Miracle-dz/UniFAR-FTUs huggingface dataset:
Margin-Based Transfer Bounds for Meta Learning with Deep Feature Embedding

By transferring knowledge learned from seen/previous tasks, meta learning aims to generalize well to unseen/future tasks. Existing meta-learning approaches have shown promising empirical performance on various multiclass classification problems, but few provide theoretical analysis on the classifiers' generalization ability on future tasks. In this paper, under the assumption that all classification tasks are sampled from the same meta-distribution, we leverage margin theory and statistical learning theory to establish three margin-based transfer bounds for meta-learning based multiclass classification (MLMC). These bounds reveal that the expected error of a given classification algorithm for a future task can be estimated with the average empirical error on a finite number of previous tasks, uniformly over a class of preprocessing feature maps/deep neural networks (i.e. deep feature embeddings). To validate these bounds, instead of the commonly-used cross-entropy loss, a multi-margin loss is employed to train a number of representative MLMC models. Experiments on three benchmarks show that these margin-based models still achieve competitive performance, validating the practical value of our margin-based theoretical analysis.
Veillonella nakazawae sp. nov., an anaerobic Gram-negative coccus isolated from the oral cavity of Japanese children.

Two strains of previously unknown Gram-negative cocci, T1-7T and S6-16, were isolated from the oral cavity of healthy Japanese children. The two strains showed atypical phenotypic characteristics of members of the genus Veillonella, including catalase production. Sequencing of their 16S rRNA genes confirmed that they belong to genus Veillonella. Under anaerobic conditions, the two strains produced acetic acid and propionic acid as metabolic end-products in a trypticase-yeast extract-haemin medium containing 1 % (w/v) glucose, 1 % (w/v) fructose and 1 % (v/v) sodium lactate. Comparative analysis of the 16S rRNA, dnaK, rpoB and gltA gene sequences revealed that the two strains are phylogenetically homogeneous and comprise a distinct, novel lineage within the genus Veillonella. The sequences from the two strains shared the highest similarity, at 99.9, 95.8, 96.9 and 96.7 %, using the partial 16S rRNA, dnaK, rpoB and gltA gene sequences, respectively, with the type strains of the two most closely related species, Veillonella dispar ATCC 17748T and Veillonella infantium JCM 31738T. Furthermore, strain T1-7T shared the highest average nucleotide identity (ANI) value (94.06 %) with type strain of the most closely related species, V. infantium. At the same time, strain T1-7T showed the highest digital DNA-DNA hybridization (dDDH) value (55.5 %) with the type strain of V. infantium. The two strains reported in this study were distinguished from the previously reported species from the genus Veillonella based on catalase production, partial dnaK, rpoB and gltA sequences, average ANI and dDDH values. Based on these observations, the two strains represent a novel species, for which the name Veillonella nakazawae sp. nov. is proposed. The type strain is T1-7T (JCM 33966T=CCUG 74597T).
Diagnosis and treatment of gastro-oesophageal junction abnormalities in dogs with brachycephalic syndrome.

OBJECTIVES To determine whether there is a benefit of using pre- and postoperative antacid treatment in dogs undergoing surgery for brachycephalic syndrome. To assess the use of an obstruction manoeuvre during endoscopy for the detection of dynamic gastro-oesophageal junction abnormalities. MATERIALS AND METHODS Thirty-six client-owned brachycephalic dogs were prospectively included in a randomised trial. Antacid treatment was randomly prescribed in 18 dogs before and after surgery while the other 18 dogs did not receive any gastrointestinal medical treatment. At presentation, at the time of surgery and at recheck, digestive clinical signs and gastro-oesophageal junction abnormalities were assessed using specific scores. Gastro-oesophageal junction abnormalities were assessed during endoscopy in standard conditions as well as during endotracheal tube obstruction. This manoeuvre was also applied in an unrelated control group. RESULTS The results suggest a beneficial effect of antacid treatment on the improvement of digestive clinical signs and lesions in dogs with brachycephalic syndrome undergoing surgery. At postsurgical control 83% of dogs had a digestive clinical score ≤1 in the treated group in contrast to 44% in the non-treated group and 39% of dogs had a gastro-oesophageal abnormalities score (during obstruction manoeuvre) ≤1 in the treated group in contrast to 16.7% in the non-treated group. The use of the obstruction manoeuvre during endoscopic assessment in a control group revealed that gastro-oesophageal junction movements are negligible in healthy animals. CLINICAL SIGNIFICANCE The addition of antacid treatment during the pre- and postoperative period for brachycephalic dogs undergoing surgery may result in a faster and greater improvement in treated dogs. The obstruction manoeuvre is an interesting technique to improve detection of gastro-oesophageal junction abnormalities.
Protective Effects of Melatonin against Severe Burn-Induced Distant Organ Injury: A Systematic Review and Meta-Analysis of Experimental Studies

Extensive burns result in a local wound response and distant-organ injury (DOI) caused by oxidative-stress and inflammation. Melatonin (MT) shows promise in alleviating oxidative-stress and inflammation, but its role in thermal injury is largely unexplored. The present systematic review and meta-analysis were designed to assess the effects of MT on oxidative-stress and inflammatory markers against severe burn-induced DOI. Mean difference (MD)/standard mean difference (SMD) with 95% confidence interval (CI) were estimated using fixed-effect/random-effects models. Eighteen experimental studies met the inclusion criteria. Compared with the control group, MT significantly decreased the levels of malondialdehyde (SMD, −1.03; 95% CI, −1.30, −0.76, p < 0.00001) and 4-hydroxynonenal (MD, −1.06; 95% CI, −1.57, −0.56, p < 0.0001). Additionally, MT increased the levels of glutathione (SMD, 1.94; 95% CI, 1.27, 2.61, p < 0.00001) and superoxide-dismutase (SMD, 0.76; 95% CI, 0.08, 1.45, p = 0.03). Finally, MT significantly decreased the levels of tumor necrosis factor-α (SMD, −1.34; 95% CI, −1.92 to −0.77; p < 0.00001) and C-reactive protein (MD, −12.67; 95% CI, −16.72 to −8.62; p < 0.00001). Meta-analysis indicates that severe burn followed by immediate MT (10 mg/kg) intervention shows significant beneficial effects after 24-h against DOI by regulating oxidative-stress and the inflammatory response.
A no-go theorem on the nature of the gravitational field beyond quantum theory

Recently, table-top experiments involving massive quantum systems have been proposed to test the interface of quantum theory and gravity. In particular, the crucial point of the debate is whether it is possible to conclude anything on the quantum nature of the gravitational field, provided that two quantum systems become entangled solely due to the gravitational interaction. Typically, this question has been addressed by assuming a specific physical theory to describe the gravitational interaction, but no systematic approach to characterise the set of possible gravitational theories which are compatible with the observation of entanglement has been proposed. Here, we remedy this by introducing the framework of Generalised Probabilistic Theories (GPTs) to the study of the nature of the gravitational field. This framework enables us to systematically study all theories compatible with the detection of entanglement generated via the gravitational interaction between two systems. We prove a no-go theorem stating that the following statements are incompatible: i) gravity is able to generate entanglement; ii) gravity mediates the interaction between the systems; iii) gravity is classical. We analyse the violation of each condition, in particular with respect to alternative non-linear models such as the Schrödinger-Newton equation and Collapse Models.
Improving KernelSHAP: Practical Shapley Value Estimation via Linear Regression

The Shapley value solution concept from cooperative game theory has become popular for interpreting ML models, but efficiently estimating Shapley values remains challenging, particularly in the model-agnostic setting. We revisit the idea of estimating Shapley values via linear regression to understand and improve upon this approach. By analyzing KernelSHAP alongside a newly proposed unbiased estimator, we develop techniques to detect its convergence and calculate uncertainty estimates. We also find that that the original version incurs a negligible increase in bias in exchange for a significant reduction in variance, and we propose a variance reduction technique that further accelerates the convergence of both estimators. Finally, we develop a version of KernelSHAP for stochastic cooperative games that yields fast new estimators for two global explanation methods.
Spin-canting driven Weyl physics in EuCd$_2$As$_2$.

Though rare, magnetic Weyl semi-metals stand as the best platform to study elusive Weyl physics as they can host the minimal allowable number of Weyl points. Here we present neutron diffraction and density functional theory work elucidating the magnetic structure realized in the candidate magnetic Weyl semi-metal EuCd$_2$As$_2$ . Our work shows an unanticipated magnetic structure (magnetic space group $C2'/m'$) with an in-plane [210] moment direction and a slight out-of-plane canting. This canted structure indicates that subtle tuning (rather than a phase transition) may be able to stabilize the sought c-polarized state. Our density functional theory work shows that though Weyl physics should exist for a purely in-plane [210] structure, even a slight canting drastically alters the relevant bands leading to well defined Weyl points. Furthermore, we find that relative to the \textit{c}-polarized state the [210] order with a small canting brings the Weyl points closer to the Fermi level and thus may lead to clearer signatures of the Weyl physics.
Nanoliposomes and Nanoemulsions Based on Chia Seed Lipids: Preparation and Characterization

Polyunsaturated fatty acids (PUFA) are important in reducing the risk for cardiovascular, metabolic and neurodegenerative diseases. Chia (Salvia hispanica L.) seeds contain high levels of omega-3 PUFA, α-linolenic acid (ALA) in particular, and are a potential source for development of omega-3 PUFA-based products. Our objective was to obtain and characterize chia seed lipids, focusing on phospholipid fraction, and to investigate their use in the formulation of nanoemulsions (NE) and nanoliposomes (NL). Solvent-based lipid extraction was performed on the ORURO variety of chia seeds, followed by lipid composition analysis using GC and LC-MS and physico-chemical characterization of chia NL and NE. Folch extraction led to a slightly higher yield of ALA as compared to Soxhlet extraction. Lipid, phospholipid, and fatty acid composition analysis of the oil and residue revealed that the residue was rich in phospholipids; these were used to prepare NE and NL. Physico-chemical characterization showed that NE and NL were generally spherical (transmission electron microscopy), with a size of <120 nm under hydrated conditions that remained stable over 5 days. In conclusion, chia oil and phospholipid-rich residue can be used to obtain stable NL or NE using a simple method that involves spontaneous emulsification during lipid hydration, which potentially may be useful in cosmetics, pharmaceutical, and other health applications.
A non-inferiority study evaluating a new extended-release preparation of tilmicosin injected subcutaneously vs. ceftiofur administered intramammary, as dry-cow therapy in Holstein Friesian cows

Background A new, extended long-acting tilmicosin (TLAe) preparation was tested against intramammary ceftiofur (CEF) using a non-inferiority trial model during dry-cow therapy (DCT) in a farm with high bovine population density and deficient hygiene application. Objectives To evaluate the possibility that TLAe administered parenterally can achieve non-inferiority status compared to CEF administered intramammary for DCT. Methods Cows were randomly assigned to TLAe (20 mg/kg subcutaneous; n = 53) or CEF (CEF-HCl, 125 mg/quarter; n = 38 cows) treatment groups. California mastitis testing, colony-forming unit assessment (CFU/mL), and number of cases positive for Staphylococcus aureus were quantified before DCT and 7 d after calving. A complete cure was defined as no bacteria isolated; partial cure when CFU/mL ranged from 150 to 700, and cure-failure when CFU/mL was above 700. Results TLAe and CEF had overall cure rates of 57% and 53% (p > 0.05) and S. aureus cure rates of 77.7% and 25%, respectively (p < 0.05). The pathogens detected at DCT and 7 days after calving were S. aureus (62.71% and 35.55%), Staphylococcus spp. (22.03% and 35.55%), Streptococcus uberis (10.16% and 13.33%), and Escherichia coli (5.08% and 15.55%). Non-inferiority and binary logistic regression analyses revealed a lack of difference in overall efficacies of TLAe and CEF. Apart from S. aureus, S. uberis was the predominant pathogen found in both groups. Conclusions This study is the first successful report of parenteral DCT showing comparable efficacy as CEF, the gold-standard. The extended long-term pharmacokinetic activity of TLAe explains these results.
Solvent-Resistant Photocurable “Liquid Teflon” for Microfluidic Device Fabrication

We report the first fabrication of a solvent-compatible microfluidic device based on photocurable “Liquid Teflon” materials. The materials are highly fluorinated functionalized perfluoropolyethers (PFPEs) that have liquidlike viscosities that can be cured into tough, highly durable elastomers that exhibit the remarkable chemical resistance of fluoropolymers such as Teflon. Poly(dimethylsiloxane) (PDMS) elastomers have rapidly become the material of choice for many recent microfluidic device applications. Despite the advantages of PDMS in relation to microfluidics technology, the material suffers from a serious drawback in that it swells in most organic solvents. The swelling of PDMS-based devices in organic solvents greatly disrupts the micrometer-sized features and makes it impossible for fluids to flow inside the channels. Our approach to this problem has been to replace PDMS with photocurable perfluoropolyethers. Device fabrication and valve actuation were accomplished using established procedures for .
Oesophageal cancer magnitude and presentation in Ethiopia 2012–2017

The aim of this study was to assess the magnitude, socio-demographic, and clinical characteristics of oesophageal cancer patients in selected referral hospitals of Ethiopia. A retrospective document review was employed in ten referral hospitals in different regions of Ethiopia. A structured data extraction tool was used to extract data from clinical care records of all clinically and pathologically confirmed oesophageal cancer patients who were diagnosed and treated in those hospitals from 2012 to 2017. During the study period, a total of 777 oesophageal cancer cases were identified, and the median age of these patients was 55 years, with an interquartile range of 19. More than half (55.1%, n = 428) of the cases were males, and the majority of them were reported from Oromia (49.9%, n = 388) and Somali (25.9%, n = 202) regional states. The highest numbers of oesophageal cancer cases were recorded in 2016 (23.8%, n = 185), while the lowest were in 2012 (12.6%, n = 98). Eighty per cent of oesophageal cancer cases were diagnosed in later stages of the disease. More than one-fourth (27.0%, n = 210) of patients had surgical procedures where the majority (74.3%, n = 156) required insertion of a feeding tube followed by transhiatal oesophagectomy (10.9%, n = 23). Of the 118 patients for which there was histology data, squamous cell carcinoma (56.7%, n = 67) and adenocarcinoma (36.4%, n = 43) were the predominant histologic type. One-fourth (25.0%, n = 194) of the patients were alive, and more than two-thirds (71.7%, n = 557) of the patients’ current status was unknown at the time of the review. In these referral hospitals of Ethiopia, many oesophageal cancer patients presented during later stages of the disease and needed palliative care measures. The number of patients seen in Oromia and Somali hospitals by far exceeded hospitals of the other regions, thus postulating possibly unique risk factors in those geographic areas.
Generating private data with user customization

Personal devices such as mobile phones can produce and store large amounts of data that can enhance machine learning models; however, this data may contain private information specific to the data owner that prevents the release of the data. We want to reduce the correlation between user-specific private information and the data while retaining the useful information. Rather than training a large model to achieve privatization from end to end, we first decouple the creation of a latent representation, and then privatize the data that allows user-specific privatization to occur in a setting with limited computation and minimal disturbance on the utility of the data. We leverage a Variational Autoencoder (VAE) to create a compact latent representation of the data that remains fixed for all devices and all possible private labels. We then train a small generative filter to perturb the latent representation based on user specified preferences regarding the private and utility information. The small filter is trained via a GAN-type robust optimization that can take place on a distributed device such as a phone or tablet. Under special conditions of our linear filter, we disclose the connections between our generative approach and renyi differential privacy. We conduct experiments on multiple datasets including MNIST, UCI-Adult, and CelebA, and give a thorough evaluation including visualizing the geometry of the latent embeddings and estimating the empirical mutual information to show the effectiveness of our approach.
A Multi-Omics Protocol for Swine Feces to Elucidate Longitudinal Dynamics in Microbiome Structure and Function

Swine are regarded as promising biomedical models, but the dynamics of their gastrointestinal microbiome have been much less investigated than that of humans or mice. The aim of this study was to establish an integrated multi-omics protocol to investigate the fecal microbiome of healthy swine. To this end, a preparation and analysis protocol including integrated sample preparation for meta-omics analyses of deep-frozen feces was developed. Subsequent data integration linked microbiome composition with function, and metabolic activity with protein inventories, i.e., 16S rRNA data and expressed proteins, and identified proteins with corresponding metabolites. 16S rRNA gene amplicon and metaproteomics analyses revealed a fecal microbiome dominated by Prevotellaceae, Lactobacillaceae, Lachnospiraceae, Ruminococcaceae and Clostridiaceae. Similar microbiome compositions in feces and colon, but not ileum samples, were observed, showing that feces can serve as minimal-invasive proxy for porcine colon microbiomes. Longitudinal dynamics in composition, e.g., temporal decreased abundance of Lactobacillaceae and Streptococcaceae during the experiment, were not reflected in microbiome function. Instead, metaproteomics and metabolomics showed a rather stable functional state, as evident from short-chain fatty acids (SCFA) profiles and associated metaproteome functions, pointing towards functional redundancy among microbiome constituents. In conclusion, our pipeline generates congruent data from different omics approaches on the taxonomy and functionality of the intestinal microbiome of swine.
Controversial Regulation of Gene Expression and Protein Transduction of Aquaporins under Drought and Salinity Stress

Enhancement of the passage of water through membranes is one of the main mechanisms via which cells can maintain their homeostasis under stress conditions, and aquaporins are the main participants in this process. However, in the last few years, a number of studies have reported discrepancies between aquaporin messenger RNA (mRNA) expression and the number of aquaporin proteins synthesised in response to abiotic stress. These observations suggest the existence of post-transcriptional mechanisms which regulate plasma membrane intrinsic protein (PIP) trafficking to the plasma membrane. This indicates that the mRNA synthesis of some aquaporins could be modulated by the accumulation of the corresponding encoded protein, in relation to the turnover of the membranes. This aspect is discussed in terms of the results obtained: on the one hand, with isolated vesicles, in which the level of proteins present provides the membranes with important characteristics such as resistance and stability and, on the other, with isolated proteins reconstituted in artificial liposomes as an in vitro method to address the in vivo physiology of the entire plant.
Genome-Wide Identification of the Vacuolar H+-ATPase Gene Family in Five Rosaceae Species and Expression Analysis in Pear (Pyrus bretschneideri)

Vacuolar H+-ATPases (V-ATPase) are multi-subunit complexes that function as ATP hydrolysis-driven proton pumps. They play pivotal roles in physiological processes, such as development, metabolism, stress, and growth. However, there have been very few studies on the characterisation of V-ATPase (VHA) genes in Rosaceae species. Therefore, in the present study, we performed a genome-wide analysis and identified VHA gene family members in five Rosaceae species (Pyrus bretschneideri, Malus domestica, Prunus persica, Fragaria vesca, and Prunus mume). A total of 159 VHA genes were identified, and were classified into 13 subfamilies according to the phylogenetic analysis. The structure of VHA proteins revealed high similarity among different VHA genes within the same subgroup. Gene duplication event analysis revealed that whole-genome duplications represented the major pathway for expansion of the Pyrus bretschneideri VHA genes (PbrVHA genes). The tissue-specific expression analysis of the pear showed that 36 PbrVHA genes were expressed in major tissues. Seven PbrVHA genes were significantly downregulated when the pollen tube growth stopped. Moreover, many PbrVHA genes were differentially expressed during fruit development and storage, suggesting that VHA genes play specific roles in development and senescence. The present study provides fundamental information for further elucidating the potential roles of VHA genes during development and senescence.
Cosmic-Ray Diffusion Suppression in Star-forming Regions Inhibits Clump Formation in Gas-rich Galaxies

Observations of the γ-ray emission around star clusters, isolated supernova remnants, and pulsar wind nebulae indicate that the cosmic-ray (CR) diffusion coefficient near acceleration sites can be suppressed by a large factor compared to the Galaxy average. We explore the effects of such local suppression of CR diffusion on galaxy evolution using simulations of isolated disk galaxies with regular and high gas fractions. Our results show that while CR propagation with constant diffusivity can make gaseous disks more stable by increasing the midplane pressure, large-scale CR pressure gradients cannot prevent local fragmentation when the disk is unstable. In contrast, when CR diffusivity is suppressed in star-forming regions, the accumulation of CRs in these regions results in strong local pressure gradients that prevent the formation of massive gaseous clumps. As a result, the distribution of dense gas and star formation changes qualitatively: a globally unstable gaseous disk does not violently fragment into massive star-forming clumps but maintains a regular grand-design spiral structure. This effect regulates star formation and disk structure and is qualitatively different from and complementary to the global role of CRs in vertical hydrostatic support of the gaseous disk and in driving galactic winds.