Miracle-dz/UniFAR-FTUs huggingface dataset:
Rayleigh-Sommerfeld scalar diffraction by apertures moving at relativistic speeds

We have analytically obtained the theoretical results for Rayleigh-Sommerfeld (R-S) scalar diffraction by apertures such as single-slit, double-slit, grating, and circular apertures, moving at relativistic speeds with velocities perpendicular to the direction of incidence. We also have studied diffraction by the single slit of an oscillatory shutter. Significantly, our study probes the relativistic transverse Doppler effect on the intensity pattern of the diffracted field.
Non-protein-coding RNAs

1 General Information 1 1.1 Identification of ncRNAs in the wet-lab . 2 1.1.1 ncRNA flavors . 3 1.2 Computational identification of ncRNAs . 3 1.2. 1 ncRNAs and small peptide-coding genes databases . 5 1.3 Small peptides and ncRNAs in A. thaliana . 6
CURI: A Benchmark for Productive Concept Learning Under Uncertainty

Humans can learn and reason under substantial uncertainty in a space of infinitely many concepts, including structured relational concepts ("a scene with objects that have the same color") and ad-hoc categories defined through goals ("objects that could fall on one's head"). In contrast, standard classification benchmarks: 1) consider only a fixed set of category labels, 2) do not evaluate compositional concept learning and 3) do not explicitly capture a notion of reasoning under uncertainty. We introduce a new few-shot, meta-learning benchmark, Compositional Reasoning Under Uncertainty (CURI) to bridge this gap. CURI evaluates different aspects of productive and systematic generalization, including abstract understandings of disentangling, productive generalization, learning boolean operations, variable binding, etc. Importantly, it also defines a model-independent "compositionality gap" to evaluate the difficulty of generalizing out-of-distribution along each of these axes. Extensive evaluations across a range of modeling choices spanning different modalities (image, schemas, and sounds), splits, privileged auxiliary concept information, and choices of negatives reveal substantial scope for modeling advances on the proposed task. All code and datasets will be available online.
Determination for minimum symbol-pair and RT weights of repeated-root cyclic codes

In this paper, we determine the minimum symbol-pair weight and RT weight of repeated-root cyclic codes over $\mathfrak R=\mathbb F_{p^m}[u]/\langle u^4\rangle$ of length $n=p^k$. For the determination, we explicitly present a third torsional degree for all different types of cyclic codes over $\mathfrak R$ of length $n$.
Learning to Generalize for Sequential Decision Making

We consider problems of making sequences of decisions to accomplish tasks, interacting via the medium of language. These problems are often tackled with reinforcement learning approaches. We find that these models do not generalize well when applied to novel task domains. However, the large amount of computation necessary to adequately train and explore the search space of sequential decision making, under a reinforcement learning paradigm, precludes the inclusion of large contextualized language models, which might otherwise enable the desired generalization ability. We introduce a teacher-student imitation learning methodology and a means of converting a reinforcement learning model into a natural language understanding model. Together, these methodologies enable the introduction of contextualized language models into the sequential decision making problem space. We show that models can learn faster and generalize more, leveraging both the imitation learning and the reformulation. Our models exceed teacher performance on various held-out decision problems, by up to 7% on in-domain problems and 24% on out-of-domain problems.
Recyclable Gaussian Processes

We present a new framework for recycling independent variational approximations to Gaussian processes. The main contribution is the construction of variational ensembles given a dictionary of fitted Gaussian processes without revisiting any subset of observations. Our framework allows for regression, classification and heterogeneous tasks, i.e. mix of continuous and discrete variables over the same input domain. We exploit infinite-dimensional integral operators based on the Kullback-Leibler divergence between stochastic processes to re-combine arbitrary amounts of variational sparse approximations with different complexity, likelihood model and location of the pseudo-inputs. Extensive results illustrate the usability of our framework in large-scale distributed experiments, also compared with the exact inference models in the literature.
Lactobacillus Plantarum HFY15 Helps Prevent Retinoic Acid-Induced Secondary Osteoporosis in Wistar Rats

A rat model of secondary osteoporosis was constructed using retinoic acid as an inducer, and the genes, proteins, and bone mass of the rats were analyzed. qPCR detection of the Wnt/β-catenin and OPG/RANK/RANKL signaling pathway-related gene expression levels showed that Lactobacillus plantarum HFY15 played a positive role in regulating both pathways. HFY15 significantly increased β-catenin, Lrp5, Lrp6, Wnt10b, OPG, RANKL, and Runx2 expression and downregulated DKK1, RANK, CTSK, TRACP, and ALP expression. Enzyme-linked immunosorbent assays further confirmed the qPCR results. Tartrate-resistant acid phosphatase staining showed that HFY15 slowed retinoic acid-induced osteoclast formation. Microcomputed tomography showed that HFY15 reduced trabecular separation and increased the percent bone volume, trabecular numbers, trabecular thickness, and bone mineral density in the rats in vivo. These findings indicate that HFY15 may help prevent retinoic acid-induced secondary osteoporosis in vivo.
Toward an information theoretical description of communication in brain networks

Abstract Modeling communication dynamics in the brain is a key challenge in network neuroscience. We present here a framework that combines two measurements for any system where different communication processes are taking place on top of a fixed structural topology: path processing score (PPS) estimates how much the brain signal has changed or has been transformed between any two brain regions (source and target); path broadcasting strength (PBS) estimates the propagation of the signal through edges adjacent to the path being assessed. We use PPS and PBS to explore communication dynamics in large-scale brain networks. We show that brain communication dynamics can be divided into three main “communication regimes” of information transfer: absent communication (no communication happening); relay communication (information is being transferred almost intact); and transducted communication (the information is being transformed). We use PBS to categorize brain regions based on the way they broadcast information. Subcortical regions are mainly direct broadcasters to multiple receivers; Temporal and frontal nodes mainly operate as broadcast relay brain stations; visual and somatomotor cortices act as multichannel transducted broadcasters. This work paves the way toward the field of brain network information theory by providing a principled methodology to explore communication dynamics in large-scale brain networks.
Influenza A Virus Induces Autophagy by Its Hemagglutinin Binding to Cell Surface Heat Shock Protein 90AA1

Autophagy can be utilized by the influenza A virus (IAV) to facilitate its replication. However, whether autophagy is induced at the stage of IAV entry is still unclear. Here, we report that IAV induces autophagy by hemagglutinin (HA) binding to heat shock protein 90AA1 (HSP90AA1) distributed on the cell surface. Virus overlay protein binding assay and pull-down assay indicated that IAV HA bound directly to cell surface HSP90AA1. Knockdown of HSP90AA1 weakened H1N1 infection. Incubation of IAV viral particles with recombinant HSP90AA1 or prior blockade of A549 cells with an anti-HSP90AA1 antibody could inhibit attachment of IAV. Moreover, we found that recombinant HA1 protein binding to cell surface HSP90AA1 was sufficient to induce autophagy through the AKT-MTOR pathway. Our study reveals that the HSP90AA1 on cell surface participates in IAV entry by directing binding to the HA1 subunit of IAV and subsequently induces autophagy.
From the Gut to the Brain and Back: Therapeutic Approaches for the Treatment of Network Dysfunction in Parkinson's Disease

Parkinson's disease (PD) is a complex, multisystem, progressive, degenerative disorder characterized by severe, debilitating motor dysfunction, cognitive impairments, and mood disorders. Although preclinical research has traditionally focused on the motor deficits resulting from the loss of nigrostriatal dopaminergic neurons, up to two thirds of PD patients present separate and distinct behavioral changes. Loss of basal forebrain cholinergic neurons occurs as early as the loss of dopaminergic cells and contributes to the cognitive decline in PD. In addition, attentional deficits can limit posture control and movement efficacy caused by dopaminergic cell loss. Complicating the picture further is intracellular α-synuclein accumulation beginning in the enteric nervous system and diffusing to the substantia nigra through the dorsal motor neurons of the vagus nerve. It seems that α-synuclein's role is that of mediating dopamine synthesis, storage, and release, and its function has not been completely understood. Treating a complex, multistage network disorder, such as PD, likely requires a multipronged approach. Here, we describe a few approaches that could be used alone or perhaps in combination to achieve a greater mosaic of behavioral benefit. These include (1) using encapsulated, genetically modified cells as delivery vehicles for administering neuroprotective trophic factors, such as GDNF, in a direct and sustained means to the brain; (2) immunotherapeutic interventions, such as vaccination or the use of monoclonal antibodies against aggregated, pathological α-synuclein; (3) the continuous infusion of levodopa-carbidopa through an intestinal gel pad to attenuate the loss of dopaminergic function and manage the motor and non-motor complications in PD patients; and (4) specific rehabilitation treatment programs for drug-refractory motor complications.
Reinforcing Fisheries Management through Semantic Data Integration

The European project BlueCloud is developing pilot demonstrator applications with the goal of establishing a marine-themed European Open Science Cloud (EOSC) for the blue economy and marine environment. “Fish, a matter of scales” is one of these demonstrators that aims to improve data management and analytical capabilities of fisheries. Fisheries management is a laborious task that relies on data analysis using complex models and fine-grained software over several sources of information in order to deduce certain facts with the overall aim of improving the sustainability of fisheries. It includes the usually manual process of identifying and combining different parts of information, which is an extremely time-consuming and error-prone process. The key indicators for efficient fisheries management are stocks and fisheries. Stocks refer to groups or individuals of a species occupying a well-defined spatial range (e.g. swordfish in the Mediterranean Sea). Fisheries describe the activities leading to the harvesting of the fish within a particular area, using a particular method or equipment and purpose of activity (e.g. the Atlantic cod fishery in the area of East and South Greenland). The knowledge of the status and the trends of stocks and fisheries at regional, national and local levels is the key factor for highly reliable fisheries management. To this end, the Global Record of Stocks and Fisheries (GRSF) [1], developed within the context of the EU H2020 project BlueBRIDGE (GA no: 675680, 2015-2018), has collated stocks and fisheries information from three distinct data sources: FIRMS from the Food and Agriculture Organization of the United Nations (FAO), RAM Legacy Stock Assessment database and FishSource from the Sustainable Fisheries Partnership. These sources were chosen because they contain complementary information both conceptually and geographically. By collating these sources, the reporting coverage of any of the single entities is increased. To achieve this, we have defined a workflow of activities that semantically integrate these sources in order to deliver a single source of
Experimental evidence that hyperthermia limits offspring provisioning in a temperate-breeding bird

In many vertebrates, parental care can require long bouts of daily exercise that can span several weeks. Exercise, especially in the heat, raises body temperature, and can lead to hyperthermia. Typical strategies for regulating body temperature during endurance exercise include modifying performance to avoid hyperthermia (anticipatory regulation) and allowing body temperature to rise above normothermic levels for brief periods of time (facultative hyperthermia). Facultative hyperthermia is commonly employed by desert birds to economize on water, but this strategy may also be important for chick-rearing birds to avoid reducing offspring provisioning when thermoregulatory demands are high. In this study, we tested how chick-rearing birds balance their own body temperature against the need to provision dependent offspring. We experimentally increased the heat dissipation capacity of breeding female tree swallows (Tachycineta bicolor) by trimming their ventral feathers and remotely monitored provisioning rates, body temperature and the probability of hyperthermia. Birds with an experimentally increased capacity to dissipate heat (i.e. trimmed treatment) maintained higher feeding rates than controls at high ambient temperatures (greater than or equal to 25°C), while maintaining lower body temperatures. However, at the highest temperatures (greater than or equal to 25°C), trimmed individuals became hyperthermic. These results provide evidence that chick-rearing tree swallows use both anticipatory regulation and facultative hyperthermia during endurance performance. With rising global temperatures, individuals may need to increase their frequency of facultative hyperthermia to maintain nestling provisioning, and thereby maximize reproductive success.
Cementless Metaphyseal Sleeve Fixation in Revision Knee Arthroplasty: Our Experience with an Arabic Population at the Midterm

Objective Metaphyseal sleeve (MS) fixation in revision knee arthroplasty (RKA) among Western populations has been reported with very encouraging outcomes. The aim of this study was to report our experience with the use of MS in RKA among an Arabic population. Clinical and radiographic outcomes and implant survivorship were reported at a minimum follow-up of 2 years and a mean follow-up of 4.1 years. Methods A retrospective analysis was conducted on prospectively collected data of patients who underwent RKA with a MS in combination with a cementless stem (femoral or tibial). Range of motion (ROM) and Knee Society Score (KSS) were obtained pre- and postoperatively. Complications, occurrence of stem-tip pain, and implant survival were documented. Knee radiographs were obtained to evaluate the alignment and osseointegration or loosening of the MS. Results A total of 52 sleeves (27 tibial and 25 femoral) implanted in 27 RKAs (27 patients) were included. The mean follow-up period was 4.1 ± 1.8 (2–7.5) years. Postoperatively, the ROM improved from 89.3 ± 9.2 to 106.3 ± 11.4 (p = 0.19) and the KSS also significantly improved, from 102.9 ± 35.6 to 130.2 ± 33.7 (p < 0.001). One patient (3.7%) developed heterotopic ossification, and another one (3.7 %) had a stem-tip pain on the tibial side; both were managed conservatively. One patient (3.7 %) sustained a fracture and required reoperation. None of the sleeves showed progressive radiolucent lines, and none required revision. The aseptic survivorship and overall survivorship at a mean of 4.1 years were 100% and 96.3%, respectively. Conclusion MS provided successful midterm outcomes that were maintained in obese patients with different levels of constraint. Our series supports their use as a viable option in RKA.
DNA from resin-embedded organisms: Past, present and future

Past claims have been made for fossil DNA recovery from various organisms (bacteria, plants, insects and mammals, including humans) dating back in time from thousands to several million years BP. However, many of these recoveries, especially those described from million-year-old amber (fossil resin), have faced criticism as being the result of modern environmental contamination and for lack of reproducibility. Using modern genomic techniques, DNA can be obtained with confidence from a variety of substrates (e.g. bones, teeth, gum, museum specimens and fossil insects) of different ages, albeit always less than one million years BP, and results can also be obtained from much older materials using palaeoproteomics. Nevertheless, new attempts to determine if ancient DNA (aDNA) is present in insects preserved in 40 000-year old sub-fossilised resin, the precursor of amber, have been unsuccessful or not well documented. Resin-embedded specimens are therefore regarded as unsuitable for genetic studies. However, we demonstrate here, for the first time, that although a labile molecule, DNA is still present in platypodine beetles (Coleoptera: Curculionidae) embedded in six-year-old and two-year-old resin pieces from Hymenaea verrucosa (Angiospermae: Fabaceae) collected in Madagascar. We describe an optimised method which meets all the requirements and precautions for aDNA experiments for our purpose: to explore the DNA preservation limits in resin. Our objective is far from starting an uncontrolled search for aDNA in amber as it was in the past, but to start resolving basic aspects from the DNA preservation in resin and search from the most modern samples to the ancient ones, step by step. We conclude that it is therefore possible to study genomics from resin-embedded organisms, although the time limits remain to be determined.
Designing a quantum network protocol

The second quantum revolution brings with it the promise of a quantum internet. As the first quantum network hardware prototypes near completion new challenges emerge. A functional network is more than just the physical hardware, yet work on scalable quantum network systems is in its infancy. In this paper we present a quantum network protocol designed to enable end-to-end quantum communication in the face of the new fundamental and technical challenges brought by quantum mechanics. We develop a quantum data plane protocol that enables end-to-end quantum communication and can serve as a building block for more complex services. One of the key challenges in near-term quantum technology is decoherence --- the gradual decay of quantum information --- which imposes extremely stringent limits on storage times. Our protocol is designed to be efficient in the face of short quantum memory lifetimes. We demonstrate this using a simulator for quantum networks and show that the protocol is able to deliver its service even in the face of significant losses due to decoherence. Finally, we conclude by showing that the protocol remains functional on the extremely resource limited hardware that is being developed today underlining the timeliness of this work.
Effects of ACEIs and ARBs on the Residual Renal Function in Peritoneal Dialysis Patients: A Meta-Analysis of Randomized Controlled Trials

Background In peritoneal dialysis (PD) patients, whether angiotensin-converting enzyme inhibitors (ACEIs) and angiotensin receptor blockers (ARBs) could protect residual renal function is still controversial. To assess the effects of ACEIs and ARBs on the residual renal function and cardiovascular (CV) events in peritoneal dialysis patients, we performed a meta-analysis of randomized controlled trials. Materials and Methods We searched PubMed, EMBASE, the Cochrane Library, the CNKI database, and the Wanfang database for relevant articles from database inception to November 30, 2019. Randomized controlled trials were included. The primary outcome was the decline in the residual renal function (RRF). Results Thirteen trials with 625 participants were included in the meta-analysis. The average residual GFR declined by 1.79 ml/min per 1.73 m2 in the ACEI/ARB group versus 1.44 ml/min per 1.73 m2 in the placebo or active control group at 3 mo. The average residual GFR declined by 2.02 versus 2.06, 2.16 versus 2.72, and -0.04 versus 2.74 ml/min per 1.73 m2 in the placebo or active control group at 6 months (mo), 12 mo, and 24 mo, respectively. The decline in residual GFR showed a significant difference between the ACEI/ARB group and the placebo or active control group at 12 mo (MD = −0.64 ml/min per 1.73 m2; 95% CI: -0.97~-0.32; I2 = 44%; P < 0.0001). No significant difference was observed in Kt/V, urinary protein excretion, weekly creatinine clearance, CV events, or serum potassium levels. Conclusions In the present study, we found that the use of ACEIs and ARBs, especially long-term treatment, decreased the decline of RRF in patients on PD. ACEIs and ARBs do not cause an additional risk of side effects.
Biological Activity of IGRs Against Four Stored-Product Coleopterans

Four insect growth regulators (IGRs), BAY SIR 8514 [1-4-trifluoromethoxyphenyl)- 3-(2-chlorobenzoyl) urea], diflubenzuron, methoprene, and MV-678 [2-methoxy 9-( p isopropylphenyl)-2,6-dimethylnonane], applied at 5 ppm to wheat flour or grain, were evaluated against Oryzaephilus surinamensis (L.), Tribolium castaneum (Herbst), Rhyzopertha dominica (F.), and Sitophilus oryzae (L.). BAY SIR 8514 and diflubenzuron zuron were highly active against the eggs and younger larvae of O. surinamensis, T. castaneum , and R. dominica Methoprene, besides its ovicidal action against O. surinamensis and R. dominica , caused substantial mortality in the full-grown larvae of the three species. BAY SIR 8514 and methoprene also affected the subsequent progeny production of parent adults preexposed to IGR-treated food for 2 weeks. MV-678 appeared to be the least active compound tested. Diflubenzuron and methoprene had no adverse effects on the development of S. oryzae inside grain kernels infested with parent adults 1 day after grain was treated. However, in grain treated with BAY SIR 8514, diflubenzuron, and methoprene and infested with this insect after 12 months of posttreatment storage, the development of this species was arrested significantly. BAY SIR 8514 and diflubenzuron were more active against the eggs and younger larvae, with methoprene showing activity against all stages from egg to preemergence adults of this species. In testing IGRs against internal feeders, it is important to allow for penetration of the active ingredients into the inner portions of grain kernels before assessing effects.
Differences in stress defence mechanisms in germinating seeds of Pinus sylvestris exposed to various lead chemical forms

Exposure to lead (Pb) can have serious toxic effects on the physiological and biochemical processes of plants. The chemical form of the metal determines the degree of its toxicity. In our research, we examined the effect of lead in the form of lead nitrate [Pb(NO3)2] and lead chloride (PbCl2) in concentrations of 12.5 mM and 25 mM on pine (Pinus sylvestris) seed germination. Nitrogen salt causes more severe changes than chloride salt. Increasing levels of electrolyte leakage, malondialdehyde, and hydrogen peroxide were detected during germination processes. The high levels of ROS lead to redox changes in the cell. We observed a reduction in the level of the reduced form of glutathione (GSH), and at the same time observed increased levels of the oxidised form of glutathione (GSSG) depending on the concentration and also the time of exposure to lead compounds. At the beginning of germination processes, the effective non-enzymatic activity of the antioxidant cycle was dominant, and at the late stage the enzymatic activity was noticed in the presence of Pb compounds. CAT activity significantly increased after Pb compound exposition.