Miracle-dz/UniFAR-FTUs huggingface dataset:
Long Noncoding RNA JHDM1D-AS1 Promotes Tumor Growth by Regulating Angiogenesis in Response to Nutrient Starvation

ABSTRACT Long noncoding RNAs play a pivotal role in tumor progression, but their role in cancer cells in the nutrient-starved tumor microenvironment remains unknown. Here, we show that a nutrient starvation-responsive long noncoding RNA, JHDM1D antisense 1 (JHDM1D-AS1), promotes tumorigenesis by regulating angiogenesis in response to nutrient starvation. Expression of JHDM1D-AS1 was increased in cancer cells. In addition, expression of JHDM1D-AS1 was increased in clinical tumor samples compared to that in normal tissue. Stable expression of JHDM1D-AS1 in human pancreatic cancer (PANC-1 and AsPC-1) cells promoted cell growth in vitro. Remarkably, these JHDM1D-AS1-expressing cells showed a significant increase in tumor growth in vivo that was associated with increased formation of CD31+ blood vessels and elevated infiltration of CD11b+ macrophage lineage cells into tumor tissues. Genome-wide analysis of tumor xenografts revealed that expression of genes for tumor-derived angiogenic factors such as hHGF and hFGF1 concomitant with host-derived inflammation-responsive genes such as mMmp3, mMmp9, mS100a8, and mS100a9 was increased in tumor xenografts of JHDM1D-AS1-expressing pancreatic cancer cells, leading to a poor prognosis. Our results provide evidence that increased JHDM1D-AS1 expression under nutrient starvation accelerates tumor growth by upregulating angiogenesis, thus laying the foundation for improved therapeutic strategies.
Hadron spectrum with domain-wall valence quarks on an improved staggered sea

The hadron spectrum is computed in full QCD using domain-wall valence fermions on an improved staggered sea, for pion masses down to around $$350{approx}(/rm MeV)$$. Emphasis is laid on the low-lying baryon spectrum. All possible baryon correlators obtainable from local and quasi-local quark sources are computed, using lattice group-theory methods Results are presented for the lowest-lying states in each isospin channel.
A Practice-Based Study of the Variation of Diagnostics of Dental Caries in New and Old Patients of Different Ages

Data mining of digital dental records provides possibilities for analysing the variation between dentists when diagnosing caries. A total of 71,317 male and 82,302 female subjects visited the health centres in Vantaa and Kemi during the ‘digital era’ (1994–2005). As subjects were classified as ‘new patients’ at the first examination, all re-examinations of the same subjects thereafter by the same dentist produced ‘old patients’. A mean number of decayed surfaces (DS) was counted as a function of the age of the subject during the follow-up. The significance of the difference between old and new patients was determined by the Mann-Whitney test for each age cohort at the cross sections, and for the whole follow-up. Caries was seen to affect new patients more than the old ones in both health centres after the age of 20 years. The mean DS values were the same, reaching about 1 for new and old patients at the age of 15 years. The mean DS had a peak for new patients in both health centres at the age of 25 years and another peak around 45–50 years in Kemi. With a few exceptions there was a significant difference between the DS values of new and old patients at most cross sections and for the whole follow-up time. Evidently dentists examine new patients more carefully than their old patients. After the age of 18 years patients may have changed their dentists because they have finished the free-of-charge treatment period.
Economic gains of a home fortification program: evaluation of "Sprinkles" from the provider's perspective.

INTRODUCTION This paper models the effects of a home-fortification program (using Sprinkles which contain zinc and iron and other micronutrients), in Pakistan, a country with high levels of infant mortality, anemia, and diarrhea. It uses the results of randomized trials of the effect of Sprinkles on anemia and on longitudinal prevalence of diarrhea. METHODS Based on previous literature, the effect of Sprinkles on intermediate outcomes (diarrhea and anemia) is linked to longer-term outcomes (infant and young child mortality, and cognitive achievement and hence adult wages). Three different measures of cost effectiveness are presented: the cost per death averted (effect via zinc supplementation on reduction of longitudinal prevalence of diarrhea); the cost per 'disability adjusted life year' (DALY) saved (same modality); and the gain in earnings due to higher cognitive functioning for each dollar spent (effect via iron supplementation on reduced anemia). RESULTS We estimated that the cost per death averted is dollars406 (dollars273-dollars3248), the cost per DALY saved is dollars12.2 (dollars8-dollars97) and the present value of the gain in earnings is dollars37 (dollars18-dollars51) for each dollar spent on the Sprinkles program. These estimates were developed for a low-income country (GDP per capita = dollars417) with a high infant mortality rate (IMR = 83/1000), high prevalence of anemia (93%), and high mean longitudinal prevalence of diarrhea (17%). DISCUSSION These outcomes are particularly favourable in Pakistan. The outcomes are more favourable when used with children 6-12 months. Further longer-run field trials of Sprinkles with larger populations would be helpful.
Attentive Memory Networks: Efficient Machine Reading for Conversational Search

Recent advances in conversational systems have changed the search paradigm. Traditionally, a user poses a query to a search engine that returns an answer based on its index, possibly leveraging external knowledge bases and conditioning the response on earlier interactions in the search session. In a natural conversation, there is an additional source of information to take into account: utterances produced earlier in a conversation can also be referred to and a conversational IR system has to keep track of information conveyed by the user during the conversation, even if it is implicit. We argue that the process of building a representation of the conversation can be framed as a machine reading task, where an automated system is presented with a number of statements about which it should answer questions. The questions should be answered solely by referring to the statements provided, without consulting external knowledge. The time is right for the information retrieval community to embrace this task, both as a stand-alone task and integrated in a broader conversational search setting. In this paper, we focus on machine reading as a stand-alone task and present the Attentive Memory Network (AMN), an end-to-end trainable machine reading algorithm. Its key contribution is in efficiency, achieved by having an hierarchical input encoder, iterating over the input only once. Speed is an important requirement in the setting of conversational search, as gaps between conversational turns have a detrimental effect on naturalness. On 20 datasets commonly used for evaluating machine reading algorithms we show that the AMN achieves performance comparable to the state-of-the-art models, while using considerably fewer computations.
Error analysis in a learner corpus: what are the learners' strategies?

This corpus-based work is intended to find transfer and intralingual errors made by native Spanish speakers with a high proficiency level of the English language, particularly when the production is written. Recent trends in language teaching are in tune with second language acquisition (SLA) research results, so studying learner outputs is important to help define parameters on the way a second language is learned. At the same time, this means a contribution to teaching. By analyzing errors of learners' production it is possible to distinguish the strategies they trigger in their process of SLA. The learner corpus used for this research is named ICLE (International Corpus of Learner English) and belongs to the Center for English Corpus Linguistics from the Universite Catholique de Louvain (UCL). This corpus contains over three million words, a collection of essays written by learners of English with diverse mother tongues. The Spanish sub-corpus was error-tagged by researchers at the UCL, this was the material used for the study.
Inclusion: What Progress is Being Made across States?

Where α Student with α disabilHy lives is one of the most significant factors in determining the placement setting in which the student will be educated. Data from the Annual Reports to Con­ gress, however, reveal that these trends vary dramatically from state to state. Some states have made significant progress toward moving students with disabilities to less restrictive settings, whereas others have made very little progress. The final article in this series addresses this issue by examining place­ ment rates across the 50 states and the District of Columbia.
Combination of Collagen-Based Scaffold and Bioactive Factors Induces Adipose-Derived Mesenchymal Stem Cells Chondrogenic Differentiation In vitro

Recently, multipotent mesenchymal stem cells (MSCs) have attracted much attention in the field of regenerative medicine due to their ability to give rise to different cell types, including chondrocytes. Damaged articular cartilage repair is one of the most challenging issues for regenerative medicine, due to the intrinsic limited capability of cartilage to heal because of its avascular nature. While surgical approaches like chondral autografts and allografts provide symptoms and function improvement only for a short period, MSC based stimulation therapies, like microfracture surgery or autologous matrix-induced chondrogenesis demonstrate to be more effective. The use of adult chondrocytes, which are the main cellular constituent of cartilage, in medical practice, is indeed limited due to their instability in monolayer culture and difficulty to collect donor tissue (articular and nasal cartilage). The most recent cartilage engineering approaches combine cells, biomaterial scaffold and bioactive factors to promote functional tissue replacements. Many recent evidences demonstrate that scaffolds providing specific microenvironmental conditions can promote MSCs differentiation toward a functional phenotype. In the present work, the chondrogenic potential of a new Collagen I based 3D scaffold has been assessed in vitro, in combination with human adipose-derived MSCs which possess a higher chondrogenic potential compared to MSCs isolated from other tissues. Our data indicate that the scaffold was able to promote the early stages of chondrogenic commitment and that supplementation of specific soluble factors was able to induce the complete differentiation of MSCs in chondrocytes as demonstrated by the appearance of cartilage distinctive markers (Sox 9, Aggrecan, Matrilin-1, and Collagen II), as well as by the cartilage-specific Alcian Blue staining and by the acquisition of typical cellular morphology. Such evidences suggest that the investigated scaffold formulation could be suitable for the production of medical devices that can be beneficial in the field of articular cartilage engineering, thus improving the efficacy and durability of the current therapeutic options.
Diamond optomechanical crystals

Cavity-optomechanical systems realized in single-crystal diamond are poised to benefit from its extraordinary material properties, including low mechanical dissipation and a wide optical transparency window. Diamond is also rich in optically active defects, such as the nitrogen-vacancy (NV) and silicon-vacancy (SiV) centers, which behave as atom-like systems in the solid state. Predictions and observations of coherent coupling of the NV electronic spin to phonons via lattice strain has motivated the development of diamond nanomechanical devices aimed at realization of hybrid quantum systems, in which phonons provide an interface with diamond spins. In this work, we demonstrate diamond optomechanical crystals (OMCs), a device platform to enable such applications, wherein the co-localization of ~ 200 THz photons and few to 10 GHz phonons in a quasi-periodic diamond nanostructure leads to coupling of an optical cavity field to a mechanical mode via radiation pressure. In contrast to other material systems, diamond OMCs operating in the resolved-sideband regime possess large intracavity photon capacity (> 10$^5$) and sufficient optomechanical coupling rates to reach a cooperativity of ~ 20 at room temperature, allowing for the observation of optomechanically induced transparency and the realization of large amplitude optomechanical self-oscillations.
Presence of Viral Genome in Urine and Development of Hematuria and Pathological Changes in Kidneys in Common Marmoset (Callithrix jacchus) after Inoculation with Dengue Virus

Common marmosets (Callithrix jacchus) developed high levels of viremia, clinical signs including fever, weight loss, a decrease in activity and hematuria upon inoculation with dengue virus (DENV). Presence of DENV genome in urine samples and pathological changes in kidneys were examined in the present study. Levels of DENV genome were determined in 228 urine samples from 20 primary DENV-inoculated marmosets and in 56 urine samples from four secondary DENV-inoculated marmosets. DENV genome was detected in 75% (15/20) of marmosets after primary DENV infection. No DENV genome was detected in urine samples from the marmosets with secondary infection with homologous DENV (0%, 0/4). Two marmosets demonstrated hematuria. Pathological analysis of the kidneys demonstrated non-suppressive interstitial nephritis with renal tubular regeneration. DENV antigen-positive cells were detected in kidneys. In human dengue virus infections, some patients present renal symptoms. The results indicate that marmosets recapitulate some aspects of the involvement of kidneys in human DENV infection, and suggest that marmosets are potentially useful for the studies of the pathogenesis of DENV infection, including kidneys.
IMPROVED ARITHMETIC CODING IN H.264/AVC USING CONTEXT-TREE WEIGHTING METHOD *

In this paper, an improvement of coding efficiency of the Context-based Adaptive Binary Arithmetic Coding (CABAC) is proposed for applications in Advanced Video Codecs (H.264/AVC). In the paper, more accurate estimation technique for conditional probabilities of symbols is proposed. To achieve that, the well-known data modeling technique of the Context-Tree Weighting (CTW) is used. A novel method of incorporating CTW into the H.264/AVC codec is proposed. The compression efficiency of the modified H.264/AVC codec (with CTW) has been thoroughly tested and compared against the coding efficiency of the original H.264/AVC (with CABAC). Experimental results show that the use of CTW with CABAC allows for up to 2.5% compression efficiency increase with respect to the original CABAC.
Childhood adiposity trajectories and risk of nonalcoholic fatty liver disease in adolescents

Nonalcoholic fatty liver disease (NAFLD) and its metabolic risk factors are recognized during childhood and adolescence. Identification of adolescents at risk of NAFLD from childhood anthropometry may expose opportunities to influence the hepatic and metabolic destinies of individuals. We sought associations between NAFLD diagnosed during adolescence and earlier life trajectories of anthropometry, in a population‐based cohort of predominantly Caucasian adolescents.
Comparison of Leukocytic Pyrogen and Leukocytic Endogenous Mediator

Summary Leukocytic pyrogen was subjected to a five-step purification scheme, and quantitative assays for both leukocytic pyrogen and leukocytic endogenous mediator (LEM) were made. At each step of the purification scheme, the active fractions, in addition to producing fever, lowered plasma iron and zinc concentrations, elevated fi-brinogen concentrations, and caused a release of neutrophils from bone marrow. It appears, therefore, that LEM and leukocytic pyrogen are the same molecule.
Specificity Protein 1 Transcription Factor Regulates Human ARTS Promoter Activity through Multiple Binding Sites

Apoptosis-related protein in the TGF-β signaling pathway (ARTS) is an unusual mitochondrial Septin-like protein which functions as a tumor suppressor. There are various splice variants derived from the human Septin4 gene, one of which is ARTS, also known as Septin4_i2. Unlike other Septin4 members, ARTS can induce apoptosis in many cells, however, the underlying molecular mechanism for the transcriptional regulation of ARTS has yet to be deciphered. In this study, we attempted to analyze the promoter region of ARTS in cultured HEK-293T and LX-2 cells with the purpose of elucidating the underlying transcriptional mechanisms driving ARTS expression. We effectively demonstrated that the -824 to -5 bp region of the ARTS promoter was essential for ARTS transcription and identified four putative specificity protein 1 (Sp1) binding sites within this core promoter region. ChIP analysis showed that Sp1 protein could bind to two of these sites (-735/-718 and -173/-157) and mutation of each Sp1 binding site led to a significant decrease in ARTS promoter activity. In conclusion, all the results indicated that the Sp1 transcription factor could contribute to ARTS gene transcription. The underlying molecular events of the specific promoter of ARTS could also be used to explain why ARTS is selectively silenced during some human diseases. This would provide basis for further study on the function of ARTS on cell apoptosis.
Journal of Graph Algorithms and Applications Superpatterns and Universal Point Sets

An old open problem in graph drawing asks for the size of a universal point set, a set of points that can be used as vertices for straight-line drawings of all n-vertex planar graphs. We connect this problem to the theory of permutation patterns, where another open problem concerns the size of superpatterns, permutations that contain all patterns of a given size. We generalize superpatterns to classes of permutations determined by forbidden patterns, and we construct superpatterns of size n 2 /4 + Θ(n) for the 213-avoiding permutations, half the size of known superpatterns for unconstrained permutations. We use our superpatterns to construct universal point sets of size n 2 /4−Θ(n), smaller than the previous bound by a 9/16 factor. We prove that every proper subclass of the 213-avoiding permutations has superpatterns of size O(n log O(1) n), which we use to prove that the planar graphs of bounded pathwidth have near-linear universal point sets.
Adaptive Nonlinear Estimation Based on Parallel Projection Along Affine Subspaces in Reproducing Kernel Hilbert Space

We propose a novel algorithm using a reproducing kernel for adaptive nonlinear estimation. The proposed algorithm is based on three ideas: projection-along-subspace, selective update, and parallel projection. The projection-along-subspace yields excellent performances with small dictionary sizes. The selective update effectively reduces the complexity without any serious degradation of performance. The parallel projection leads to fast convergence/tracking accompanied by noise robustness. A convergence analysis in the non-selective-update case is presented by using the adaptive projected subgradient method. Simulation results exemplify the benefits from the three ideas as well as showing the advantages over the state-of-the-art algorithms. The proposed algorithm bridges the quantized kernel least mean square algorithm of Chen et al. and the sparse sequential algorithm of Dodd et al.
Convergence Rates of Efficient Global Optimization Algorithms

Efficient global optimization is the problem of minimizing an unknown function f, using as few evaluations f(x) as possible. It can be considered as a continuum-armed bandit problem, with noiseless data and simple regret. Expected improvement is perhaps the most popular method for solving this problem; the algorithm performs well in experiments, but little is known about its theoretical properties. Implementing expected improvement requires a choice of Gaussian process prior, which determines an associated space of functions, its reproducing-kernel Hilbert space (RKHS). When the prior is fixed, expected improvement is known to converge on the minimum of any function in the RKHS. We begin by providing convergence rates for this procedure. The rates are optimal for functions of low smoothness, and we modify the algorithm to attain optimal rates for smoother functions. For practitioners, however, these results are somewhat misleading. Priors are typically not held fixed, but depend on parameters estimated from the data. For standard estimators, we show this procedure may never discover the minimum of f. We then propose alternative estimators, chosen to minimize the constants in the rate of convergence, and show these estimators retain the convergence rates of a fixed prior.
Conjectured Statistics for the Higher q, t-Catalan Sequences

This article describes conjectured combinatorial interpretations for the higher $q,t$-Catalan sequences introduced by Garsia and Haiman, which arise in the theory of symmetric functions and Macdonald polynomials. We define new combinatorial statistics generalizing those proposed by Haglund and Haiman for the original $q,t$-Catalan sequence. We prove explicit summation formulas, bijections, and recursions involving the new statistics. We show that specializations of the combinatorial sequences obtained by setting $t=1$ or $q=1$ or $t=1/q$ agree with the corresponding specializations of the Garsia-Haiman sequences. A third statistic occurs naturally in the combinatorial setting, leading to the introduction of $q,t,r$-Catalan sequences. Similar combinatorial results are proved for these trivariate sequences.
Design of maximally decimated near-perfect-reconstruction DFT filter banks with allpass-based analysis filters

In this paper we address a maximally decimated IIR DFT filter bank, where all polyphase components are replaced by all pass filters. Generally a perfect reconstruction (PR) solution leads to a synthesis filter bank with unstable subband filters. As a novelty we show that by using closed form FIR phase compensation filters as polyphase components in the synthesis filter bank we obtain a stable near-PR analysis-synthesis system. Furthermore, the remaining linear and aliasing distortions only depend on the overall system delay and can be made arbitrarily small.