Miracle-dz/UniFAR-FTUs huggingface dataset:
Structural Insights into the Mechanism of Protein O-Fucosylation

Protein O-fucosylation is an essential post-translational modification, involved in the folding of target proteins and in the role of these target proteins during embryonic development and adult tissue homeostasis, among other things. Two different enzymes are responsible for this modification, Protein O-fucosyltransferase 1 and 2 (POFUT1 and POFUT2, respectively). Both proteins have been characterised biologically and enzymatically but nothing is known at the molecular or structural level. Here we describe the first crystal structure of a catalytically functional POFUT1 in an apo-form and in complex with GDP-fucose and GDP. The enzyme belongs to the GT-B family and is not dependent on manganese for activity. GDP-fucose/GDP is localised in a conserved cavity connected to a large solvent exposed pocket, which we show is the binding site of epidermal growth factor (EGF) repeats in the extracellular domain of the Notch Receptor. Through both mutational and kinetic studies we have identified which residues are involved in binding and catalysis and have determined that the Arg240 residue is a key catalytic residue. We also propose a novel SN1-like catalytic mechanism with formation of an intimate ion pair, in which the glycosidic bond is cleaved before the nucleophilic attack; and theoretical calculations at a DFT (B3LYP/6-31+G(d,p) support this mechanism. Thus, the crystal structure together with our mutagenesis studies explain the molecular mechanism of POFUT1 and provide a new starting point for the design of functional inhibitors to this critical enzyme in the future.
Resource Ecology of Virulence in a Planktonic Host‐Parasite System: An Explanation Using Dynamic Energy Budgets

Parasites steal resources that a host would otherwise direct toward its own growth and reproduction. We use this fundamental notion to explain resource‐dependent virulence in a fungal parasite (Metschnikowia)–zooplankton host (Daphnia) system and in a variety of other disease systems with invertebrate hosts. In an experiment, well‐fed hosts died faster and produced more parasites than did austerely fed ones. This resource‐dependent variation in virulence and other experimental results (involving growth and reproduction rate/timing of hosts) readily emerged from a model based on dynamic energy budgets. This model follows energy flow through the host, from ingestion of food, to internal energy storage, to allocation toward growth and reproduction or to a parasite that consumes these reserves. Acting as a consumer, the parasite catalyzes its own extinction, persistence with an energetically compromised host, or death of the host. In this last case, more resources for the host inadvertently fuels faster parasite growth, thereby accelerating the demise of the host (although the opposite result arises with different resource kinetics of the parasite). Thus, this model can explain how resource supply drives variation in virulence. This ecological dependence of virulence likely rivals and/or interacts with genetic mechanisms that often garner more attention in the literature on disease.
Comparison of Clinicopathological Features and Treatments between Young (≤40 Years) and Older (>40 Years) Female Breast Cancer Patients in West China: A Retrospective, Epidemiological, Multicenter, Case Only Study

The incidence of young cases of breast cancer is higher in China compared to the western world. We aimed to explore differences in risk factors, clinicopathological features and treatment modes of young female breast cancer compared to older patients in West China. We collected clinical information from 12,209 female breast cancer patients in West China, including risk factors, clinicopathological features and treatment modes, from January 2010 to December 2012. Chi-square tests and the multivariate logistic regression analysis were applied for statistical analysis. There were 2,682 young (≤40 years) cases and 9,527 older cases at the time of breast cancer diagnosis. Young patients had a greater tumor diameter at diagnosis, and a higher probability of axillary lymph node and distant metastasis (P < 0.05). The progesterone receptor positive expression rate, estrogen receptor/progesterone receptor double positive expression rate, and human epidermal growth factor receptor 2 (HER2) negative expression rate was higher in young patients compared to older patients (P < 0.05). For young patients, the age at menarche was earlier, they had lower marriage rates, fewer pregnancies and births, and a lower breastfeeding rate (P < 0.05). A higher proportion of young patients underwent advanced operations, neoadjuvant and adjuvant chemotherapy, radiotherapy, and endocrine therapy compared to older patients (P < 0.05). We found significant differences in the clinicopathological features, risk factors and treatment modes between young (≤40 years) and older (>40 years) female breast cancer patients in West China. As some of these results differ from those found in the western female population, it is likely that the mechanism of tumorigenesis of young female breast cancer patients in West China may differ from that in western developed countries. Further investigation into the regional differences in breast cancer tumorigenesis is warranted.
Speech enhancement using generalized maximum a posteriori spectral amplitude estimator

This paper proposes a generalized maximum a posteriori spectral amplitude (GMAPA) algorithm to spectral restoration for speech enhancement. The proposed GMAPA algorithm dynamically adjusts the scale of prior information to calculate the gain function for spectral restoration. In higher signal-to-noise ratio (SNR) conditions, GMAPA adopts a smaller scale to prevent overcompensations that may result in speech distortions. On the other hand, in lower SNR conditions, GMAPA uses a larger scale to enable the gain function to more effectively remove noise components from noisy speech. We also develop a mapping function to optimally determine the prior information scale according to the SNR of speech utterances. Two standardized speech databases, Aurora-4 and Aurora-2, are used to conduct objective and recognition evaluations, respectively, to test the proposed GMAPA algorithm. For comparison, three conventional spectral restoration algorithms are also evaluated; they are minimum mean-square error spectral estimator (MMSE), maximum likelihood spectral amplitude estimator (MLSA), and maximum a posteriori spectral amplitude estimator (MAPA). The experimental results first confirm that GMAPA provides better objective evaluation scores than MMSE, MLSA, and MAPA in lower SNR conditions, with comparable scores to MLSA in higher SNR conditions. Moreover, our recognition results indicate that GMAPA outperforms the three conventional algorithms consistently over different testing conditions.
Illuminating the principles of social exchange theory with Hawthorne studies

Purpose The purpose of this paper is to suggest Homans’ social exchange theory (SET), a management theory, as an explanation for some of the findings of some of the Hawthorne experiments (1924-1933), which demonstrated how social situations play an important role in task performance and productivity and how social exchanges can facilitate it. The authors also use SET to investigate Elton Mayo’s inquiry as to what caused spontaneous cooperation in Hawthorne. Design/methodology/approach The authors used a combination of published work by Homans, Roethlisberger and Dickson, Mayo and others, as well as oral histories conducted by Greenwood and Bolton in 1982-1984, to argue that some of the Hawthorne studies illustrate the principles of SET. Homans’ SET brought together concepts from multiple disciplines and offered a framework to explain social behaviors. Findings The relay assembly room and the bank wiring tests of Hawthorne studies can illustrate SET as developed by Homans. With the development of SET, Homans not only provided explanations for the creation of strong feelings of affiliation and trust through interactions and mutual dependence between group members but also provided evidence to Mayo’s concept of spontaneous collaboration. Research limitations/implications The limitations of the paper are that the studies themselves can lend themselves to multiple perspectives due to design flaws. Therefore, our argument is only one interpretation – even if it is something that the researchers would have supported. Originality/value The paper augments the ongoing discussion about the Hawthorne studies in the literature and in the development of management theories such as SET. The authors provide support that it is through the attempts to explain the Hawthorne studies and the post-Second World War controversies over the studies that Homans developed social exchange. Building on previous work, the methods show perspectives beyond the motivations and sentiments of Homans by demonstrating observable behaviors from the Hawthorne studies.
Showing our seams: A reply to Eric Funkhouser

ABSTRACT In a recent paper published in this journal, Eric Funkhouser argues that some of our beliefs have the primary function of signaling to others, rather than allowing us to navigate the world. Funkhouser’s case is persuasive. However, his account of beliefs as signals is underinclusive, omitting both beliefs that are signals to the self and less than full-fledged beliefs as signals. The latter set of beliefs, moreover, has a better claim to being considered as constituting a psychological kind in its own right than the set of beliefs Funkhouser identifies.
Drawn to the light: Predicting religiosity using “God is light” metaphor.

A prominent class of metaphors depicts that which is sacred (God, a spiritual path) in terms of lightness rather than darkness. Metaphors of this type should have systematic implications for religious cognition according to conceptual metaphor theory (CMT) and a new extension of this theory termed balanced CMT. Five studies (total N = 761) derived predictions from these models and then tested them. Consistent with balanced CMT, Studies 1-3 found that people who preferred light to dark believed in God to a greater extent and were more religious. Furthermore, priming thoughts related to God shifted perceptual responses in a light-ward direction (Study 4) and models wearing lighter, relative to darker, shirts were inferred to be more religious (Study 5). The findings provide novel evidence for the importance of light-dark metaphors in religious representations while highlighting a new class of processes that covary with, and therefore predict, religious belief.
Children living in residential care from teachers’ voices

ABSTRACT Teachers have the potential to be key figures in the educational progress of children in care. This study is based on semi-structured interviews with 16 primary school teachers of children in residential care. It explores the teachers’ understandings of their pupils in residential care as well as the main issues they recalled from their experiences working with said population. It also enquires into the possible requirements suggested by teachers in order to improve their educational intervention. Results suggest that teachers had more knowledge and control over the academic aspect than over emotional and behavioural issues of children in residential care. They found difficulties to address emotional and behavioural needs of these children. This fact is related to a lack of structural support and constitutes a significant barrier to the education of children residential in care.
The role of fetal calf serum in the primary immune response in vitro

The mode of action of 2-mercaptoethanol (2-ME) on the primary immune response in vitro was investigated. Fetal calf serum (FCS) was preincubated with 2-ME and lyophilized to remove free 2-ME. This 2-ME- treated FCS was able to substitute the function of adherent cells in the primary immune response against sheep red blood cells (SRBC) in vitro; Fractionation of 2-tme-treated FCS on a Sephadex G-100 column showed that 2-ME acted on a high molecular serum component which after activation, could substitute for macrophages. In order to obtain a humoral immune response against SRBC in vitro, spleen cells require selected FCS. These "good" sera could be distinguished from "deficient" sera by their higher content of this 2-ME-activated factor. The height of the in vitro immune response to SRBC was dependent on the amount of activated factor added to the culture medium. FCS normally required in the culture medium could be completely replaced by the factor- containing fraction without deleterious effect on the culture medium. The factor should be added to the spleen cells during the first 24 h of culture and remain there for 72 h in order to obtain an optimal immune response. The factor could be partially absorbed by spleen cells but not by SRBC. The relationship between macrophage, 2-ME, and FCS in eliciting an in vitro primary immune response is discussed.
Low-frequency noise figures-of-merit in RF SiGe HBT technology

We present the first systematic experimental and modeling results of corner frequency (f/sub C/) and the corner frequency to cut-off frequency ratio (f/sub C//f/sub T/) for SiGe HBTs in a commercial SiGe RF technology. The f/sub C//f/sub T/ ratio is examined as a function of biasing current for SiGe HBTs featuring multiple collector doping profiles (breakdown voltages) and multiple SiGe profiles.
Parallel Symbolic Computing with the Shared Dataspace Coordination Model

Shared Prolog is a language for symbolic computing that combines distributed coordination based on a shared dataspace with sequential symbolic computation based on logic programming. Shared Prolog includes a concept of logically shared dataspace, thus introducing in parallel logic programming a coordination model different from the stream-based communication model of Flat Concurrent Prolog and Strand. We demonstrate how Shared Prolog can be used for expressing a number of different parallel symbolic computing schemata such as: pipeline, divide et impera, and distributed problem solving. We also discuss a number of topics in implementing such a programming model.
PENGARUH KECERDASAN INTELEKTUAL, KECERDASAN EMOSIONAL, KECERDASAN SPIRITUAL DAN PERILAKU BELAJAR TERHADAP TINGKAT PEMAHAMAN AKUNTANSI

Penelitian ini bertujuan untuk mengetahui pengaruh Kecerdasan Intelektual, Kecerdasan Emosional, Kecerdasan Spiritual dan Perilaku Belajar terhadap Tingkat Pemahaman Akuntansi pada Mahasiswa Akuntansi FE UNY. Responden penelitian ini adalah Mahasiswa Akuntansi FE UNY yang sudah menempuh mata kuliah Akuntansi Pengantar 1, Akuntansi Pengantar 2, Akuntansi Keuangan Menengah 1, Akuntansi Keuangan Menengah 2, Akuntansi Keuangan Lanjutan 1, Akuntansi Keuangan Lanjutan 2, Pengauditan 1, Pengauditan 2, Akuntansi Biaya, Sistem Akuntansi, Akuntansi Manajemen, Akuntansi Sektor Publik dan Sistem Informasi Akuntansi dan diambil sampel sebanyak 120 dengan menggunakan teknik Purposive Sampling . Teknik pengumpulan data menggunakan kuesioner. Uji coba instrumen dilakukan pada 30 Mahasiswa Akuntansi dari populasi dan tidak digunakan kembali sebagai responden data penelitian. Uji prasyarat analisis terdiri dari uji normalitas, uji linearitas, uji multikolinearitas, dan uji heteroskedastisitas. Uji hipotesis terdiri dari analisis regresi sederhana dan analisis regresi berganda. Hasil penelitian ini terdapat pengaruh positif Kecerdasan Intelektual, Kecerdasan Emosional, Kecerdasan Spiritual dan Perilaku Belajar terhadap Tingkat Pemahaman Akuntansi pada Mahasiswa Akuntansi FE UNY dengan nilai R2 = 0,640; F hitung = 51,108; dan F tabel = 1,658. Kata kunci: Tingkat Pemahaman Akuntansi, Kecerdasan Intelektual, Kecerdasan Emosional, Perilaku Belajar
Cognitive Load and Working Memory in Multimedia Learning: Conceptual and Measurement Issues

This article reviews contemporary research on multimedia learning that uses cognitive load theory as the major theoretical framework. In particular, we address the extent to which working memory has been conceptualized and measured in this research, what kind of subjective measures of cognitive load have been used and whether such measures are combined with other measures of cognitive load, and how results from subjective measures have been related to learning and achievement. The findings show that most of the reviewed studies did not include any clear conceptualization or measurement of working memory, used only general subjective measures containing one or very few items, and did not report findings consistent with the hypothesized relationship between cognitive load and multimedia learning. The findings are discussed in relation to the broader goal of improving research on cognitive load in the context of multimedia learning.
Optimising file delivery in a maritime environment through inter-vessel connectivity predictions

It is well known that the Internet infrastructure is experiencing an ever growing demand for large file/data transfers. To date, Delay Tolerant Networking (DTN) seems as the only economically viable over-the-sea communications paradigm to support bulk data transfers between seagoing vessels and the fixed Internet. In this work, we construct an architectural prototype of this DTN overlay to connect sailing vessels to the fixed Internet infrastructure. The proposed architecture integrates elements of the existing vessel Automatic Identification System (AIS) to fetch and manipulate mobility and trip related data of every vessel that could come into close contact (at any future instance in time) with a destination node and therefore assist in message forwarding. Considering both current and future contact opportunities all within the same optimization strategy allows for the maximization of routing performance. Ultimately, it is shown that the proposed architecture allows for computationally efficient routing solutions to be generated with variable optimization objectives. As an initial assessment of the performance of the routing functions of this architecture we illustrate the optimal minimum delay routing paths that deliver messages from an arbitrary infrastructure node to a target destination mobile host.
Developmental Trajectories and Milestones of Sexual-Minority Youth

It was not until the early 1970s that scientists – spearheaded by clinical and public health professionals – recognized and, in a sense created, a unique sexual population that was labeled gay youth. To find these youth, researchers recruited from locations and organizations that served the needs of compromised youth. Although the methodology was flawed, conclusions from these convenience samples were instrumental in founding a field of study. Not surprisingly, gay youth were perceived as having an exceptional developmental profile and consequently to be in dire need of immediate medical, psychiatric, and social interventions (Roesler & Deisher, 1972). By contrast, over the past two decades an increasingly broad array of biological, social, and behavioral scientists has produced data on which to build a developmental perspective on sexual-minority youth. This was possible primarily through social media recruitment and the inclusion of sexual status measures in large-scale surveys, giving researchers access to diverse and likely more representative populations of sexual-minority youth. A major consequence of the improved methodology was that many initial clinical findings were challenged, modulated, or, in some cases, repudiated (e.g., that one-third to half of sexual-minority youths attempt suicide, see Remafedi, 1987 vs. Savin-Williams, 2001a). Although the early research has limited relevance for understanding contemporary sexual-minority youth, especially during their child and adolescent years, few social scientists produced data-based research that illuminated the developmental processes of same-sex sexual and romantic growth prior to adulthood. Presented in this chapter is this limited literature, which must, by its very nature, be suggestive rather than confirmatory regarding the qualities and experiences of millennial sexual-minority youths as they navigate from their first memories of same-sex sexuality to their self-acceptance, expression, and integration of that sexuality. It is
Scene Labeling using Gated Recurrent Units with Explicit Long Range Conditioning

Recurrent neural network (RNN), as a powerful contextual dependency modeling framework, has been widely applied to scene labeling problems. However, this work shows that directly applying traditional RNN architectures, which unfolds a 2D lattice grid into a sequence, is not sufficient to model structure dependencies in images due to the "impact vanishing" problem. First, we give an empirical analysis about the "impact vanishing" problem. Then, a new RNN unit named Recurrent Neural Network with explicit long range conditioning (RNN-ELC) is designed to alleviate this problem. A novel neural network architecture is built for scene labeling tasks where one of the variants of the new RNN unit, Gated Recurrent Unit with Explicit Long-range Conditioning (GRU-ELC), is used to model multi scale contextual dependencies in images. We validate the use of GRU-ELC units with state-of-the-art performance on three standard scene labeling datasets. Comprehensive experiments demonstrate that the new GRU-ELC unit benefits scene labeling problem a lot as it can encode longer contextual dependencies in images more effectively than traditional RNN units.
Automatic transcription of drum loops

Recent efforts in audio indexing and retrieval in music databases mostly focus on melody. If this is appropriate for polyphonic music signals, specific approaches are needed for systems dealing with percussive audio signals such as those produced by drums, tabla or djembe. Most studies of drum signal transcription focus on sounds taken in isolation. In this paper, we propose several methods for drum loop transcription where the drums signals dataset reflects the variability encountered in modern audio recordings (real and natural drum kits, audio effects, simultaneous instruments, etc.). The approaches described are based on hidden Markov models (HMM) and support vector machines (SVM). Promising results are obtained with a 83.9% correct recognition rate for a simplified taxonomy.