Miracle-dz/UniFAR-FTUs huggingface dataset:
Review Paper on Enzyme Supplementation in Poultry Ration

This review paper is prepared with objective of to revise the available scientific information about the role and source of enzyme supplementation in poultry ration. The biggest single expense in any system of poultry production is feed accounting for up to 70% of total production cost per bird. The poultry industry readily accepts enzymes as a standard dietary component, especially in wheat and barley-based rations. Enzymes are biological catalyst composed of amino acids with vitamins and minerals. They bring about biochemical reactions without themselves undergoing any change. Poultry naturally produce enzymes to aid the digestion of feed nutrients. However, they do not have enzyme to break down fiber completely and need exogenous enzymes in feed to aid digestion. According to the purpose of application, feed enzymes can be fundamentally divided in to enzymes which are to quantitatively supplement endogenous digestive enzymes of mono gastric animals (Proteases, lipases, Amylases) and enzymes which are not produced by mono gastric animals (β-glucanases, Pentosanases and Phytases). Specific degradation site in the molecule, PH value, temperature, and presence of aerators / inhibitorsare some factors affecting the activity of enzyme. Bacteria, fungi and yeast are micro-organisms used as a source of enzyme in poultry ration. Some of the enzymes that have been used over the past several years or have potential for use in the poultry feed industry include cellulase (s-glucanases), xylanases and associated enzymes, phytases, proteases, lipases, and galactosidases. The benefits of using enzymes in poultry diets include not only enhanced bird performance and feed conversion but also less environmental problems due to reduced output of excreta, including reducing the gut viscosity, increasing the effectiveness of host (endogenous) enzymes, alteration in feed passage rate, effect on excreta characteristics, effect on litter problems, release of nutrients, availability of phosphorus, increase in available energy, and improvement in nutrient digestibility. The degree of improvement obtained by adding enzymes to the diet depends on many factors including the type and amount of cereal in the diet, the level of anti-nutritive factor in the cereal which can vary within a given cereal (for example, low-versus high-s-glucan barley), the spectrum and concentration of enzymes used, the type of animal (poultry tend to be more responsive to enzyme treatment than pigs), and the age of the animal (young animals tend to respond better to enzymes than older animals), type of gut micro flora present and the physiology of the bird.
Improved Synthetic Training for Reading Comprehension

Automatically generated synthetic training examples have been shown to improve performance in machine reading comprehension (MRC). Compared to human annotated gold standard data, synthetic training data has unique properties, such as high availability at the possible expense of quality. In view of such differences, in this paper, we explore novel applications of synthetic examples to MRC. Our proposed pre-training and knowledge distillation strategies show significant improvements over existing methods. In a particularly surprising discovery, we observe that synthetic distillation often yields students that can outperform the teacher model.
The third realization of the International Celestial Reference Frame by very long baseline interferometry

A new realization of the International Celestial Reference Frame (ICRF) is presented based on the work achieved by a working group of the International Astronomical Union (IAU) mandated for this purpose. This new realization follows the initial realization of the ICRF completed in 1997 and its successor, ICRF2, adopted as a replacement in 2009. The new frame, referred to as ICRF3, is based on nearly 40 years of data acquired by very long baseline interferometry at the standard geodetic and astrometric radio frequencies (8.4 and 2.3 GHz), supplemented with data collected at higher radio frequencies (24 GHz and dual-frequency 32 and 8.4 GHz) over the past 15 years. State-of-the-art astronomical and geophysical modeling has been used to analyze these data and derive source positions. The modeling integrates, for the first time, the effect of the galactocentric acceleration of the solar system (directly estimated from the data) which, if not considered, induces significant deformation of the frame due to the data span. The new frame includes positions at 8.4 GHz for 4536 extragalactic sources. Of these, 303 sources, uniformly distributed on the sky, are identified as “defining sources” and as such serve to define the axes of the frame. Positions at 8.4 GHz are supplemented with positions at 24 GHz for 824 sources and at 32 GHz for 678 sources. In all, ICRF3 comprises 4588 sources, with three-frequency positions available for 600 of these. Source positions have been determined independently at each of the frequencies in order to preserve the underlying astrophysical content behind such positions. They are reported for epoch 2015.0 and must be propagated for observations at other epochs for the most accurate needs, accounting for the acceleration toward the Galactic center, which results in a dipolar proper motion field of amplitude 0.0058 milliarcsecond yr−1 (mas yr−1). The frame is aligned onto the International Celestial Reference System to within the accuracy of ICRF2 and shows a median positional uncertainty of about 0.1 mas in right ascension and 0.2 mas in declination, with a noise floor of 0.03 mas in the individual source coordinates. A subset of 500 sources is found to have extremely accurate positions, in the range of 0.03–0.06 mas, at the traditional 8.4 GHz frequency. Comparing ICRF3 with the recently released Gaia Celestial Reference Frame 2 in the optical domain, there is no evidence for deformations larger than 0.03 mas between the two frames, in agreement with the ICRF3 noise level. Significant positional offsets between the three ICRF3 frequencies are detected for about 5% of the sources. Moreover, a notable fraction (22%) of the sources shows optical and radio positions that are significantly offset. There are indications that these positional offsets may be the manifestation of extended source structures. This third realization of the ICRF was adopted by the IAU at its 30th General Assembly in August 2018 and replaced the previous realization, ICRF2, on January 1, 2019.
Borrelia miyamotoi Serology in a Clinical Population With Persistent Symptoms and Suspected Tick-Borne Illness

Eighty-two patients seeking consultation for long-term sequalae after suspected tick-borne illness were consecutively tested for Borrelia miyamotoi antibodies using a recombinant glycerophosphodiester phosphodiesterase (GlpQ) enzyme immunoassay. Twenty-one of the 82 patients (26%) tested positive on the GlpQ IgG ELISA. Nearly all of the patients (98%) had no prior B. miyamotoi testing, indicating that clinicians rarely test for this emerging tick-borne pathogen. Compared to patients who solely tested positive for Lyme disease antibodies, patients with B. miyamotoi antibodies presented with significantly more sleepiness and pain. A prospective study is needed to ascertain the relationship between the presence of B. miyamotoi antibodies and persistent symptoms.
Lightning-Fast Gravitational Wave Parameter Inference through Neural Amortization

Gravitational waves from compact binaries measured by the LIGO and Virgo detectors are routinely analyzed using Markov Chain Monte Carlo sampling algorithms. Because the evaluation of the likelihood function requires evaluating millions of waveform models that link between signal shapes and the source parameters, running Markov chains until convergence is typically expensive and requires days of computation. In this extended abstract, we provide a proof of concept that demonstrates how the latest advances in neural simulation-based inference can speed up the inference time by up to three orders of magnitude -- from days to minutes -- without impairing the performance. Our approach is based on a convolutional neural network modeling the likelihood-to-evidence ratio and entirely amortizes the computation of the posterior. We find that our model correctly estimates credible intervals for the parameters of simulated gravitational waves.
Zero-Shot Learning from scratch (ZFS): leveraging local compositional representations

Zero-shot classification is a generalization task where no instance from the target classes is seen during training. To allow for test-time transfer, each class is annotated with semantic information, commonly in the form of attributes or text descriptions. While classical zero-shot learning does not explicitly forbid using information from other datasets, the approaches that achieve the best absolute performance on image benchmarks rely on features extracted from encoders pretrained on Imagenet. This approach relies on hyper-optimized Imagenet-relevant parameters from the supervised classification setting, entangling important questions about the suitability of those parameters and how they were learned with more fundamental questions about representation learning and generalization. To remove these distractors, we propose a more challenging setting: Zero-Shot Learning from scratch (ZFS), which explicitly forbids the use of encoders fine-tuned on other datasets. Our analysis on this setting highlights the importance of local information, and compositional representations.
Flexible Piecewise Curves Estimation for Photo Enhancement

This paper presents a new method, called FlexiCurve, for photo enhancement. Unlike most existing methods that perform image-to-image mapping, which requires expensive pixel-wise reconstruction, FlexiCurve takes an input image and estimates global curves to adjust the image. The adjustment curves are specially designed for performing piecewise mapping, taking nonlinear adjustment and differentiability into account. To cope with challenging and diverse illumination properties in real-world images, FlexiCurve is formulated as a multi-task framework to produce diverse estimations and the associated confidence maps. These estimations are adaptively fused to improve local enhancements of different regions. Thanks to the image-to-curve formulation, for an image with a size of 512*512*3, FlexiCurve only needs a lightweight network (150K trainable parameters) and it has a fast inference speed (83FPS on a single NVIDIA 2080Ti GPU). The proposed method improves efficiency without compromising the enhancement quality and losing details in the original image. The method is also appealing as it is not limited to paired training data, thus it can flexibly learn rich enhancement styles from unpaired data. Extensive experiments demonstrate that our method achieves state-of-the-art performance on photo enhancement quantitively and qualitatively.
A Dynamical View on Optimization Algorithms of Overparameterized Neural Networks

When equipped with efficient optimization algorithms, the over-parameterized neural networks have demonstrated high level of performance even though the loss function is non-convex and non-smooth. While many works have been focusing on understanding the loss dynamics by training neural networks with the gradient descent (GD), in this work, we consider a broad class of optimization algorithms that are commonly used in practice. For example, we show from a dynamical system perspective that the Heavy Ball (HB) method can converge to global minimum on mean squared error (MSE) at a linear rate (similar to GD); however, the Nesterov accelerated gradient descent (NAG) only converges to global minimum sublinearly. Our results rely on the connection between neural tangent kernel (NTK) and finite over-parameterized neural networks with ReLU activation, which leads to analyzing the limiting ordinary differential equations (ODE) for optimization algorithms. We show that, optimizing the non-convex loss over the weights corresponds to optimizing some strongly convex loss over the prediction error. As a consequence, we can leverage the classical convex optimization theory to understand the convergence behavior of neural networks. We believe our approach can also be extended to other loss functions and network architectures.
Revisiting Neural Language Modelling with Syllables

Language modelling is regularly analysed at word, subword or character units, but syllables are seldom used. Syllables provide shorter sequences than characters, they can be extracted with rules, and their segmentation typically requires less specialised effort than identifying morphemes. We reconsider syllables for an open-vocabulary generation task in 20 languages. We use rule-based syllabification methods for five languages and address the rest with a hyphenation tool, which behaviour as syllable proxy is validated. With a comparable perplexity, we show that syllables outperform characters, annotated morphemes and unsupervised subwords. Finally, we also study the overlapping of syllables concerning other subword pieces and discuss some limitations and opportunities.
Human Decidual Stromal Cells in Early Pregnancy Induce Functional Re-Programming of Monocyte-Derived Dendritic Cells via Crosstalk Between G-CSF and IL-1β

Accumulation of dendritic cells (DCs) is a special characteristic of the decidual microenvironment. Decidua-infiltrated DCs show unique phenotypes and functions that promote the establishment of fetal-maternal tolerance. However, the regulatory mechanisms yet to be fully investigated. Decidual stromal cells (DSCs) are the major cellular component of decidua tissue. The interactions between DSCs and decidua-infiltrated immunocytes dictate immune tolerance in early pregnancy. Therefore, in the present study, we explore the effect of early pregnancy DSCs on monocyte-derived DCs and the relevant mechanisms. DSC-conditioned DCs showed altered phenotypes, secretion profiles and Th2 priming potential. G-CSF concentration was significantly up-regulated in the co-culture supernatant between DSCs and DCs. Supplementation of G-CSF neutralizing antibody partly reversed the reprogramming of DCs mediated by DSCs. Furthermore, G-CSF production was promoted by IL-1β, which was mainly produced by DCs and significantly up-regulated after their cultivation with DSCs. Interestingly, the effects of DSC on IL-1β production of DCs occurred in their immature stage but not their mature stage. Lastly, no significant difference of G-CSF was found in DSCs from healthy early pregnancy women and spontaneous abortions (SA) patients. However, DSCs from SA patients secreted less G-CSF in response to exogenous rhIL-1β or DC cultivation. In conclusion, our study bolster the understanding of the decidual immunomodulatory microenvironment during early pregnancy, and brings new insight into the potential clinical value of G-CSF in pregnancy disorders.
Ruminant Beslemede Alternatif Yem Katkı Maddelerinin Kullanımı: 1. Probiyotik, Prebiyotik ve Enzim

Hayvan beslemede antibiyotiklerin kullaniminin sinirlandirilmasi, organik urunlerin tuketiciler tarafindan dahafazla tercih edilmesi, bilim adamlarini alternatif yem katki maddelerinin kullanimiyla ilgili calismalar yapmaya yonlendirmistir. Probiyotikler, prebiyotikler ve enzimler alternatif yem katki maddelerinden bazilaridir. Bu alternatif yem katkimaddelerinin genc ve ergin ruminantlarda saglik, performans ve rumen fermentasyonu gibi degerler uzerinde olusturabilecekleri etkiler ve bunun ruminant besleme acisindan onemi uzerinde durulacaktir
A System Dynamics Approach to the Analysis of the Intra- Organisational Ecology Theory

This paper describes how System Dynamics simulation has been used to interpret, test and refine a theoretical framework grounded on a case study. The case analised is Burgelman's account of Intel strategic reorientation which led to the development of the intra-organisational ecology theory of strategy-making. The article explains how System Dynamics simulation has been employed and discusses advantages of coupling simulation, case study analysis and theory building. Introduction Simulation studies have a long tradition in organisational and strategy research, dating back to the seminal works in the area of the behavioural theory of the firm and Modelling and simulation may constitute fundamental elements of a research design. Modelling helps clarify concepts and sharpen the comprehension of a theory. Simulation helps rigorously to deduce consequences from modelled assumptions and to refine hypotheses. An empirical case, for example, coupled with a simulation study, provides a laboratory to test the coherence of theoretical approaches eventually generated. Alternative hypothetical, though dormant, trajectories can be activated by modifying the underlying modelled assumptions and therefore the computer simulation model can be used as a laboratory [Forrester, 1961] thereby providing an appropriate setting to conduct controlled experiments. History can be rerun , showing how small, ab-initio modifications in parameter values can be amplified over time, to yield firms with distinct characteristics. In this light, simulation is a unique methodology to perform this journey backward in history.
The development and hepatotoxicity of acetaminophen: reviewing over a century of progress

Abstract Acetaminophen (APAP) was first synthesized in the 1800s, and came on the market approximately 65 years ago. Since then, it has become one of the most used drugs in the world. However, it is also a major cause of acute liver failure. Early investigations of the mechanisms of toxicity revealed that cytochrome P450 enzymes catalyze formation of a reactive metabolite in the liver that depletes glutathione and covalently binds to proteins. That work led to the introduction of N-acetylcysteine (NAC) as an antidote for APAP overdose. Subsequent studies identified the reactive metabolite N-acetyl-p-benzoquinone imine, specific P450 enzymes involved, the mechanism of P450-mediated oxidation, and major adducted proteins. Significant gaps remain in our understanding of the mechanisms downstream of metabolism, but several events appear critical. These events include development of an initial oxidative stress, reactive nitrogen formation, altered calcium flux, JNK activation and mitochondrial translocation, inhibition of mitochondrial respiration, the mitochondrial permeability transition, and nuclear DNA fragmentation. Additional research is necessary to complete our knowledge of the toxicity, such as the source of the initial oxidative stress, and to greatly improve our understanding of liver regeneration after APAP overdose. A better understanding of these mechanisms may lead to additional treatment options. Even though NAC is an excellent antidote, its effectiveness is limited to the first 16 hours following overdose.
Chemical sensing of microhabitat by pueruli of the reef-dwelling Caribbean spiny lobster Panulirus argus: testing the importance of red algae, juveniles, and their interactive effect

Although our knowledge about the early life of the Caribbean spiny lobster, Panulirus argus (Latreille, 1804), has increased considerably during recent decades, little is known about chemical sensing used by pueruli during settlement. Considering previously-reported benefits of inhabiting red algae Laurencia spp. , such as increased growth rate and costs of close proximity to already settled benthic juveniles from predators, we predicted that the pueruli of P. argus will be attracted to the metabolites produced by red algae and repulsed by metabolites produced by juvenile conspecifics. We also expected that any preference for Laurencia spp. would cease or decrease if this cue was presented together with metabolites produced by conspecific given the reported costs of associating with them after settlement. Our results were not consistent with the predictions above. Our experiments suggest that pueruli do not display any preference for the metabolites produced by red algae or avoidance of metabolites produced by juvenile conspecifics. Unexpectedly, settling stages were attracted to water with a combination of metabolites produced by red algae and juveniles. We also examined the influence of conspecific and red algae abundance on pueruli settlement in Florida Bay, the most important nursery ground of P. argus in the USA. Partially consistent with our experiments, field data indicated that juvenile lobster density had a positive influence on pueruli settlement, as did a synergistic effect of juvenile lobster density and Laurencia spp. algae cover. Altogether, our field and laboratory data suggest that the interplay of environmental cues drives settlement of the Caribbean spiny lobster in a more complex manner than originally thought. Additional studies on the settling behavior of P. argus pueruli are needed to improve our understanding of the relationship between recruitment and fishery stocks in this heavily exploited species.
Revealing the therapeutic effects of aminolevulinate mediated femtosecond laser induced photo-chemotherapy in different cancer cells

Abstract Photodynamic therapy (PDT) is a photo chemotherapeutic strategy that is the application of photosensitizing agent and light on disease or tumor site. The aim of this study is to confirm the feasibility for femtosecond (fs) laser for aminolevulinate (ALA) mediated PDT on skin, breast and bladder cancer cells. Also the remarkable aspects of ALA mediated and laser induced PDT with respect to other literally known applications were investigated. Metastatic melanoma cells SK-MEL30, mammary epithelial carcinoma cells MCF-7 and bladder cancer cells UMUC-3 were treated with ALA and then the cells were irradiated by fs laser at thirty wavelengths in between 230 and 800 nm for 30s and 60s. Anti-cancer effects of ALA phototherapy on different cancer cell lines were determined. Protoporphyrin IX (PpIX) accumulation was visualized by confocal microscopy. The effective PDT wavelengths were applied to evaluate the degree of apoptosis and necrosis in cells. The viability tests demonstrated that wavelengths 400-440 nm and 600-630 nm were found to decrease the viability on three model cell lines. PDT at 630 nm exerted cell death by necrosis and apoptosis after 30 s and 60 s periods. This paper confirms that ALA and femtosecond laser mediated PDT may be used together as therapeutic and diagnostic method to target breast, skin and urinary bladder cancer cells. The use of fs laser allows the flexibility for optimization of wavelength for photosensitizing agents.
Caveolae as Potential Hijackable Gates in Cell Communication

Caveolae are membrane microdomains described in many cell types involved in endocytocis, transcytosis, cell signaling, mechanotransduction, and aging. They are found at the interface with the extracellular environment and are structured by caveolin and cavin proteins. Caveolae and caveolins mediate transduction of chemical messages via signaling pathways, as well as non-chemical messages, such as stretching or shear stress. Various pathogens or signals can hijack these gates, leading to infectious, oncogenic and even caveolin-related diseases named caveolinopathies. By contrast, preclinical and clinical research have fallen behind in their attempts to hijack caveolae and caveolins for therapeutic purposes. Caveolae involvement in human disease is not yet fully explored or understood and, of all their scaffold proteins, only caveolin-1 is being considered in clinical trials as a possible biomarker of disease. This review briefly summarizes current knowledge about caveolae cell signaling and raises the hypothesis whether these microdomains could serve as hijackable “gatekeepers” or “gateways” in cell communication. Furthermore, because cell signaling is one of the most dynamic domains in translating data from basic to clinical research, we pay special attention to translation of caveolae, caveolin, and cavin research into clinical practice.