Miracle-dz/UniFAR-FTUs huggingface dataset:
A Deep Learning Model for Structured Outputs with High-order Interaction

Many real-world applications are associated with structured data, where not only input but also output has interplay. However, typical classification and regression models often lack the ability of simultaneously exploring high-order interaction within input and that within output. In this paper, we present a deep learning model aiming to generate a powerful nonlinear functional mapping from structured input to structured output. More specifically, we propose to integrate high-order hidden units, guided discriminative pretraining, and high-order auto-encoders for this purpose. We evaluate the model with three datasets, and obtain state-of-the-art performances among competitive methods. Our current work focuses on structured output regression, which is a less explored area, although the model can be extended to handle structured label classification.
Metric recovery from directed unweighted graphs

We analyze directed, unweighted graphs obtained from $x_i\in \mathbb{R}^d$ by connecting vertex $i$ to $j$ iff $|x_i - x_j| < \epsilon(x_i)$. Examples of such graphs include $k$-nearest neighbor graphs, where $\epsilon(x_i)$ varies from point to point, and, arguably, many real world graphs such as co-purchasing graphs. We ask whether we can recover the underlying Euclidean metric $\epsilon(x_i)$ and the associated density $p(x_i)$ given only the directed graph and $d$. We show that consistent recovery is possible up to isometric scaling when the vertex degree is at least $\omega(n^{2/(2+d)}\log(n)^{d/(d+2)})$. Our estimator is based on a careful characterization of a random walk over the directed graph and the associated continuum limit. As an algorithm, it resembles the PageRank centrality metric. We demonstrate empirically that the estimator performs well on simulated examples as well as on real-world co-purchasing graphs even with a small number of points and degree scaling as low as $\log(n)$.
Introduction to the Special Issue on Case Studies

Case studies create a bridge between practice and research. They provide a method for research in which the complexity of the process and outcome of psychotherapy and counseling can be explored and examined. At the same time, they tell the story of an individual therapeutic experience, offering an opportunity for practitioners to reflect on and develop their understanding of theory and practice. They enable and promote communication between proponents of therapeutic approaches as descriptions of theories and practice can be explored for shared understanding and alternative perspectives. Moreover, case studies offer a medium for enabling non-therapists, such as potential clients and commissioners of services, to gain insight into what actually happens inside the therapy room.
Investigation of Heat-Assisted Magnetic Recording Media Films in Four Dimensions

Heat-assisted magnetic recording is one of the most promising approaches to achieve extremely high density magnetic recording. A laser is used to temporarily heat the recording media film to render its switching field to become lower than the magnetic field of the writing head. After writing, the film material is cooled down to room temperature for data storage. In this dynamic writing process, the challenge is to tailor and optimize the time resolved structural/thermal/magnetic properties of the media films and their correlations during/after the laser heating. In this paper, the four dimensions of current progress in HAMR media research, i.e., structure, magnetic properties, thermal properties and time, are briefly overviewed and discussed. Their correlations are also emphasized.
Researching language teaching: Understanding practice through situated classroom research

In this article we argue that second language acquisition (SLA) research and theory have a significant role to play in teacher education, especially at the masters level. The danger of overly practical approaches is that they cannot challenge current practice in ways that are both critical and rigorous. However, to engage critically with practice, SLA research must be situated in its institutional, social and cultural settings. We argue that situated research into classroom interaction provides second language teachers with opportunities to theorize and improve practice.
A systematic method to guide the choice of ridge parameter in ridge extreme learning machine

Extreme Learning Machine (ELM) has attracted many researchers as a universal function approximator because of its extremely fast learning speed and good generalization performance. Recently, a new trend in ELM emerges to combine it with ridge regression, which has been shown improved stability and generalization performance. However, this ridge parameter is determined through a trial-and-error manner, an unsatisfactory approach for automatic learning applications. In this paper, the differences between ridge ELM and ordinary Neural Networks are discussed as well as special properties of ridge ELM and various approaches to derive the ridge parameter. Furthermore, a semi-cross-validation ridge parameter selection procedure based on the special properties of ridge ELM is proposed. This approach, termed as Semi-Cross-validation Ridge ELM (SC-R-ELM), is also demonstrated to achieve robust and reliable results in 11 regression data sets.
A deterministic plus stochastic model of the residual signal for improved parametric speech synthesis

Speech generated by parametric synthesizers generally suffers from a typical buzziness, similar to what was encountered in old LPC-like vocoders. In order to alleviate this problem, a more suited modeling of the excitation should be adopted. For this, we hereby propose an adaptation of the Deterministic plus Stochastic Model (DSM) for the residual. In this model, the excitation is divided into two distinct spectral bands delimited by the maximum voiced frequency. The deterministic part concerns the low-frequency contents and consists of a decomposition of pitch-synchronous residual frames on an orthonormal basis obtained by Principal Component Analysis. The stochastic component is a high-pass filtered noise whose time structure is modulated by an energy-envelope, similarly to what is done in the Harmonic plus Noise Model (HNM). The proposed residual model is integrated within a HMM-based speech synthesizer and is compared to the traditional excitation through a subjective test. Results show a significative improvement for both male and female voices. In addition the proposed model requires few computational load and memory, which is essential for its integration in commercial applications. Index Terms: HMM-based speech synthesis, residual modeling, Deterministic plus Stochastic model
Proteomic Differences between Developmental Stages of Toxoplasma gondii Revealed by iTRAQ-Based Quantitative Proteomics

Toxoplasma gondii has a complex two-host life-cycle between intermediate host and definitive host. Understanding proteomic variations across the life-cycle stages of T. gondii may improve the understanding of molecular adaption mechanism of T. gondii across life-cycle stages, and should have implications for the development of new treatment and prevention interventions against T. gondii infection. Here, we utilized LC–MS/MS coupled with iTRAQ labeling technology to identify differentially expressed proteins (DEPs) specific to tachyzoite (T), bradyzoites-containing cyst (C) and sporulated oocyst (O) stages of the cyst-forming T. gondii Prugniuad (Pru) strain. A total of 6285 proteins were identified in the three developmental stages of T. gondii. Our analysis also revealed 875, 656, and 538 DEPs in O vs. T, T vs. C, and C vs. O, respectively. The up- and down-regulated proteins were analyzed by Gene Ontology enrichment, KEGG pathway and STRING analyses. Some virulence-related factors and ribosomal proteins exhibited distinct expression patterns across the life-cycle stages. The virulence factors expressed in sporulated oocysts and the number of up-regulated virulence factors in the cyst stage were about twice as many as in tachyzoites. Of the 79 ribosomal proteins identified in T. gondii, the number of up-regulated ribosomal proteins was 33 and 46 in sporulated oocysts and cysts, respectively, compared with tachyzoites. These results support the hypothesis that oocyst and cystic stages are able to adapt to adverse environmental conditions and selection pressures induced by the host's immune response, respectively. These findings have important implications for understanding of the developmental biology of T. gondii, which may facilitate the discovery of novel therapeutic targets to better control toxoplasmosis.
Approximation trade-offs in Markovian stream processing: An empirical study

A large amount of the world's data is both sequential and imprecise. Such data is commonly modeled as Markovian streams; examples include words/sentences inferred from raw audio signals, or discrete location sequences inferred from RFID or GPS data. The rich semantics and large volumes of these streams make them difficult to query efficiently. In this paper, we study the effects-on both efficiency and accuracy-of two common stream approximations. Through experiments on a realworld RFID data set, we identify conditions under which these approximations can improve performance by several orders of magnitude, with only minimal effects on query results. We also identify cases when the full rich semantics are necessary.
PSP: Parallel sub-pipelined architecture for high throughput AES on FPGA and ASIC

As the technology is growing day by day, information security plays a very important role in our lives. In order to protect the information, several cryptographic algorithms have been proposed. The aim of this paper is to present an effective Advanced Encryption Standard (AES) architecture to achieve high throughput for security applications. The Parallel Sub-Pipelined architecture (PSP) is proposed in order to obtain high throughput. The proposed architecture is also compared with loop unrolled, pipelined, sub-pipelined, parallel and parallel pipelined architecture in terms of throughput. The AES algorithm using Parallel Sub-Pipelined architecture was prototyped in FPGA (Field Programmable Gate Array) and ASIC (Application Specific Integrated Circuit). The proposed architecture yielded a throughput of 59.59 Gbps at a frequency of 450.045 MHz on FPGA Virtex XC6VLX75T which is higher than the throughput yielded in other architectures. In ASIC 0.13 µm technology, the proposed architecture yielded a throughput of 25.60 Gbps and in 0.18 µm, it yielded a throughput of 20.56 Gbps.
Influence of serum on the immune recognition of a synthetic lipopeptide mimetic of the 19-kDa lipoprotein from Mycobacterium tuberculosis

The innate immune response provides a critical first-line defense against Mycobacterium tuberculosis, an intracellular pathogen that represents a major health threat world-wide. A synthetic lipopeptide (LP) mimicking the lipid moiety of the cell-wall associated 19-kDa lipoprotein from M. tuberculosis has recently been assigned an important role in the induction of an antibacterial immune response in host macrophages. Here, we present experimental data on the biological activities and the biophysical mechanisms underlying cell activation by synthetic 19-kDa M. tuberculosis-derived lipopeptide (Mtb-LP). Investigation of the geometry of the LP (i.e. the molecular conformation and supramolecular aggregate structure) and the preference for membrane intercalation provide an explanation for the biological activities of the mycobacterial LP. Cell activation by low concentrations of Mtb-LP was enhanced by the lipopolysaccharide—binding protein and CD14. However, surprisingly, we found that activation of human macrophages to induce pro- as well as antiinflammatory mediators (tumor necrosis factor(TNF)-α, Interleukin(IL)-6, IL-8, and IL-10) in response to the Mtb-LP is strongly reduced in the presence of serum. This observation could be confirmed for the immune response of murine macrophages which showed a strongly enhanced TNF-α release in the absence of serum, suggesting that the molecular mechanisms of immune recognition of the Mtb-LP are tailored to the ambient conditions of the lung.
Functional Polymorphism of the CK2α Intronless Gene Plays Oncogenic Roles in Lung Cancer

Protein kinase CK2 is frequently up-regulated in human cancers, although the mechanism of CK2 activation in cancer remains unknown. In this study, we investigated the role of the CK2α intronless gene (CSNK2A1P, a presumed CK2α pseudogene) in the pathogenesis of human cancers. We found evidence of amplification and over-expression of the CSNK2A1P gene in non- small cell lung cancer and leukemia cell lines and 25% of the lung cancer tissues studied. The mRNA expression levels correlated with the copy numbers of the CSNK2A1P gene. We also identified a novel polymorphic variant (398T/C, I133T) of the CSNK2A1P gene and showed that the 398T allele is selectively amplified over the 398C allele in 101 non-small cell lung cancer tissue samples compared to those in 48 normal controls (p = 0.013<0.05). We show for the first time CSNK2A1P protein expression in transfected human embryonic kidney 293T and mouse embryonic fibroblast NIH-3T3 cell lines. Both alleles are transforming in these cell lines, and the 398T allele appears to be more transforming than the 398C allele. Moreover, the 398T allele degrades PML tumor suppressor protein more efficiently than the 398C allele and shows a relatively stronger binding to PML. Knockdown of the CSNK2A1P gene expression with specific siRNA increased the PML protein level in lung cancer cells. We report, for the first time, that the CSNK2A1P gene is a functional proto-oncogene in human cancers and its functional polymorphism appears to degrade PML differentially in cancer cells. These results are consistent with an important role for the 398T allele of the CSNK2A1P in human lung cancer susceptibility.
Strategy compatibility, scale compatibility, and the prominence effect.

Ss expressed preferences between pairs of decision alternatives characterized by 2 attributes, for example, price and quality. They were more likely to prefer the alternative that was superior with respect to the most important attribute when making choices and strength-of-preference judgments than when making matching and monetary-equivalent value judgments. Rating scale judgments fell between these two extremes. These findings extend the previously established choice versus matching prominence effect (Tversky, Sattath, & Slovic, 1988) to a more general qualitative versus quantitative task prominence effect. The data support the strategy-compatibility interpretation of the prominence effect. They also show that in riskless decision making, the generalized prominence effect is much stronger than simple scale-compatibility effects
3D structure of the Yersinia entomophaga toxin complex and implications for insecticidal activity

Toxin complex (Tc) proteins are a class of bacterial protein toxins that form large, multisubunit complexes. Comprising TcA, B, and C components, they are of great interest because many exhibit potent insecticidal activity. Here we report the structure of a novel Tc, Yen-Tc, isolated from the bacterium Yersinia entomophaga MH96, which differs from the majority of bacterially derived Tcs in that it exhibits oral activity toward a broad range of insect pests, including the diamondback moth (Plutella xylostella). We have determined the structure of the Yen-Tc using single particle electron microscopy and studied its mechanism of toxicity by comparative analyses of two variants of the complex exhibiting different toxicity profiles. We show that the A subunits form the basis of a fivefold symmetric assembly that differs substantially in structure and subunit arrangement from its most well characterized homologue, the Xenorhabdus nematophila toxin XptA1. Histopathological and quantitative dose response analyses identify the B and C subunits, which map to a single, surface-accessible region of the structure, as the sole determinants of toxicity. Finally, we show that the assembled Yen-Tc has endochitinase activity and attribute this to putative chitinase subunits that decorate the surface of the TcA scaffold, an observation that may explain the oral toxicity associated with the complex.
Increasing native English vocabulary recognition through Spanish immersion : Cognate transfer from foreign to first language

Effects of Spanish immersion on children's native English vocabulary were studied. Matched on grade, sex, and verbal scores on a 4th-grade Cognitive Abilities Test (CAT), 30 5th- and 6th-grade immersion students and 30 English monolinguals did 60 consecutive Peabody Picture Vocabulary Test (PPVT) items. They also did a 20-item Spanish-English Cognate Test (SECT), similar to PPVT, on recognizing low-frequency English words with high-frequency Spanish cognates. The CAT and conventionally scored PPVT revealed comparable verbal ability between groups, but on 60 consecutive PPVT items, immersion did better than control (p = .002) because of cognates. On SECT, immersion significantly outperformed control (p <.001; effect sizes: 5th grade = 1.72, 6th grade = 1.45). Findings support the idea that Spanish immersion has English-language benefits and that positive transfer (crosslinguistic influence) occurs from Spanish as a foreign language to native English receptive vocabulary.
Arabidopsis Mutants Define a Central Role for the Xanthophyll Cycle in the Regulation of Photosynthetic Energy Conversion

A conserved regulatory mechanism protects plants against the potentially damaging effects of excessive light. Nearly all photosynthetic eukaryotes are able to dissipate excess absorbed light energy in a process that involves xanthophyll pigments. To dissect the role of xanthophylls in photoprotective energy dissipation in vivo, we isolated Arabidopsis xanthophyll cycle mutants by screening for altered nonphotochemical quenching of chlorophyll fluorescence. The npq1 mutants are unable to convert violaxanthin to zeaxanthin in excessive light, whereas the npq2 mutants accumulate zeaxanthin constitutively. The npq2 mutants are new alleles of aba1, the zeaxanthin epoxidase gene. The high levels of zeaxanthin in npq2 affected the kinetics of induction and relaxation but not the extent of nonphotochemical quenching. Genetic mapping, DNA sequencing, and complementation of npq1 demonstrated that this mutation affects the structural gene encoding violaxanthin deepoxidase. The npq1 mutant exhibited greatly reduced nonphotochemical quenching, demonstrating that violaxanthin deepoxidation is required for the bulk of rapidly reversible nonphotochemical quenching in Arabidopsis. Altered regulation of photosynthetic energy conversion in npq1 was associated with increased sensitivity to photoinhibition. These results, in conjunction with the analysis of npq mutants of Chlamydomonas, suggest that the role of the xanthophyll cycle in nonphotochemical quenching has been conserved, although different photosynthetic eukaryotes rely on the xanthophyll cycle to different extents for the dissipation of excess absorbed light energy.
MicroRNA-7 Modulates CD98 Expression during Intestinal Epithelial Cell Differentiation*

The transmembrane glycoprotein CD98 regulates multiple cellular functions, including extracellular signaling, epithelial cell adhesion/polarity, amino acid transport, and cell-cell interactions. MicroRNAs post-transcriptionally regulate gene expression, thereby functioning as modulators of numerous cellular processes, such as cell differentiation, proliferation, and apoptosis. Here, we investigated if microRNAs regulate CD98 expression during intestinal epithelial cell differentiation and inflammation. We found that microRNA-7 repressed CD98 expression in Caco2-BBE cells by directly targeting the 3′-untranslated region of human CD98 mRNA. Expression of CD98 was decreased, whereas that of microRNA-7 was increased in well-differentiated Caco2-BBE cells compared with undifferentiated cells. Undifferentiated crypt cells isolated from mouse jejunum showed higher CD98 levels and lower levels of mmu-microRNA-706, a murine original microRNA candidate for CD98, than well-differentiated villus cells. Importantly, microRNA-7 decreased Caco2-BBE cell attachment on laminin-1, and CD98 overexpression recovered this inhibition, suggesting that microRNA-7 modulates epithelial cell adhesion to extracellular matrix, which in turn could affect proliferation and differentiation during the migration of enterocytes across the crypt-villus axis, by regulating CD98 expression. In a pathological context, the pro-inflammatory cytokine interleukin 1-β increased CD98 expression in Caco2-BBE cells by decreasing microRNA-7 levels. Consistent with the in vitro findings, microRNA-7 levels were decreased in actively inflamed Crohn disease colonic tissues, where CD98 expression was up-regulated, compared with normal tissues. Together, these results reveal a novel mechanism underlying regulation of CD98 expression during patho-physiological states. This study raises microRNAs as a promising target for therapeutic modulations of CD98 expression in intestinal inflammatory disorders.
Motivators for and barriers against workplace flexibility: comparing nonprofit, for-profit, and public sector organizations

Despite growing interest in workplace flexibility, relatively little is known about how the dynamics of flexible options might differ in for-profit, nonprofit, and public sector organizations. This short report evaluates the relative importance of various barriers against and motivators for flexible options in the public, nonprofit private, and for-profit private sectors using two similar surveys of private sector (2006 National Study of Business Strategy and Workforce Development Survey) and public sector (2008 States as Employers-of-Choice Survey) organizations in the USA. While there are some differences in what motivates organizations in each sector to adopt flexible work options, the differences in barriers to flexibility are more noticeable. For instance, the three groups of organizations differ significantly in the importance of implementation costs, employee pressures to adopt these policies and programs, and the extent to which more pressing issues prevent a focus on workplace flexibility. The results of this short report, while preliminary, suggest that understanding both what motivates organizations to adopt flexible work options and what prevents them from doing so should help advocates of workplace flexibility to design policies and programs better suited to each sector.