Miracle-dz/UniFAR-FTUs huggingface dataset:
Carbohydrate Intake Interacts With SNP276G>T Polymorphism in the Adiponectin Gene to Affect Fasting Blood Glucose, HbA1C, and HDL Cholesterol in Korean Patients With Type 2 Diabetes

Background/Objective: The SNP276G>T polymorphism in the adiponectin gene has been reported to be associated with type 2 diabetes and impaired glucose tolerance. The objective of this study was to examine whether SNP276G>T polymorphism influences the blood glucose levels in relation to dietary carbohydrate intake. Subjects/Methods: In an ongoing, prospective study, 673 patients with type 2 diabetes (339 men and 334 women, aged 40–85 years) were recruited from one of two diabetes clinics in Seoul, Korea. The levels of carbohydrate intake were categorized as <55%, 55%–65%, and >65% of total energy intake. Results: Significant gene–nutrient interactions between SNP276G>T polymorphism and the level of carbohydrate intake were found, which modulated plasma fasting blood glucose ( p = 0.0277), HbA1C ( p = 0.0407), and high-density lipoprotein (HDL) cholesterol ( p = 0.0134) concentrations. The G allele was associated with higher fasting blood glucose only in subjects consuming a low-carbohydrate diet (<55% of energy). However, when carbohydrate intake was intermediate (55%–65%), carriers of the T allele had greater fasting blood glucose and HbA1C concentrations. When carbohydrate intake was high (>65%), carriers of the T allele had greater HDL cholesterol concentrations. This interaction was significant even when carbohydrate intake was considered a continuous variable ( p = 0.0200 for fasting blood glucose, p = 0.0408 for HbA1C, and p = 0.0254 for HDL cholesterol), suggesting a strong dose–response relation. Conclusions: Our data show that the effect of the SNP276G>T polymorphism on plasma fasting blood glucose, HbA1C, and HDL cholesterol concentrations depends on dietary carbohydrate intake.
The Great Billion‐year War between Ribosome‐ and Capsid‐encoding Organisms (Cells and Viruses) as the Major Source of Evolutionary Novelties

Our conceptions on the origin, nature, and role of viruses have been shaken recently by several independent lines of research. There are many reasons to believe now that viruses are more ancient than modern cells and have always been more abundant and diverse than their cellular targets. Viruses can be defined as capsid‐encoding organisms that transform their “host” cell into a viral factory. If capsid‐encoding organisms (viruses) and ribosome‐encoding organisms (cells) are the major types of living entities on our planet, it seems logical to conclude that their conflict has been a major engine of biological evolution (in the framework of natural selection). In particular, many novelties first selected in the viral world might have been transferred to cells as a consequence of the continuous flow of viral genes into cellular genomes. We discuss recent observations and hypotheses suggesting that viruses have played a major role at different stages of biological evolution, such as the RNA to DNA transition, the origin of the eukaryotic nucleus, or, alternatively, the origin of unique features in multicellular macrobes.
Training Mixture Models at Scale via Coresets

How can we train a statistical mixture model on a massive data set? In this paper, we show how to construct coresets for mixtures of Gaussians and natural generalizations. A coreset is a weighted subset of the data, which guarantees that models fitting the coreset also provide a good fit for the original data set. We show that, perhaps surprisingly, Gaussian mixtures admit coresets of size polynomial in dimension and the number of mixture components, while being independent of the data set size. Hence, one can compute a (1 + ε)-approximation for the optimal model on a significantly smaller data set. More importantly, such coresets can be efficiently constructed both in distributed and streaming settings. Our results rely on a novel reduction of statistical estimation to problems in computational geometry and new complexity results for mixtures of Gaussians. As a by-product of our analysis, we prove that the pseudo-dimension of arbitrary mixtures of Gaussians is polynomial in the ambient dimension. Empirical evaluation on several real-world datasets suggest that our coreset-based approach enables significant reduction in training-time with negligible approximation error.
The Differentiation of Soft Tissue Infiltration and Surrounding Edema in an Animal Model of Malignant Bone Tumor: Evaluation by Dual-Energy CT

To study the value of dual energy computed tomography in distinguishing soft tissue infiltration from surrounding soft tissue edema in rabbit malignant bone tumor, a malignant bone tumor model was established through implantation of VX2 tumor fragments into the tibiae of rabbits. Tumor adjacent soft tissues were divided into 3 areas according to pathology and computed tomography images. Computed tomography spectral curve slopes and iodine and water concentrations were assessed. Statistical analyses were performed using the Mann-Whitney U test and t test. The spectral curve of the soft tissue infiltration areas has a slope (1.30 ± 0.41) higher than that of the soft tissue edema areas (0.71 ± 0.23; P < .001). The iodine concentration in the soft tissue infiltration areas (8.56 ± 2.15) was higher than that in the in soft tissue edema areas (6.09 ± 1.02; P < .001). Water concentration was similar in the soft tissue infiltration areas (1033.86 ± 10.50) to that of the edema areas (1031.45 ± 12.83; P < .05). Spectral curve analysis and iodine–water concentration are helpful in the differentiation of bone tumor soft tissue infiltration and soft tissue edema.
Analysis and Processing of Lecture Audio Data: Preliminary Investigations

In this paper we report on our recent efforts to collect a corpus of spoken lecture material that will enable research directed towards fast, accurate, and easy access to lecture content. Thus far, we have collected a corpus of 270 hours of speech from a variety of undergraduate courses and seminars. We report on an initial analysis of the spontaneous speech phenomena present in these data and the vocabulary usage patterns across three courses. Finally, we examine language model perplexities trained from written and spoken materials, and describe an initial recognition experiment on one course.
On the Learnability of Two Representations of Equivalence Partitioning and Boundary Value Analysis

Currently, equivalence partitioning and boundary value analysis are taught at La Trobe University using Myers' original representation of these black-box testing methods. We previously proposed an alternative representation called atomic rules. In this paper we present the statistical results of two similar experiments that examine which of these approaches enable students to write more complete and correct black-box test sets and which approach students prefer to use. We compare the results of these experiments and discuss how the results could change the teaching of black-box testing methods at La Trobe University and in industry.
Effects of allophones on the performance of Korean speech recognition

This paper investigates the effects of allophones on the performance of Korean speech recognition systems. Along with a baseline phone-like unit (PLU) set consisting of phonemes, 31 allophone-based PLU sets are designed by systematically considering 5 major Korean allophonic constraints which can describe all the PLU sets currently used for Korean speech recognition systems. Experiments for phone, word, and continuous speech recognition are performed using the proposed PLU sets. The results show that the allophone-based PLU sets improve recognition performance compared to using a baseline phoneme-based PLU set. The performance improvement is clearly evident in phone recognition for isolated speech and in isolated word and continuous speech recognition using context independent units. As predicted, the performance improvement is less evident when context dependent (CD) units are used in the experiments, since the allophonic information is internalized in the CD units. Finally, the constraint V OICING -L AX is observed as playing a positive role compared to other constraints that are only partly influential.
Binding of Copper(I) by the Wilson Disease Protein and Its Copper Chaperone*

The Wilson disease protein (WND) is a transport ATPase involved in copper delivery to the secretory pathway. Mutations in WND and its homolog, the Menkes protein, lead to genetic disorders of copper metabolism. The WND and Menkes proteins are distinguished from other P-type ATPases by the presence of six soluble N-terminal metal-binding domains containing a conserved CXXC metal-binding motif. The exact roles of these domains are not well established, but possible functions include exchanging copper with the metallochaperone Atox1 and mediating copper-responsive cellular relocalization. Although all six domains can bind copper, genetic and biochemical studies indicate that the domains are not functionally equivalent. One way the domains could be tuned to perform different functions is by having different affinities for Cu(I). We have used isothermal titration calorimetry to measure the association constant (Ka) and stoichiometry (n) values of Cu(I) binding to the WND metal-binding domains and to their metallochaperone Atox1. The association constants for both the chaperone and target domains are ∼105 to 106 m–1, suggesting that the handling of copper by Atox1 and copper transfer between Atox1 and WND are under kinetic rather than thermodynamic control. Although some differences in both n and Ka values are observed for variant proteins containing less than the full complement of six metal-binding domains, the data for domains 1–6 were best fitted with a single site model. Thus, the individual functions of the six WND metal-binding domains are not conferred by different Cu(I) affinities but instead by fold and electrostatic surface properties.
Handover in UMTS networks with hybrid access femtocells

Femtocells enable in-home cell phone coverage and provide access to high speed wireless broadband services. The Femtocell network architecture is very different from the existing based on the UMTS macrocell network architecture. Hence, a modified handover procedure for existing networks is needed to support macrocell/femtocell integrated networks. Voice call services are an essential part of mobile communications and studies of mobile usage show that more than 50 percent of all voice calls are placed indoors. Frequent and unnecessary handovers are another problem of heterogeneous network environments. In this paper, we propose a modified handover procedure for voice call service between 3GPP UMTS-based macrocell and femtocell networks. And Call Admission Control (CAC) to reduce the unnecessary handover in the hybrid access mode is proposed.
A Subharmonic Injection-Locked Self-Oscillating Mixer

A subharmonic injection-locked self-oscillating mixer (s-ILSOM) at 1 GHz is reported in this paper. The proposed circuit which combines both injection-locking and mixing functions is described theoretically and experimentally. In contrast to previously reported works, only one input port is required for both the RF/IF signal and the injection signal. Furthermore, the injection signal which is used to stabilize the oscillation is at a subharmonic of the oscillation frequency (fLO/4), with a power level as low as -20 dBm. Phase noise calculations and mixing characteristics are reported, indicating a noise improvement, and a high up-conversion gain for both fundamental and harmonic mixing. The circuit is implemented, using a GaAs FET, exhibiting an up-conversion gain of 13 dB, a phase noise of -93 dBc/Hz at 100 KHz offset, a P1dB of -18 dBm, an IP3 of -5 dBm, and a power consumption of 24 mW.
Role for Escherichia coli YidD in Membrane Protein Insertion

ABSTRACT YidC has an essential but poorly defined function in membrane protein insertion and folding in bacteria. The yidC gene is located in a gene cluster that is highly conserved in Gram-negative bacteria, the gene order being rpmH, rnpA, yidD, yidC, and trmE. Here, we show that Escherichia coli yidD, which overlaps with rnpA and is only 2 bp upstream of yidC, is expressed and localizes to the inner membrane, probably through an amphipathic helix. Inactivation of yidD had no discernible effect on cell growth and viability. However, compared to control cells, ΔyidD cells were affected in the insertion and processing of three YidC-dependent inner membrane proteins. Furthermore, in vitro cross-linking showed that YidD is in proximity of a nascent inner membrane protein during its localization in the Sec-YidC translocon, suggesting that YidD might be involved in the insertion process.
Longitudinal Dynamics of 3-Dimensional Components of Selfhood After Severe Traumatic Brain Injury: A qEEG Case Study

In this report, we describe the case of a patient who sustained extremely severe traumatic brain damage with diffuse axonal injury in a traffic accident and whose recovery was monitored during 6 years. Specifically, we were interested in the recovery dynamics of 3-dimensional components of selfhood (a 3-dimensional construct model for the complex experiential selfhood has been recently proposed based on the empirical findings on the functional-topographical specialization of 3 operational modules of brain functional network responsible for the self-consciousness processing) derived from the electroencephalographic (EEG) signal. The analysis revealed progressive (though not monotonous) restoration of EEG functional connectivity of 3 modules of brain functional network responsible for the self-consciousness processing, which was also paralleled by the clinically significant functional recovery. We propose that restoration of normal integrity of the operational modules of the self-referential brain network may underlie the positive dynamics of 3 aspects of selfhood and provide a neurobiological mechanism for their recovery. The results are discussed in the context of recent experimental studies that support this inference. Studies of ongoing recovery after severe brain injury utilizing knowledge about each separate aspect of complex selfhood will likely help to develop more efficient and targeted rehabilitation programs for patients with brain trauma.
Delirium in the intensive care unit

Delirium is a serious complication that commonly occurs in critically ill patients in the intensive care unit (ICU). Delirium is frequently unrecognized or missed despite its high incidence and prevalence, and leads to poor clinical outcomes and an increased cost by increasing morbidity, mortality, and hospital and ICU length of stay. Although its pathophysiology is poorly understood, numerous risk factors for delirium have been suggested. To improve clinical outcomes, it is crucial to perform preventive measures against delirium, to detect delirium early using valid and reliable screening tools, and to treat the underlying causes or hazard symptoms of delirium in a timely manner.
Consistent Partial Identification

This study contrasts consistent partial identification with learning in the limit. Here partial identification means that the learner outputs an infinite sequence of conjectures in which one correct hypothesis occurs infinitely often and all other hypotheses occur only finitely often. Consistency means that every conjecture is correct on all the data seen so far. Learning in the limit means that the learner outputs from some time on always the same correct hypothesis. As the class of all total-recursive functions can be partially identified, the constraint of consistency has to be added to make a meaningful comparison to learning in the limit. For the version of consistency where the learner has to be defined and consistent on all inputs, it is shown that the power of the learning criterion depends on whether the function to be learnt is fed in canonical order or in arbitrary order. In the first case, consistent partial identification is incomparable to learning in the limit; in the second case, it is equivalent to consistent learning in the limit with arbitrarily fed input. Furthermore, the inference degrees of these criteria are investigated. For the case where the function is fed in canonical order, there are just two inference degrees: the trivial one which contains all oracles of hyperimmune free Turing degree and the omniscient one which contains all oracles of hyperimmune Turing degree. In the case that the function is fed in arbitrary order, the picture is more complicated and the omniscient inference degree contains exactly all oracles of high Turing degree.
Cohort profile: Growing Up in Singapore Towards healthy Outcomes (GUSTO) birth cohort study.

Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Department of Obstetrics & Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, National University Health System, Singapore, Singapore Institute for Clinical Sciences, Agency for Science and Technology Research (A*STAR), Brenner Centre for Molecular Medicine, Singapore, Liggins Institute, University of Auckland, Auckland, New Zealand, Medical Research Council Lifecourse Epidemiology Unit, Southampton, UK, NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Foundation Trust, Southampton, UK, Biostatistics Unit, Yong Loo Lin School of Medicine, National University of Singapore, Singapore and KK Women’s and Children’s Hospital, Singapore
Elevated Blood Lead Concentrations and Vitamin D Deficiency in Winter and Summer in Young Urban Children

Background It is widely recognized that blood lead concentrations are higher in the summer than in winter. Although the effects of some environmental factors such as lead in dust on this phenomenon have been studied, relationships to sunlight-induced vitamin D synthesis have not been adequately investigated. Vitamin D status is influenced by the diet, sunlight exposure, age, skin pigmentation, and other factors, and may modify gastrointestinal lead absorption or release of lead stored in bones into the bloodstream. Objective and Methods We collected paired blood samples from 142 young, urban African-American and Hispanic children in the winter and summer to study the seasonal increase in blood lead and its relationships to vitamin D nutrition, age, and race. Results A winter/summer (W/S) increase in blood lead concentrations of 32.4% was found for children 1–3 years of age. There was a smaller W/S increase of 13.0% in children 4–8 years of age. None of the 51 Hispanic children had an elevated blood lead concentration (≥ 10 μg/dL) during the winter, and only one had an elevated summertime concentration. In contrast, elevated blood lead concentrations were frequent in the 91 African-American children, especially those 1–3 years of age. For the latter, the percentage with elevated blood lead levels increased from 12.2% in winter to 22.5% in summer. A 1.2% W/S increase in serum 25-hydroxy-vitamin D (serum 25-OH-D) concentrations was found for children 1–3 years of age. However, in children 4–8 years of age the W/S increase in serum 25-OH-D was much larger—33.6%. The percentages of children with low (< 16 μg/L) serum 25-OH-D concentrations were 12.0% in winter and 0.7% in summer and were consistently greater in African-American than in Hispanic children. The seasonal increases in blood lead and serum 25-OH-D in children 4–8 years of age were significantly associated. Conclusion The higher summertime serum 25-OH-D concentrations for the 4- to 8-year-old children are likely caused by increased sunlight-induced vitamin D synthesis and may contribute to the seasonal increase in blood lead. Age and race are key factors that affect blood lead and vitamin D nutrition, as well as their interactions, in young urban children.
The analysis of fault diagnosis tasks : do verbal reports speak for themselves?

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Analysis of HTTP Performance

We discuss the performance effects of using per-transaction TCP connections for HTTP access, and the proposed optimizations of avoiding per-transaction re-connection and TCP slow-start restart overheads. We analyzed the performance penalties of the interaction of HTTP and TCP. Our observations indicate that the proposed optimizations do not affect Web access for the vast majority of users. Most users see end-to-end latencies of about 100-250 ms and use modem lines, resulting in only 1-2 packets in transit. At these rates, the optimizations reduce the overall transaction time by 13%. Rates over 240 Kbps are required in order to achieve user-noticeable performance enhancement, reducing the time per transaction by half.
Automatic Tune Family Identification by Musical Sequence Alignment

Musics, like languages and genes, evolve through a process of transmission, variation, and selection. Evolution of musical tune families has been studied qualitatively for over a century, but quantitative analysis has been hampered by an inability to objectively distinguish between musical similarities that are due to chance and those that are due to descent from a common ancestor. Here we propose an automated method to identify tune families by adapting genetic sequence alignment algorithms designed for automatic identification and alignment of protein families. We tested the effectiveness of our method against a high-quality ground-truth dataset of 26 folk tunes from four diverse tune families (two English, two Japanese) that had previously been identified and aligned manually by expert musicologists. We tested different combinations of parameters related to sequence alignment and to modeling of pitch, rhythm, and text to find the combination that best matched the ground-truth classifications. The best-performing automated model correctly grouped 100% (26/26) of the tunes in terms of overall similarity to other tunes, identifying 85% (22/26) of these tunes as forming distinct tune families. The success of our approach on a diverse, cross-cultural ground-truth dataset suggests promise for future automated reconstruction of musical evolution on a wide scale.