Miracle-dz/UniFAR-FTUs huggingface dataset:
Assembly of Synthetic Locked Phycocyanobilin Derivatives with Phytochrome in Vitro and in Vivo in Ceratodon purpureus and Arabidopsis[C][W]

This article shows that two synthetic “locked” chromophores, termed 15ZaPCB and 15EaPCB, are incorporated into recombinant phytochrome and that feeding of 15EaPCB to the moss Ceratodon purpureus and the seed plant Arabidopsis thaliana results in an onset of phytochrome effects in darkness. Thus, the 15EaPCB phytochrome adduct mimics Pfr, the physiologically active form of phytochrome. Phytochromes are photoreceptors with a bilin chromophore in which light triggers the conversion between the red light–absorbing form, Pr, and the far-red-light–absorbing form, Pfr. Here we performed in vitro and in vivo studies using locked phycocyanobilin derivatives, termed 15 Z anti phycocyanobilin (15ZaPCB) and 15 E anti PCB (15EaPCB). Recombinant bacterial and plant phytochromes incorporated either chromophore in a noncovalent or covalent manner. All adducts were photoinactive. The absorption spectra of the 15ZaPCB and 15EaPCB adducts were comparable with those of the Pr and Pfr form, respectively. Feeding of 15EaPCB, but not 15ZaPCB, to protonemal filaments of the moss Ceratodon purpureus resulted in increased chlorophyll accumulation, modulation of gravitropism, and induction of side branches in darkness. The effect of locked chromophores on phytochrome responses, such as induction of seed germination, inhibition of hypocotyl elongation, induction of cotyledon opening, randomization of gravitropism, and gene regulation, were investigated in wild-type Arabidopsis thaliana and the phytochrome-chromophore–deficient long hypocotyl mutant hy1. All phytochrome responses were induced in darkness by 15EaPCB, not only in the mutant but also in the wild type. These studies show that the 15Ea stereochemistry of the chromophore results in the formation of active Pfr-like phytochrome in the cell. Locked chromophores might be used to investigate phytochrome responses in many other organisms without the need to isolate mutants. The induction of phytochrome responses in the hy1 mutant by 15EaPCB were however less efficient than by red light irradiation given to biliverdin-rescued seeds or seedlings.
The role of mast cells in oral squamous cell carcinoma

The mast cells are initial effective lineage in both humoral and adaptive immunity. They are ubiquitous in skin, mucosa, and in function. They contain biologically essential and dynamic mediators in healthy and harmful conditions of tissue. Mast cell malfunctioning could be attributed to various chronic allergic diseases. Considerately, emerging evidence of mast cell involvement in various cancers shows them to have both positive and negative roles in tumour growth. It mostly indulges in tumour progression and metastasis via angiogenesis, extracellular matrix degradation, and mitogenic activity in the tumour microenvironment. The current paper reviewed research papers on mast cells in oral squamous cell carcinoma through the PubMed database from 1980 to the present date. The present paper is an attempt to summarise the research reports on the role of mast cells in oral squamous cell carcinoma. Further to this note, this paper also outlines the role of mast cells in normal physiological processes and tumour biology.
AFRICAN RACE-INFLUENCED BILATERAL AMBLYOPIA AMONG WEST INDIAN IMMIGRANTS IN THE UNITED KINGDOM*

, but ophthalmoscopic examination was substantially negative. Visual acuity was 6/36 in each eye. Because of recurrent urticaria, he was examined for evidence of filariasis and onchocerciasis. These examinations, as also haematological, cerebro-spinal fluid, and routine radiological investigations, were negative, except for the presence of cysts of Fentamoeba histolytica in the stools (Prof. Woodruff). The patient was re-examined 5 years later, when the ophthalmological status was found to be entirely unchanged.
Consequences of NMO-IgG binding to aquaporin-4 in neuromyelitis optica

Hinson et al. (1) suggested a unique mechanism for the pathogenesis of neuromyelitis optica (NMO), a neuroinflammatory disease caused by binding of an autoantibody (NMO-IgG) to aquaporin-4 (AQP4) on astrocyte plasma membranes. AQP4 is expressed as long (called M1) and short (called M23) isoforms, the latter forming orthogonal arrays of particles (OAPs). Hinson et al. (1) reported that M1-AQP4 is rapidly internalized in cells whereas M23-AQP4 resists internalization, and that NMO-IgG inhibits AQP4 water permeability. They propose that NMO pathogenesis involves NMO-IgG–induced internalization of M1-AQP4 and direct inhibition of AQP4 water permeability, resulting in increased OAP size, enhanced complement-dependent cytotoxicity, and tissue swelling. Although their mechanism is unique and interesting, data from our laboratory and others challenge each of their major findings and hence the validity of their model.
Susceptibility of Mycobacteria to p-nitrobenzoic acid in relation to their niacin production.

Investigations were carried out on the indirect and direct susceptibility of mycobacteria to p-nitrobenzoic acid as a means of identifying them. Three concentrations of p-aminobenzoic acid in 7H10 medium and one concentration in Lowenstein-Jensen medium were used. Most cultures that produced niacin were susceptible to p-nitrobenzoic acid, and most cultures that did not produce niacin were resistant to this compound. Among the concentrations studied, 500 μg of p-nitrobenzoic acid per ml in 7H10 medium gave the best results in the indirect tests; in direct susceptibility tests in 7H10, 125 μg per ml might be useful.
Measuring and Mitigating AS-level Adversaries Against Tor

The popularity of Tor as an anonymity system has made it a popular target for a variety of attacks. We focus on traffic correlation attacks, which are no longer solely in the realm of academic research with recent revelations about the NSA and GCHQ actively working to implement them in practice. Our first contribution is an empirical study that allows us to gain a high fidelity snapshot of the threat of traffic correlation attacks in the wild. We find that up to 40% of all circuits created by Tor are vulnerable to attacks by traffic correlation from Autonomous System (AS)-level adversaries, 42% from colluding AS-level adversaries, and 85% from statelevel adversaries. In addition, we find that in some regions (notably, China and Iran) there exist many cases where over 95% of all possible circuits are vulnerable to correlation attacks, emphasizing the need for AS-aware relay-selection. To mitigate the threat of such attacks, we build Astoria‐an AS-aware Tor client. Astoria leverages recent developments in network measurement to perform path-prediction and intelligent relay selection. Astoria reduces the number of vulnerable circuits to 2% against AS-level adversaries, under 5% against colluding AS-level adversaries, and 25% against state-level adversaries. In addition, Astoria load balances across the Tor network so as to not overload any set of relays.
Sorghum extract exerts an anti-diabetic effect by improving insulin sensitivity via PPAR-γ in mice fed a high-fat diet

This study investigated the hypothesis that a sorghum extract exerts anti-diabetic effects through a mechanism that improves insulin sensitivity via peroxisome proliferator-activated receptor gamma (PPAR-γ) from adipose tissue. Seven C57BL/6 mice were fed an AIN-93M diet with fat consisting of 10% of total energy intake (LF) for 14 weeks, and 21 mice were fed a high-fat AIN diet with 60% of calories derived from fat (HF). From week 8, the HF diet-fed mice were orally administered either saline (HF group), 0.5% (0.5% SE group), or 1% sorghum extract (1% SE group) for 6 weeks (n = 7/group). Perirenal fat content was significantly lower in the 0.5% SE and 1% SE groups than that in the HF mice. Levels of total and low-density lipoprotein cholesterol, triglycerides, glucose, and the area under the curve for glucose were significantly lower in mice administered 0.5% SE and 1% SE than those in HF mice. Serum insulin level was significantly lower in mice administered 1% SE than that in HF mice or those given 0.5% SE. PPAR-γ expression was significantly higher, whereas the expression of tumor necrosis factor-α was significantly lower in mice given 1% SE compared to those in the HF mice. Adiponectin expression was also significantly higher in mice given 0.5% SE and 1% SE than that in the HF mice. These results suggest that the hypoglycemic effect of SE may be related with the regulation of PPAR-γ-mediated metabolism in this mouse model.
The Order Dimension of Convex Polytopes

With a convex polytope ${\text{M}}$ in $\mathbb{R}^3$, a partially ordered set ${\text{P}}_{\text{M}} $ is associated whose elements are the vertices, edges, and faces of ${\text{M}}$ ordered by inclusion. This paper shows that the order dimension of ${\text{P}}_{\text{M}} $ is exactly 4 for every convex polytope ${\text{M}}$. In fact, the subposet of ${\text{P}}_{\text{M}} $ determined by the vertices and faces is critical in the sense that deleting any element leaves a poset of dimension 3.
Immunogenicity and Efficacy of Cryptococcus neoformans Capsular Polysaccharide Glucuronoxylomannan Peptide Mimotope-Protein Conjugates in Human Immunoglobulin Transgenic Mice

ABSTRACT Peptide mimotopes of capsular polysaccharides have been proposed as antigens for vaccines against encapsulated pathogens. In this study, we determined the antibody response to and efficacy of P13, a peptide mimetic of the Cryptococcus neoformans capsular polysaccharide glucuronoxylomannan (GXM), in mice that produce human antibodies. P13 was conjugated to tetanus toxoid (TT) or diphtheria toxoid (DT) and administered subcutaneously in Alhydrogel with or without CpG to mice transgenic for human immunoglobulin loci (XenoMouse mice) and expressing either immunoglobulin G2 (IgG2) (G2 mice) or IgG4 (G4 mice). Mice were vaccinated and revaccinated two or three times. The serum antibody responses of the mice to GXM and P13 and antibody idiotype expression were analyzed by an enzyme-linked immunosorbent assay. The results showed that both P13-TT and P13-DT were antigenic, inducing a mimetic response to P13 in both G2 and G4 mice, and immunogenic, inducing a mimotope response including VH3 (idiotype)-positive antibodies to GXM in G2 but not G4 mice. CpG led to higher titers of IgG to P13 and GXM in P13-TT-vaccinated G2 mice. C. neoformans challenge of P13-protein conjugate-vaccinated and control G2 mice induced anamnestic IgG- and VH3-positive responses to GXM and was associated with a significantly decreased risk of death and a prolongation of survival in P13-DT-vaccinated mice compared to phosphate-buffered saline-treated or protein carrier-vaccinated mice. These findings reveal that P13 elicited a human antibody response with VH3 expression in human immunoglobulin transgenic mice that has been observed for human antibodies to GXM and support the concept that peptide mimotope-based vaccines may hold promise for the treatment of C. neoformans infections.
Phonological patterns in Mandarin–English bilingual children

Adele Miccio recognized the paucity of information on the phonological development of children from diverse linguistic and cultural backgrounds, and emphasized the need to apply advances in bilingual phonological research toward an appropriate phonological measure for bilingual children. In the spirit of her pioneering work, the present study investigated both Mandarin and English phonological patterns in typically-developing 5-year-old bilingual children in an English-immersion programme in Taiwan. Consonant and vowel accuracy, number and types of phonological processes, and Mandarin-influenced English patterns were assessed on a single-word assessment in each language. Results indicated comparable levels of phoneme accuracy and similar rates and types of phonological processes for bilinguals and their monolingual counterparts. A number of English phonological processes for bilinguals, however, suggested a possible Mandarin influence. The present results reiterate Dr Miccio's call for interdisciplinary collaboration to enhance one's understanding of bilingual language development, to advance successful intervention for bilingual children.
Nongenomic Effects of Aldosterone in the Human Heart: Interaction With Angiotensin II

Aldosterone exerts rapid “nongenomic” effects in various nonrenal tissues. Here, we investigated whether such effects occur in the human heart. Trabeculae and coronary arteries obtained from 57 heart valve donors (25 males; 32 females; 17 to 66 years of age) were mounted in organ baths. Aldosterone decreased contractility in atrial and ventricular trabeculae by maximally 34±3% and 15±4%, respectively, within 5 to 15 minutes after its application. The protein kinase C (PKC) inhibitor chelerythrine chloride, but not the mineralocorticoid receptor antagonists spironolactone and eplerenone, blocked this effect. Aldosterone also relaxed trabeculae that were prestimulated with angiotensin II (Ang II), and its negative inotropic effects were mimicked by hydrocortisone (at 10-fold lower potency) but not 17β-estradiol. Aldosterone concentrations required to reduce inotropy were present in failing but not in normal human hearts. Previous exposure of coronary arteries to 1 &mgr;mol/L aldosterone or 17β-estradiol (but not hydrocortisone) doubled the maximum contractile response (Emax) to Ang II. &Dgr;Emax correlated with extracellular signal-regulated kinase (ERK) 1/2 phosphorylation (P<0.01). Spironolactone and eplerenone did not block the potentiating effect of aldosterone. Studies in porcine renal arteries showed that potentiation also occurred at pmol/L aldosterone levels but not at 17β-estradiol levels <1 &mgr;mol/L. Aldosterone did not potentiate the α1-adrenoceptor agonist phenylephrine. In conclusion, aldosterone induces a negative inotropic response in human trabeculae (thereby antagonizing the positive inotropic actions of Ang II) and potentiates the vasoconstrictor effect of Ang II in coronary arteries. These effects are specific and involve PKC and ERK 1/2, respectively. Furthermore, they occur in a nongenomic manner, and require pathological aldosterone concentrations.
Fetal Cell Based Prenatal Diagnosis: Perspectives on the Present and Future

The ability to capture and analyze fetal cells from maternal circulation or other sources during pregnancy has been a goal of prenatal diagnostics for over thirty years. The vision of replacing invasive prenatal diagnostic procedures with the prospect of having the entire fetal genome in hand non-invasively for chromosomal and molecular studies for both clinical and research use has brought many investigators and innovations into the effort. While the object of this desire, however, has remained elusive, the aspiration for this approach to non-invasive prenatal diagnosis remains and the inquiry has continued. With the advent of screening by cell-free DNA analysis, the standards for fetal cell based prenatal diagnostics have been sharpened. Relevant aspects of the history and the current status of investigations to meet the goal of having an accessible and reliable strategy for capturing and analyzing fetal cells during pregnancy are reviewed.
Domain Separation Networks

The cost of large scale data collection and annotation often makes the application of machine learning algorithms to new tasks or datasets prohibitively expensive. One approach circumventing this cost is training models on synthetic data where annotations are provided automatically. Despite their appeal, such models often fail to generalize from synthetic to real images, necessitating domain adaptation algorithms to manipulate these models before they can be successfully applied. Existing approaches focus either on mapping representations from one domain to the other, or on learning to extract features that are invariant to the domain from which they were extracted. However, by focusing only on creating a mapping or shared representation between the two domains, they ignore the individual characteristics of each domain. We hypothesize that explicitly modeling what is unique to each domain can improve a model's ability to extract domain-invariant features. Inspired by work on private-shared component analysis, we explicitly learn to extract image representations that are partitioned into two subspaces: one component which is private to each domain and one which is shared across domains. Our model is trained to not only perform the task we care about in the source domain, but also to use the partitioned representation to reconstruct the images from both domains. Our novel architecture results in a model that outperforms the state-of-the-art on a range of unsupervised domain adaptation scenarios and additionally produces visualizations of the private and shared representations enabling interpretation of the domain adaptation process.
Temporal Hierarchical Adaptive Texture CRF for Automatic Detection of Gadolinium-Enhancing Multiple Sclerosis Lesions in Brain MRI

We propose a conditional random field (CRF) based classifier for segmentation of small enhanced pathologies. Specifically, we develop a temporal hierarchical adaptive texture CRF (THAT-CRF) and apply it to the challenging problem of gad enhancing lesion segmentation in brain MRI of patients with multiple sclerosis. In this context, the presence of many nonlesion enhancements (such as blood vessels) renders the problem more difficult. In addition to voxel-wise features, the framework exploits multiple higher order textures to discriminate the true lesional enhancements from the pool of other enhancements. Since lesional enhancements show more variation over time as compared to the nonlesional ones, we incorporate temporal texture analysis in order to study the textures of enhanced candidates over time. The parameters of the THAT-CRF model are learned based on 2380 scans from a multi-center clinical trial. The effect of different components of the model is extensively evaluated on 120 scans from a separate multi-center clinical trial. The incorporation of the temporal textures results in a general decrease of the false discovery rate. Specifically, THAT-CRF achieves overall sensitivity of 95% along with false discovery rate of 20% and average false positive count of 0.5 lesions per scan. The sensitivity of the temporal method to the trained time interval is further investigated on five different intervals of 69 patients. Moreover, superior performance is achieved by the reviewed labelings of our model compared to the fully manual labeling when applied to the context of separating different treatment arms in a real clinical trial.
How is theory of mind useful? Perhaps to enable social pretend play

Citation: Dore RA, Smith ED and Lillard AS (2015) How is theory of mind useful? Perhaps to enable social pretend play. It is often claimed that theory of mind (ToM) is facilitated by pretend play (PP), or by a particular type of PP, social pretend play (SPP). Here we challenge that view, proposing instead that ToM might be useful for driving SPP, rather than the reverse. We discuss background theory, review pertinent studies, and explain why the " ToM first " view is at least equally likely. The first form of pretend to consider is solitary PP, emerging at 12–18 months, in which one engages in three basic types of transformation: substitutes one object for another, projects imaginary characteristics onto objects, and imagines situations that do not exist (Leslie, 1987). The second form is social pretend play (SPP), which involves the same basic transformations but occurs with others, and emerges around age 3. We address these two forms of PP consecutively. There is a fundamental similarity, or isomorphism (Leslie, 1987), between PP and ToM. For all three types of transformation just described, PP involves projecting a different reality onto a situation, all while knowing what the real situation is (Lillard, 1993). For example, a child might mentally project a telephone onto a banana, engaging in both of the first two types of transformation. Similarly, understanding false belief—a foundational skill in ToM—involves understanding that someone is projecting a different reality onto a situation, when one knows what the real situation is. For example, a child might see someone as mentally projecting a chocolate bar inside a drawer, while the chocolate bar is actually in the cupboard. Theoretically, then, the ability to imagine a situation that differs from one's present reality underlies both PP and understanding others' minds, in particular, false belief argued that the cognitive architecture that enables one to engage in PP also enables one to understand false belief, suggesting that PP should be related to ToM. Hence it is possible that PP engenders ToM by giving children practice at projecting representations that differ from reality onto that reality. In pursuit of evidence on this point, many researchers have examined the correlation between PP and ToM. For example, Taylor and Carlson (1997) assessed preschoolers' PP sophistication by examining their tendency to use imaginary objects in pretend action sequences (e.g., holding an imaginary toothbrush to brush one's teeth rather than using …
Nationality Classification Using Name Embeddings

Nationality identification unlocks important demographic information, with many applications in biomedical and sociological research. Existing name-based nationality classifiers use name substrings as features and are trained on small, unrepresentative sets of labeled names, typically extracted from Wikipedia. As a result, these methods achieve limited performance and cannot support fine-grained classification. We exploit the phenomena of homophily in communication patterns to learn name embeddings, a new representation that encodes gender, ethnicity, and nationality which is readily applicable to building classifiers and other systems. Through our analysis of 57M contact lists from a major Internet company, we are able to design a fine-grained nationality classifier covering 39 groups representing over 90% of the world population. In an evaluation against other published systems over 13 common classes, our F1 score (0.795) is substantial better than our closest competitor Ethnea (0.580). To the best of our knowledge, this is the most accurate, fine-grained nationality classifier available. As a social media application, we apply our classifiers to the followers of major Twitter celebrities over six different domains. We demonstrate stark differences in the ethnicities of the followers of Trump and Obama, and in the sports and entertainments favored by different groups. Finally, we identify an anomalous political figure whose presumably inflated following appears largely incapable of reading the language he posts in.