Transferring Physical Motion Between Domains for Neural Inertial Tracking

Inertial information processing plays a pivotal role in ego-motion awareness for mobile agents, as inertial measurements are entirely egocentric and not environment dependent. However, they are affected greatly by changes in sensor placement/orientation or motion dynamics, and it is infeasible to collect labelled data from every domain. To overcome the challenges of domain adaptation on long sensory sequences, we propose a novel framework that extracts domain-invariant features of raw sequences from arbitrary domains, and transforms to new domains without any paired data. Through the experiments, we demonstrate that it is able to efficiently and effectively convert the raw sequence from a new unlabelled target domain into an accurate inertial trajectory, benefiting from the physical motion knowledge transferred from the labelled source domain. We also conduct real-world experiments to show our framework can reconstruct physically meaningful trajectories from raw IMU measurements obtained with a standard mobile phone in various attachments.
Idiosyncratic, Retinotopic Bias in Face Identification Modulated by Familiarity

Abstract The perception of gender and age of unfamiliar faces is reported to vary idiosyncratically across retinal locations such that, for example, the same androgynous face may appear to be male at one location but female at another. Here, we test spatial heterogeneity for the recognition of the identity of personally familiar faces in human participants. We found idiosyncratic biases that were stable within participants and that varied more across locations for low as compared to high familiar faces. These data suggest that like face gender and age, face identity is processed, in part, by independent populations of neurons monitoring restricted spatial regions and that the recognition responses vary for the same face across these different locations. Moreover, repeated and varied social interactions appear to lead to adjustments of these independent face recognition neurons so that the same familiar face is eventually more likely to elicit the same recognition response across widely separated visual field locations. We provide a mechanistic account of this reduced retinotopic bias based on computational simulations.