Miracle-dz/UniFAR-FTUs huggingface dataset:
IL-33 Is an Unconventional Alarmin That Stimulates IL-2 Secretion by Dendritic Cells To Selectively Expand IL-33R/ST2+ Regulatory T Cells

IL-33 is a recently characterized IL-1 family member that is proposed to function as an alarmin, or endogenous signal of cellular damage, as well as act as a pleiotropic cytokine. The ability of IL-33 to potentiate both Th1 and Th2 immunity supports its role in pathogen clearance and disease immunopathology. Yet, IL-33 restrains experimental colitis and transplant rejection by expanding regulatory T cells (Treg) via an undefined mechanism. We sought to determine the influence of IL-33 on hematopoietic cells that drives Treg expansion and underlies the therapeutic benefit of IL-33 administration. In this study, we identify a feedback loop in which conventional mouse CD11c+ dendritic cells (DC) stimulated by IL-33 secrete IL-2 to selectively expand IL-33R(ST2+)– suppressive CD4+Foxp3+ Treg. Interestingly, this occurs in the absence of classical DC maturation, and DC-derived (innate) IL-2 increases ST2 expression on both DC and interacting Treg. ST2+ Treg represent an activated subset of Foxp3+ cells, demonstrated to be ICOShighCD44high compared with their ST2− counterparts. Furthermore, although studies have shown that IL-33–exposed DC promote Th2 responses, we reveal that ST2+ DC are required for IL-33–mediated in vitro and in vivo Treg expansion. Thus, we have uncovered a relationship between IL-33 and innate IL-2 that promotes the selective expansion of ST2+ Treg over non-Treg. These findings identify a novel regulatory pathway driven by IL-33 in immune cells that may be harnessed for therapeutic benefit or for robust expansion of Treg in vitro and in vivo.
Presentation to T Cells Receptor DC-SIGN Internalizes Antigen for The Dendritic Cell-Specific Adhesion

Dendritic cells (DCs) capture Ags or viruses in peripheral tissue to transport them to lymphoid organs to induce cellular T cell responses. Recently, a DC-speciﬁc C-type lectin was identiﬁed, DC-speciﬁc ICAM-grabbing non-integrin (DC-SIGN), that functions as cell adhesion receptor mediating both DC migration and T cell activation. DC-SIGN also functions as an HIV-1R that captures HIVgp120 and facilitates DC-induced HIV transmission of T cells. Internalization motifs in the cytoplasmic tail of DC-SIGN hint to a function of DC-SIGN as endocytic receptor. In this study we demonstrate that on DCs DC-SIGN is rapidly internalized upon binding of soluble ligand. Mutating a putative internalization motif in the cytoplasmic tail reduces ligand-induced internalization. Detailed analysis using ratio ﬂuorescence imaging and electron microscopy showed that DC-SIGN-ligand complexes are targeted to late endosomes/lysosomes. Moreover, ligands internalized by DC-SIGN are efﬁciently processed and presented to CD4 (cid:1) T cells. The distinct pattern of expression of C-type lectins on DCs in situ and their nonoverlapping Ag recognition proﬁle hint to selective functions of these receptors to allow a DC to recognize a wide variety of Ags and to process these to induce T cell activation. These data point to a novel function of the adhesion receptor DC-SIGN as an efﬁcient DC-speciﬁc Ag receptor that can be used as a target to induce viral and antitumor immunity. The Journal of Immunology, 2002, 168: 2118–2126.
The general totally positive matrix completion problem with few unspecified entries.

For m by n partial totally positive matrices with exactly one unspeci ed entry the set of positions for that entry that guarantee completability to a totally positive matrix are characterized They are the positions i j i j and the positions i j i j m n In each case the set of completing entries is an open and in nite in case i j or i m j n interval In the process some new structural results about totally positive matrices are developed In addition the pairs of positions that guarantee completability in partial totally positive matrices with two unspeci ed entries are characterized in low dimensions
Armitage lecture 2010: Understanding treatment effects: the value of integrating longitudinal data and survival analysis

There is a single‐minded focus on events in survival analysis, and we often ignore longitudinal data that are collected together with the event data. This is due to a lack of methodology but also a result of the artificial distinction between survival and longitudinal data analyses. Understanding the dynamics of such processes is important but has been hampered by a lack of appreciation of the difference between confirmatory and exploratory causal inferences. The latter represents an attempt at elucidating mechanisms by applying mediation analysis to statistical data and will usually be of a more tentative character than a confirmatory analysis.
Prostaglandin E Receptors*

Prostaglandin (PG) E2 exerts its actions by acting on a group of G-protein-coupled receptors (GPCRs). There are four GPCRs responding to PGE2 designated subtypes EP1, EP2, EP3, and EP4 and multiple splicing isoforms of the subtype EP3. The EP subtypes exhibit differences in signal transduction, tissue localization, and regulation of expression. This molecular and biochemical heterogeneity of PGE receptors leads to PGE2 being the most versatile prostanoid. Studies on knock-out mice deficient in each EP subtype have defined PGE2 actions mediated by each subtype and identified the role each EP subtype plays in various physiological and pathophysiological responses. Here we review recent advances in PGE receptor research.
Evaluation of perennial ryegrass straw as a forage source for ruminants1

Two experiments were conducted to evaluate perennial ryegrass straw as a forage source for ruminants. Experiment 1 evaluated digestion and physiological variables in steers offered perennial ryegrass straw containing increasing levels of ergot alkaloid, lolitrem B. Sixteen ruminally cannulated Angus × Hereford steers (231 ± 2 kg BW) were blocked by weight and assigned randomly to one of four treatments. Steers were provided perennial ryegrass straw at 120% of the previous 5-d average intake. Before straw feeding, soybean meal was provided (0.1% BW; CP basis) to meet the estimated requirement for degradable intake protein. Low (L) and high (H) lolitrem B straws (<100 and 1,550 ppb, respectively; DM basis) were used to formulate treatment diets: 100% L; 67% L:33% H; 33% L:67% H; 100% H (DM basis). Intake and digestibility of DM and OM, and ruminal pH, total VFA, and NH3-N were not affected by increasing lolitrem B concentration. Ruminal indigestible ADF (IADF) fill increased linearly (P = 0.01) and IADF passage rate decreased linearly (P = 0.04) as lolitrem B increased. Experiment 2 evaluated performance and production by 72 Angus × Hereford cows (539 ± 5 kg BW) consuming perennial ryegrass straw containing
Determinism versus nondeterminism with arithmetic tests and computation: extended abstract

For each natural number d we consider a finite structure md whose universe is the set of all 0,1-sequence of length n=2d, each representing a natural number in the set [0,1,. ,2n-1] in binary form. The operations included in the structure are the four constants 0,1,2n-1,n, multiplication and addition modulo 2n, the unary function min[2x, 2n-1], the binary functions ⌊ x/y⌋ (with ⌊ x/0 ⌋ =0), max(x,y), min(x,y), and the boolean vector operations ∧,∨,- defined on 0,1 sequences of length n by performing the operations on all components simultaneously. These are essentially the arithmetic operations that can be performed on a RAM, with wordlength n, by a single instruction. We show that there exists a term (that is, an algebraic expression) F(x,y) built up from the mentioned operations, with the only free variables x,y, such that for all terms G(y), which is also built up from the mentioned operations, the following holds. For infinitely many positive integers d, there exists an a ∈ md such that the following two statements are not equivalent: (i) md |= ∃ x, F(x,a), (ii) md models G(a)=0. In other words, the question whether an existential statement, depending on the parameter a ∈ md is true or not, cannot be decided by evaluating an algebraic expression at a. Another way of formulating the theorem, in a slightly stronger form, is, that over the structures md, quantifier elimination is not possible in the following sense. Let calm be a first-order language with equality, containing function symbols for all of the mentioned arithmetic operations. Then there exists an existential first-order formula φ(y) of calm, containing a single existential quantifier and the only free variable y, such that for each propositional formula P(y) of calm, we have that for infinitely many positive integers d, φ(y) and P(y) are not equivalent on md, that is, md |= - ∀ y, φ(y) <-> P(y). We also show that the theorem, in both forms, remains true if the binary operation min [xy, 2n-1] is added to the structure md. A general theorem is proved as well, which describes sufficient conditions for a set of operations on a sequence of structures kd, d=1,2,. which guarantees that the analogues of the mentioned theorems holds for the structures kd too.
Rural-urban migration, welfare and employment: Comparing results from Thailand and Vietnam

This paper compares empirical findings on the motivation and welfare impacts of rural-urban migration from two comprehensive case studies conducted in Thailand and Vietnam. Panel data of around 4,000 rural households and tracking surveys of close to 1,000 migrants are used from the two countries. The studies find that outcomes depend to a large extent on the development status of the country. Rural households consider outmigration mostly as a livelihood support strategy. Given the scarcity of employment opportunities in the rural areas, migrants see themselves forced to look for jobs in the cities. Interestingly, most migrants perceive themselves to be better off in the cities. The rural households left behind benefit from migration as the remittances tend to have positive income growth effects. The research confirms the calls for improved social protection for migrants in urban areas and for quality schooling in the rural areas.
Use Of Sednet Model To Establish Sediment Export Targets For Catchments Of The Wet Tropics Draining To The Great Barrier Reef

Some of the inshore reefs of the Great Barrier Reef are showing impacts consistent with a decline in water quality as a result of increased sediments and nutrients. The Wet Tropics covers approximately 2.2 million hectares and includes 91 percent of the Wet Tropics World Heritage area. The climate and geomorphologic conditions of the region are unique in Australia and generally result in fast flowing streams with high discharge rates into the GBR. The exception is the drier Herbert River.
Adversarial queueing theory

We introduce a new approach to the study of dynamic (or continuous) packet routing, where packets are being continuously injected into a network. Our objective is to study what happens to packet routing under continuous injection as a function of network load, for various queueing policies. Our approach is based on the adversarial generation of packets, so that the results are more robust in that they do not hinge upon particular probabilistic assumptions. In suggesting a new approach to studying a classical phenomenon, it is important to give careful consideration to all the relevant previous work in packet routing, queueing theory and probabilistic analysis. We give a more detailed account of previous work in Appendix A, to permit comparison with our work. Here we summarize the salient features of prior work in order to motivate our model. Most prior work on packet routing has been in the static model in which there is a fixed initial set of packet routing requests; when these packets are delivered, the problem is considered solved and the analysis stops there. Static packet routing is a basic problem in the context of parallel computation models, but for the setting of communications networks it is essential to study the case of continuous injection of packets. While it is possible to try modelling such continuous problems statically, by delaying the entry of packets using synchronization barriers, a much more natural approach is to analyze standard (local–control) routing algorithms in this fully dynamic setting. Nearly all previous work in this regard has used probabilistic models for the generation (and sometimes, delivery) of packets. Such work can broadly be classified into: ∗Department of Computer Science, University of Toronto, Toronto, Canada M5S 1A4. Part of this work was performed while visiting the IBM T.J. Watson Research Center. †Laboratory for Computer Science, MIT, Cambridge, MA 02139. Supported by an ONR Graduate Fellowship. Part of this work was performed while visiting the IBM T.J. Watson Research Center. ‡IBM Almaden Research Center, 650 Harry Road, San Jose, CA 95120. §IBM T.J. Watson Research Center, Box 218, Yorktown Heights, NY 10598. 1. Queueing-theoretic approaches, where packets are generated by a Poisson injection process; frequently, each packet is assumed to have a random destination. A common assumption in queueing theory is that the time for a packet to pass through a server (i.e., an edge) is exponentially distributed whereas for packet routing this time is a constant. This apparently slight difference poses a world of subtle difficulties in adapting queueing theory to continuous packet routing.
The Invariance Hypothesis Implies Domain-Specific Regions in Visual Cortex

Is visual cortex made up of general-purpose information processing machinery, or does it consist of a collection of specialized modules? If prior knowledge, acquired from learning a set of objects is only transferable to new objects that share properties with the old, then the recognition system’s optimal organization must be one containing specialized modules for different object classes. Our analysis starts from a premise we call the invariance hypothesis: that the computational goal of the ventral stream is to compute an invariant-to-transformations and discriminative signature for recognition. The key condition enabling approximate transfer of invariance without sacrificing discriminability turns out to be that the learned and novel objects transform similarly. This implies that the optimal recognition system must contain subsystems trained only with data from similarly-transforming objects and suggests a novel interpretation of domain-specific regions like the fusiform face area (FFA). Furthermore, we can define an index of transformation-compatibility, computable from videos, that can be combined with information about the statistics of natural vision to yield predictions for which object categories ought to have domain-specific regions in agreement with the available data. The result is a unifying account linking the large literature on view-based recognition with the wealth of experimental evidence concerning domain-specific regions.
A pilot study of cyber security and privacy related behavior and personality traits

Recent research has begun to focus on the factors that cause people to respond to phishing attacks as well as affect user behavior on social networks. This study examines the correlation between the Big Five personality traits and email phishing response. Another aspect examined is how these factors relate to users' tendency to share information and protect their privacy on Facebook (which is one of the most popular social networking sites). This research shows that when using a prize phishing email, neuroticism is the factor most correlated to responding to this email, in addition to a gender-based difference in the response. This study also found that people who score high on the openness factor tend to both post more information on Facebook as well as have less strict privacy settings, which may cause them to be susceptible to privacy attacks. In addition, this work detected no correlation between the participants estimate of being vulnerable to phishing attacks and actually being phished, which suggests susceptibility to phishing is not due to lack of awareness of the phishing risks and that real-time response to phishing is hard to predict in advance by online users. The goal of this study is to better understand the traits that contribute to online vulnerability, for the purpose of developing customized user interfaces and secure awareness education, designed to increase users' privacy and security in the future.
Seasonal fluctuations in the flux of particulate organic matter discharged from net pens for fish farming

Fish farming using net pens consumes large amounts of food for the reared fish, resulting in organic enrichment of the sediment below the fish farm from organic discharge in the forms of fish feces and food residues. Sediment traps were set at a net pen within and outside a fish farm, and organic flux on the sea floor was compared. The year-mean organic flux to the sea floor caused by fish farming from September 2003 to September 2004 was estimated at 2.11 gC/m2/day in total organic carbon (TOC) and 0.26 gN/m2/day in total nitrogen (TN), which were 2.5 times (TOC flux) and 2.2 times (TN flux) larger than that for natural organic flux outside the fish farm. The seasonal fluctuation patterns of organic flux to the sea floor below the fish farm did not necessarily coincide with those for the amount of food spent for the fish farming. The largest organic flux to the sea floor occurred in the autumn, when the vertical mixing of the water had just started. Therefore, organic enrichment of the sediment on the sea floor of a fish farm proceeded during this season.
Possible association between vitamin D deficiency and restless legs syndrome

Background and aim Restless legs syndrome (RLS) is a distressing sleep disorder that occurs worldwide. Although there have been recent developments in understanding the pathophysiology of RLS, the exact mechanism of the disease has not been well elucidated. An increased prevalence of neurologic and psychiatric diseases involving dopaminergic dysfunction in vitamin D–deficient patients led us to hypothesize that vitamin D deficiency might result in dopaminergic dysfunction and consequently, the development of RLS (in which dopaminergic dysfunction plays a pivotal role). Thus, the aim of this study was to evaluate the relationship between vitamin D deficiency and RLS. Methods One hundred and fifty-five consecutive patients, 18–65 years of age, who were admitted to the Department of Internal Medicine with musculoskeletal symptoms and who subsequently underwent neurological and electromyography (EMG) examination by the same senior neurologist, were included in this study. The patients were divided into two groups according to serum 25-hydroxyvitamin D (25(OH)D) (a vitamin D metabolite used as a measure of vitamin D status) level: 36 patients with serum 25(OH)D levels ≥20 ng/mL comprised the normal vitamin D group, and 119 patients with serum 25(OH)D levels <20 ng/mL comprised the vitamin D deficiency group. The two groups were compared for the presence of RLS and associated factors. Results The two groups were similar in terms of mean age, sex, mean body mass index (BMI), and serum levels of calcium, phosphate, alkaline phosphatase (ALP), and ferritin. The presence of RLS was significantly higher in the vitamin D deficiency group (χ2=12.87, P<0.001). Regression analysis showed vitamin D deficiency and serum 25(OH)D level to be significantly associated with the presence of RLS (odds ratio [OR] 5.085, P<0.001 and OR 1.047, P=0.006, respectively). Conclusion The present study demonstrated a possible association between vitamin D deficiency and RLS. Given the dopaminergic effects of vitamin D, 25(OH)D depletion may lead to dopaminergic dysfunction and may have a place in the etiology of RLS. Prospective vitamin D treatment studies are needed to confirm this relationship and to evaluate the efficacy of vitamin D as a treatment for RLS patients.
Iterative learning of feed-forward corrections for high-performance tracking

We revisit a recently developed iterative learning algorithm that enables systems to learn from a repeated operation with the goal of achieving high tracking performance of a given trajectory. The learning scheme is based on a coarse dynamics model of the system and uses past measurements to iteratively adapt the feed-forward input signal to the system. The novelty of this work is an identification routine that uses a numerical simulation of the system dynamics to extract the required model information. This allows the learning algorithm to be applied to any dynamic system for which a dynamics simulation is available (including systems with underlying feedback loops). The proposed learning algorithm is applied to a quadrocopter system that is guided by a trajectory-following controller. With the identification routine, we are able to extend our previous learning results to three-dimensional quadrocopter motions and achieve significantly higher tracking accuracy due to the underlying feedback control, which accounts for non-repetitive noise.
Synonymous Codon Usage Bias in Porcine Epidemic Diarrhea Virus

ABST RACT In this study, we analyzed the synonymous codon usage bias in porcine epidemic diarrhea virus genome. The effective number of codons (ENC) and the relative synonymous codon usage (RSCU) values are used to estimate codon usage variation. The plot of ENC values against GC3s and correlation analysis revealed that mutational pressure rather than translational selection is the main factor determining the codon usage bias in porcine epidemic diarrhea virus. In addition, other factors, such as aromaticity, hydrophobicity of genes also influenced the codon usage variation among virus genomes in a minor way. Our work might contribute to the understanding of molecular evolution of codon usage variation in porcine epidemic diarrhea virus genome.
Epigenetic Matters: The Link between Early Nutrition, Microbiome, and Long-term Health Development

Epigenetic modifications are among the most important mechanisms by which environmental factors can influence early cellular differentiation and create new phenotypic traits during pregnancy and within the neonatal period without altering the deoxyribonucleic acid sequence. A number of antenatal and postnatal factors, such as maternal and neonatal nutrition, pollutant exposure, and the composition of microbiota, contribute to the establishment of epigenetic changes that can not only modulate the individual adaptation to the environment but also have an influence on lifelong health and disease by modifying inflammatory molecular pathways and the immune response. Postnatal intestinal colonization, in turn determined by maternal flora, mode of delivery, early skin-to-skin contact and neonatal diet, leads to specific epigenetic signatures that can affect the barrier properties of gut mucosa and their protective role against later insults, thus potentially predisposing to the development of late-onset inflammatory diseases. The aim of this review is to outline the epigenetic mechanisms of programming and development acting within early-life stages and to examine in detail the role of maternal and neonatal nutrition, microbiota composition, and other environmental factors in determining epigenetic changes and their short- and long-term effects.
Metaphorical reasoning with an economical set of mappings

This paper discusses the nature of the metaphorical transfer from the source domain to the target domain. More specifically, it explores the question as to how the mapping links between features of the source and the target are created. It is argued that, for many metaphors, it is incorrect to assume that all the elements of the source domain map to elements of the target domain, and that a much more economical set of mappings should be used instead.