Miracle-dz/UniFAR-FTUs huggingface dataset:
Task-Dependent Representation of Feature Binding within the Same Dimension in Visual Working Memory

Working memory (WM) serves as a neurocognitive system responsible for temporarily storing and manipulating information when its source has disappeared. Previous investigations into whether features within the same dimension were stored separately or conjoined into objects have yielded conflicting findings. Based on increasing evidence on the adaptivity of the working memory system, we conjectured that the format in which objects from the same dimension are stored in Visual Working Memory (VWM) might be contingent on the specific task demands, and subtle distinctions across experiments may account for the disparities in results. In the current study, we introduced modifications to the paradigm used by Luck and Vogel (1997) and Wheeler and Treisman (2002), where the same paradigm led to different conclusions, to assess whether implicit task requirements could influence the storage format of objects in visual working memory. In two conditions, we manipulated the relevance of conjunction between two colors by varying the proportions of Mis-conjunct probes, a probe type depending on conjunction information for accurate responses. The results showed that in both conditions, performance was primarily determined by the number of features rather than the number of objects, aligning with the results of Wheeler and Treisman. Nevertheless, we observed that Mis-conjunct probes, which require conjunction information, exhibited improved performance when tested more frequently. This suggests that the format of retention in working memory, whether in separate or conjoined form, is influenced by the task demands.
UVAE: Integration of Heterogeneous Unpaired Data with Imbalanced Classes

We introduce the Unbiasing Variational Autoencoder (UVAE), a novel computational framework developed for the integration of unpaired biomedical data streams, with a particular focus on clinical flow cytometry. UVAE effectively addresses the challenges of batch effect correction and data alignment by training a semi-supervised model on partially labeled datasets. This approach enables the simultaneous normalisation and integration of diverse data within a shared latent space. The framework is implemented in Python with a descriptive interface for the specification and incorporation of multiple, partially overlapping data series. UVAE employs a probabilistic model for batch effect normalisation, with a generative capacity for unbiased data reconstruction and inference from heterogeneous samples. Its training process strategically balances class contents during various stages, ensuring accurate representation in statistical analyses. The model’s convergence is achieved through a stable, non-adversarial training mechanism, complemented by an automated selection of hyper-parameters via Bayesian optimization. We quantitatively validate the performance of UVAE’s constituent components and consequently apply it to the real problem of integrating heterogeneous clinical flow cytometry data collected from COVID-19 patients. We show that the alignment process enhances the statistical signal of cell types associated with severity and enables clustering of subpopulations without the impediment of batch effects. Finally, we demonstrate that homogeneous data generated by UVAE can be used to improve the performance of longitudinal regression for predicting peak disease severity from temporal patient samples. Availability Framework is available at https://github.com/mikephn/UVAE. Benchmarking and clinical data with processing scripts will be made available upon completing peer review.
Cerebrovascular-balance relationships reveal mechanisms of neuromotor resilience to dual-task cognitive loading

BACKGROUND Age-related decline in cerebrovascular health precipitates cognitive dysfunction and can be attenuated by habitual physical activity. Cognitive interference in balance control is well-known clinically and reflects compromised neuromotor resilience. However, whether cerebrovascular health affects cognitive-balance dual-tasking with aging is unclear. METHODS Thirty participants (76±4years) completed clinical balance/cognitive testing under single-task and dual-task conditions. Balance performance was assessed as the total distance traversed during a challenging beam walking task. Cognitive performance was assessed as response time (RT) during a working-memory n-back test. Transcranial Doppler ultrasound was used to measure resting middle cerebral artery blood velocity (MCAv). We tested whether MCAv was associated with single-task and dual-task interference (DTI) in balance and cognitive performance and the effects of age and physical activity level on this relationship. RESULTS During single-tasking, higher MCAv associated with higher balance function (r=0.40, p=0.033), while no relationship was observed for cognitive performance. Dual-tasking strengthened relationships between MCAv and DTI across domains of balance (r=0.442, p=0.016) and cognition (r=0.328, p=0.089); for cognitive DTI, this effect was driven by individuals ≥75years old (r=0.54, p=0.031). Individuals ≥75years exhibited greater cognitive DTI (p=0.049), yet achieved similar balance DTI compared to those <75. Regardless of age, participants with higher MCAv demonstrated greater dual-task prioritization of balance control over cognitive performance (r=0.410, p=0.030). Physically-active participants with higher MCAv also showed less balance DTI (r=0.621, p=0.003), while there was no relationship in under-active/sedentary individuals or within the cognitive domain. CONCLUSIONS Our results support a key role of cerebrovascular health in neuromotor resilience to cognitive loading, which may emerge earlier in brain aging processes affecting balance control compared to cognition. Cerebrovascular health may support people’s ability to prioritize balance in the face of competing attentional demands, and may mediate the positive effects of physical activity on cortically-mediated balance control.
Cell type-specific adaptation of the SARS-CoV-2 spike

SARS-CoV-2 can infect various human tissues and cell types, principally via interaction with its cognate receptor ACE2. However, how the virus evolves in different cellular environments is poorly understood. Here, we used experimental evolution to study the adaptation of the SARS-CoV-2 spike to four human cell lines expressing different levels of key entry factors. After 20 passages, cell type-specific phenotypic changes were observed. Selected spike mutations were identified and functionally characterized in terms of entry efficiency, ACE2 affinity, spike processing, TMPRSS2 usage, entry pathway and syncytia formation. We found that the effects of these mutations varied across cell types. Interestingly, two spike mutations (L48S and A372T) that emerged in cells expressing low ACE2 levels increased receptor affinity, syncytia induction, and entry efficiency under low-ACE2 conditions. Our results demonstrate specific adaptation of the SARS-CoV-2 spike to different cell types and have implications for understanding SARS-CoV-2 tissue tropism and evolution.
Cytochrome P450 CYP72A219 is Involved in Evolution of Metabolic Resistance to Tembotrione in Amaranthus palmeri Populations

Evolution of metabolic herbicide resistance is a major issue for weed management. Few genes and regulatory mechanisms have been identified, particularly in dicotyledonous weed species. We identified putative causal genes and regulatory mechanism for tembotrione-resistance in Amaranthus palmeri. Cytochrome P450 candidate genes were identified through RNA-seq analysis. We validated their functions using heterologous expression in S. cerevisae. Promoters of the candidate P450 genes were analyzed. We performed QTL mapping to identify genomic regions associated with resistance. CYP72A219_4284 deactivated tembotrione. This gene had increased expression in other A. palmeri populations resistant to multiple herbicides, including-tembotrione. Resistant plants exhibited polymorphisms in the promoter of CYP72A219_4284. We identified QTLs linked to herbicide resistance, including one on chromosome 4 approximately 3 Mb away from CYP72A219_4284. CYP72A219_4284 is involved in tembotrione resistance in A. palmeri. Increased expression of this gene could be due to cis-regulation in the promoter, as well as trans-regulation from transcription factors. The elucidation of regulatory genes is crucial for developing innovative weed management approaches and target-based novel molecules.
Higher-order thalamocortical projections selectively control excitability via NMDAR and mGluRI-mediated mechanisms

The apical dendrites of layer (L) 2/3 pyramidal neurons in the mouse somatosensory cortex integrate synaptic input from long-range projections. Among those, inputs from the higher-order thalamic posteromedial nucleus may facilitate sensory-evoked cortical activity, but it remains elusive how this role emerges. Here we show using ex vivo dendritic recordings that these projections provide dense synaptic input to broad tufted neurons residing predominantly in L2 and cooperate with other inputs to produce NMDA spikes. They have the unique capacity to block two-pore domain potassium leak channels via group 1 metabotropic glutamate receptor (mGluRI) signaling, which increases excitability. Slender tufted L2/3 neurons and other long-range projections fail to invoke these mechanisms. In vivo imaging of calcium signals confirms the presence of mGluRI-dependent modulation of feedback-mediated spiking in L2. Our results imply that higher-order thalamocortical projections regulate neuronal excitability in a cell type and input-selective manner through fast NMDAR and mGluRI-dependent mechanisms.
The impact of transient and persistent acute kidney injury on short-term outcomes in very elderly patients

Objectives: Acute kidney injury (AKI) is a common complication in elderly patients and is associated with poor outcomes. However, the effect of transient and persistent geriatric AKI on short-term mortality is unclear. We aimed to study the incidence, clinical characteristics, and prognostic impact of transient and persistent AKI in such patients. Methods: We retrospectively enrolled very elderly patients ( $ 75 years) from the geriatric department of the Chinese PLA General Hospital between 2007 and 2015. AKI was defined according to the 2012 Kidney Disease: Improving Global Outcomes criteria. AKI patients were divided into transient or persistent AKI groups based on their renal function at 3 days post-AKI. Renal function recovery was defined as a return to the baseline serum creatinine (SCr) levels. Results: In total, 668 geriatric patients (39.0%) experienced AKI, and 652 satisfied the inclusion criteria. Of these 652 patients, 270 (41.4%) had transient AKI, and 382 (58.6%) had persistent AKI. The 90-day mortality was 5.9% in patients with transient AKI and 53.1% in patients with persistent AKI. Multivariate analysis revealed that low hemoglobin levels (odds ratio [OR] = 0.989; 95% CI: 0.980–0.999; P = 0.025), low mean aortic pressure (OR = 0.985; 95% CI: 0.971–1.000; P = 0.043), peak SCr (OR = 1.020; 95% CI: 1.015–1.026; P , 0.001) levels, high uric acid (OR = 1.002; 95% CI: 1.000–1.003; P = 0.040) levels, high blood urea nitrogen (OR = 1.028; 95% CI: 1.000–1.056; P = 0.047) levels, and mechanical ventilation requirements (OR = 1.610; 95% CI: 1.012–2.562; P = 0.044) were associated with persistent AKI. Persistent AKI (hazard ratio [HR] = 5.741; 95% CI: 3.356–9.822; P , 0.001) and more severe AKI stages (stage 2: HR = 3.363; 95% CI: 1.973–5.732; P , 0.001 and stage 3: HR = 4.741; 95% CI: 2.807–8.008; P , 0.001) were associated with 90-day mortality. Conclusion: AKI is common in very elderly patients, with transient renal injury representing close to 42% of all cases of geriatric AKI. More frequent SCr measurements may be helpful for the early diagnosis of transient geriatric AKI. Persistent geriatric AKI is independently associated with a significantly higher risk of 90-day mortality.
Quantity versus Quality in Project-Based Learning Practices

In the midst of the turbulence wrought by the global economy, it has become common to see projects as an essential medium for achieving change. However, project-based learning practices-as a subset of organizational learning practices-have not kept pace with this development. To explore this concern, we have carried out a study on practices adopted by organizations for learning through projects involving nineteen companies from across Europe and from a range of different industries. We use the concepts of variation, selection and retention in organizational learning to analyze our findings and report the challenges faced by project-based organizations in each of the areas highlighted. We conclude that time pressures, centralization and deferral are the key characteristics of learning in project-based firms and that these impede project-based members in learning from and through projects.
Comparison of temporospatial and kinetic variables of walking in small and large dogs on a pressure-sensing walkway

Objective —To compare temporospatial variables (TSVs) and kinetic variables (KVs) for fore-limbs and hind limbs of small and large dogs of various breeds during walking and to determine associations among body weight (BW), TSVs, and KVs in these groups. Animals —12 adult dogs with no evidence of lameness. Procedures —Dogs (grouped according to BW as small [ < 10 kg; n = 6] or large [ > 25 kg; 6]) were walked in a straight line at their preferred velocity on a wooden platform with an embedded pressure-sensing walkway. Five valid trials were analyzed for each dog; mean TSVs and KVs were determined for each group. The TSVs and KVs for forelimbs and hind limbs were compared between groups, and correlations among BW, TSVs, and KVs were determined. Results —Small dogs had significantly smaller TSVs and KVs than did large dogs. Temporal variables of small dogs and absolute vertical force variables of small and large dogs increased as BW increased. However, normalized peak vertical force and weight distribution values among the 4 limbs were similar between groups. Conclusions and Clinical Relevance —Substantial similarities and differences were detected in gait characteristics between small and large dogs. Results indicated TSVs and KVs can be used for comparison of the walking gait between dogs or for comparison of variables between limbs in an individual dog. Use of the pressure-sensing walkway is a simple method for acquisition of TSVs and KVs for large and small dogs. ( Am J Vet Res 2011;72:1171–1177)
Error estimates of asymptotic expansions in periodic waveguides

ABSTRACT The filtering problem of a periodically corrugated rectangular metallic waveguide of length l is used as an example to set an upper bound on the validity of the various orders of asymptotic approximation of the electromagnetic field in the waveguide. We limit the analysis to the first two orders of asymptotic expansion in powers of a small parameter δ characterising the amplitude of the periodic corrugations to minimise the detail, but the procedure is applicable to higher orders of approximation without loss of generality. The asymptotic expansions are obtained via the perturbation method of multiple scales. Following conventional practice in antenna work, a phase error of π/8 is used to set an upper bound on the phase error for each order of approximation. This bound is found by setting the difference between the results of simulation using the HFSS software package and the phase of either the first-order or the second-order approximation of the electromagnetic field equal to π/8. This bound sets an upper limit on δ for a given length I which gives the same results for a fixed (δ × I) product for the first-order expansion.
Upgrading short read animal genome assemblies to chromosome level using 1 comparative genomics and a universal probe set 2 3

If you believe this document infringes copyright then please contact the KAR admin team with the take-down information provided at http://kar.kent. ac.uk/contact.html Citation for published version Damas, J. and O'Connor, R. and Farré, Marta and Lenis, V.P.E. and Martell, H.J. and Mandawala, A. and Fowler, K. and Joseph, S. and Swain, M.T. and Griffin, D.K. and Larkin, D.M. (2016) Upgrading short read animal genome assemblies to chromosome level using comparative genomics and a universal probe set. Genome Research, 27 . pp. 875-884. ISSN 1088-9051.
dis-Identification of hypercoagulability in dogs with primary immune-mediated hemolytic anemia by means of thromboelastography

Objective —To evaluate whole blood hemostasis by means of thromboelastography in dogs with primary immune-mediated hemolytic anemia (IMHA) to determine whether these dogs had evidence of hypercoagulability prior to the administration of immunosuppressant medications, blood transfusion products, or anticoagulant agents. Design —Evaluation study. Animals
Protein arginine methyltransferase 1 is required for the maintenance of adult small intestinal and colonic epithelial cell homeostasis

The vertebrate adult intestinal epithelium has a high self-renewal rate driven by intestinal stem cells (ISCs) in the crypts, which play central roles in maintaining intestinal integrity and homeostasis. However, the underlying mechanisms remain elusive. Here we showed that protein arginine methyltransferase 1 (PRMT1), a major arginine methyltransferase that can also function as a transcription co-activator, was highly expressed in the proliferating cells of adult mouse intestinal crypts. Intestinal epithelium-specific knockout of PRMT1, which ablates PRMT1 gene starting during embryogenesis, caused distinct, region-specific effects on small intestine and colon: increasing and decreasing the goblet cell number in the small intestinal and colonic crypts, respectively, leading to elongation of the crypts in small intestine but not colon, while increasing crypt cell proliferation in both regions. We further generated a tamoxifen-inducible intestinal epithelium-specific PRMT1 knockout mouse model and found that tamoxifen-induced knockout of PRMT1 in the adult mice resulted in the same region-specific intestinal phenotypes. Thus, our studies have for the first time revealed that the epigenetic enzyme PRMT1 has distinct, region-specific roles in the maintenance of intestinal epithelial architecture and homeostasis, although PRMT1 may influence intestinal development.
Comparative studies on the efficacy of AmBisome and Fungizone in a mouse model of disseminated aspergillosis.

OBJECTIVES The efficacy of intravenous injections of a liposomal formulation of amphotericin B (AmBisome) and amphotericin B deoxycholate (Fungizone) was evaluated in immunocompetent and temporarily leucopenic mouse models of disseminated aspergillosis using seven isolates of Aspergillus. METHODS Mice were infected with the organisms via tail veins. At 4 h after infection, antifungals were administered intravenously. For 30 days the number of mice surviving was recorded. RESULTS AmBisome at 1 mg/kg or higher significantly prolonged the survival time of mice infected with five out of seven isolates of Aspergillus compared with the control group. There was no difference in in vivo activity between AmBisome and Fungizone at 1 mg/kg in six isolates of Aspergillus. At the maximum tolerated dose of antifungals, however, AmBisome (10 mg/kg) showed greater efficacy than Fungizone (1 mg/kg). CONCLUSIONS These results suggest that the overall protective activity of AmBisome against disseminated aspergillosis is superior to that of Fungizone.
Jugaad CoLab: Decolonial Poetics, Minimal Computing, and South Asian Digital Humanities

Frequently translated as “hack” or “quick fix,” the North Indian term jugaad refers to a method of solving problems by “making do” with “what is at hand. ” The mixed materialities and/or sources of these inventive solutions often destabilize conventional orders of representation. This article describes the formation of an affinity group, the Jugaad CoLab, that identifies three research foci—decolonial poetics, minimal computing, and pirate care—as central concerns at the intersection of digital humanities and Indian and South Asian Studies, especially outside of English, that benefit from jugaad-as-method. These concerns are reflected in the initial batch of projects, involving Bengali, Hindi, Punjabi, and Urdu materials, undertaken by group members as summer fellows, all of whom are graduate students and/ or citizen scholars in India and Pakistan. Adapting technologies to diverse, multilingual contexts with uneven access to resources, the projects take up the cultural practice of jugaad as efficient and creative methods for building open-access, sustainable, and future-proof sites of knowledge, especially in this moment of crisis.
Travelling for Abortion Services in Mexico Travelling for Abortion Services in Mexico 2016–2019: Community-Level Contexts of Mexico 2016–2019: Community-Level Contexts of Mexico City Public Abortion Clients City Public Abortion Clients

Objective To describe the community context of women who travel to access Mexico City’s public sector abortion programme and identify factors associated with travelling from highly marginalised settings. Methods We used data from the Interrupción Legal de Embarazo (ILE) programme (2016–2019) and identified all abortion clients who travelled from outside Mexico City. We merged in contextual information at the municipality level and used descriptive statistics to describe ILE clients’ individual characteristics and municipalities on several measures of vulnerability. We also compared municipalities that ILE clients travelled from with those where no one travelled from. We used logistic regression to identify factors associated with travelling to access ILE services from highly marginalised versus less marginalised municipalities. Results Our sample included 21 629 ILE clients who travelled to Mexico City from 491 municipalities within all 31 states outside Mexico City. The majority of clients travelled from the least marginalised (81.9%) and most populated (over 100 000 inhabitants; 91.3%) municipalities. Most (91.2%) ILE clients came from municipalities with adolescent fertility rates in the bottom three quintiles. Clients with a primary or secondary education (vs high school or more) and those from a municipality with a high adolescent fertility rate (top two quintiles) had higher odds of travelling from a highly marginalised (vs less) municipality (adjusted odds ratio (aOR) 1.46, 95% CI 1.35 to 1.58 and aOR 1.89, 95% CI 1.68 to 2.12, respectively). Conclusion ILE clients travel from geographically and socioeconomically diverse communities. There is an unmet need for legal abortion across Mexico.
Prioritizing States with Action Sensitive Return in Experience Replay

Experience replay for off-policy reinforcement learning has been shown to improve sample efficiency and stabilize training. However, typical uniformly sampled replay includes many irrelevant samples for the agent to reach good performance. We introduce Action Sensitive Experience Replay (ASER), a method to prioritize samples in the replay buffer and selectively model parts of the state-space more accurately where choosing sub-optimal actions has a larger effect on the return. We experimentally show that this can make training more sample efficient and that similar performance can be reached with smaller parametric function approximators – like neural networks with few neurons – in environments where they would otherwise struggle.