Miracle-dz/UniFAR-FTUs huggingface dataset:
Performance characteristics of NuVal and the Overall Nutritional Quality Index (ONQI).

BACKGROUND Improving diets has considerable potential to improve health, but progress in this area has been limited, and advice to increase fruit and vegetable intake has largely gone unheeded. OBJECTIVES Our objective was to test the performance characteristics of the Overall Nutritional Quality Index (ONQI), a tool designed to help improve dietary patterns one well-informed choice at a time. DESIGN The ONQI was developed by a multidisciplinary group of nutrition and public health scientists independent of food industry interests and is the basis for the NuVal Nutritional Guidance System. Dietary guidelines, existing nutritional scoring systems, and other pertinent scientific literature were reviewed. An algorithm incorporating >30 entries that represent both micro- and macronutrient properties of foods, as well as weighting coefficients representing epidemiologic associations between nutrients and health outcomes, was developed and subjected to consumer research and testing of performance characteristics. RESULTS ONQI and expert panel rankings correlated highly (R = 0.92, P < 0.001). In consumer testing, approximately 80% of >800 study participants indicated that the ONQI would influence their purchase intent. ONQI scoring distinguished the more-healthful DASH (Dietary Approaches to Stop Hypertension) diet (mean score: 46) from the typical American diet according to the National Health and Nutrition Examination Survey (NHANES) 2003-2006 (mean score: 26.5; P < 0.01). In linear regression analysis of the NHANES 2003-2006 populations (n = 15,900), the NuVal system was significantly associated with the Healthy Eating Index 2005 (P < 0.0001). Recently generated data from ongoing studies indicate favorable effects on purchase patterns and significant correlation with health outcomes in large cohorts of men and women followed for decades. CONCLUSION NuVal offers universally applicable nutrition guidance that is independent of food industry interests and is supported by consumer research and scientific evaluation of its performance characteristics.
Immunogenic and Functional Organization of Hepatitis C Virus (HCV) Glycoprotein E2 on Infectious HCV Virions

ABSTRACT Development of full-length hepatitis C virus (HCV) RNAs replicating efficiently and producing infectious cell-cultured virions, HCVcc, in hepatoma cells provides an opportunity to characterize immunogenic domains on viral envelope proteins involved in entry into target cells. A panel of immunoglobulin G1 human monoclonal antibodies (HMAbs) to three immunogenic conformational domains (designated A, B, and C) on HCV E2 glycoprotein showed that epitopes within two domains, B and C, mediated HCVcc neutralization, whereas HMAbs to domain A were all nonneutralizing. For the neutralizing antibodies to domain B (with some to conserved epitopes among different HCV genotypes), the inhibitory antibody concentration reducing HCVcc infection by 90%, IC90, ranged from 0.1 to 4 μg/ml. For some neutralizing HMAbs, HCVcc neutralization displayed a linear correlation with an antibody concentration between the IC50 and the IC90 while others showed a nonlinear correlation. The differences between IC50/IC90 ratios and earlier findings that neutralizing HMAbs block E2 interaction with CD81 suggest that these antibodies block different facets of virus-receptor interaction. Collectively, these findings support an immunogenic model of HCV E2 having three immunogenic domains with distinct structures and functions and provide added support for the idea that CD81 is required for virus entry.
The iTRAPs: Guardians of Synaptic Vesicle Cargo Retrieval During Endocytosis

The reformation of synaptic vesicles (SVs) during endocytosis is essential for the maintenance of neurotransmission in central nerve terminals. Newly formed SVs must be generated with the correct protein cargo in the correct stoichiometry to be functional for exocytosis. Classical clathrin adaptor protein complexes play a key role in sorting and clustering synaptic vesicle cargo in this regard. However it is becoming increasingly apparent that additional “fail-safe” mechanisms exist to ensure the accurate retrieval of essential cargo molecules. For example, the monomeric adaptor proteins AP180/CALM and stonin-2 are required for the efficient retrieval of synaptobrevin II (sybII) and synaptotagmin-1 respectively. Furthermore, recent studies have revealed that sybII and synaptotagmin-1 interact with other SV cargoes to ensure a high fidelity of retrieval. These cargoes are synaptophysin (for sybII) and SV2A (for synaptotagmin-1). In this review, we summarize current knowledge regarding the retrieval mechanisms for both sybII and synaptotagmin-1 during endocytosis. We also define and set criteria for a new functional group of SV molecules that facilitate the retrieval of their interaction partners. We have termed these molecules intrinsic trafficking partners (iTRAPs) and we discuss how the function of this group impacts on presynaptic performance in both health and disease.
The Culture-Work-Health model and work stress.

OBJECTIVE To describe the role of organizational culture in the etiology of workplace stress through the framework of the Culture-Work-Health model. METHODS A review of the business and health literature related to organizational culture was conducted and applied to the model. RESULTS Culture is an important component of work stress and may be a key to creating effective organizational stress interventions. CONCLUSION Work stress is as much a managerial and business concern as a health concern when it is framed in a cultural argument, and the Culture-Work-Health model provides a theoretical basis for new directions in ameliorating work stress.
The morphology of the foregut of larvae and postlarva of Sesarma curacaoense De Man, 1892: a species with facultative lecithotrophy during larval development

Previous study on the resistance of larvae of Sesarma curacaoense submitted to starvation has revealed a facultative lecithotrophy during zoeal stages, but megalopa and first juvenile stages are exclusively feeding stages. In the present study, the gross morphology and fine structure of the foregut of S. curacaoense were investigated during larval, megalopa and first juvenile stages. The foregut of the zoea I show specific setae and a filter press apparently functional. The foregut undergoes changes in the zoea II (last larval stage) with increment of setae number, mainly on the cardiopyloric valve and complexity of the filter press. After metamorphosis to megalopa stage the foregut become rather complex, with a gastric mill supporting a medial and two lateral teeth well-developed. The foregut of the first juvenile is more specialized compared to the previous stage, showing similar characteristics of the decapod adults. These results provide further evidence of facultative lecithotrophic development in the larvae of S. curacaoense.
Cell Cycle-Dependent Changes in Microtubule Dynamics in Living Cells Expressing Green Fluorescent Protein-α Tubulin

LLCPK-1 cells were transfected with a green fluorescent protein (GFP)-α tubulin construct and a cell line permanently expressing GFP-α tubulin was established (LLCPK-1α). The mitotic index and doubling time for LLCPK-1α were not significantly different from parental cells. Quantitative immunoblotting showed that 17% of the tubulin in LLCPK-1α cells was GFP-tubulin; the level of unlabeled tubulin was reduced to 82% of that in parental cells. The parameters of microtubule dynamic instability were compared for interphase LLCPK-1α and parental cells injected with rhodamine-labeled tubulin. Dynamic instability was very similar in the two cases, demonstrating that LLCPK-1α cells are a useful tool for analysis of microtubule dynamics throughout the cell cycle. Comparison of astral microtubule behavior in mitosis with microtubule behavior in interphase demonstrated that the frequency of catastrophe increased twofold and that the frequency of rescue decreased nearly fourfold in mitotic compared with interphase cells. The percentage of time that microtubules spent in an attenuated state, or pause, was also dramatically reduced, from 73.5% in interphase to 11.4% in mitosis. The rates of microtubule elongation and rapid shortening were not changed; overall dynamicity increased 3.6-fold in mitosis. Microtubule release from the centrosome and a subset of differentially stable astral microtubules were also observed. The results provide the first quantitative measurements of mitotic microtubule dynamics in mammalian cells.
Semi-Supervised Sound Source Localization Based on Manifold Regularization

Conventional speaker localization algorithms, based merely on the received microphone signals, are often sensitive to adverse conditions, such as: high reverberation or low signal-to-noise ratio (SNR). In some scenarios, e.g., in meeting rooms or cars, it can be assumed that the source position is confined to a predefined area, and the acoustic parameters of the environment are approximately fixed. Such scenarios give rise to the assumption that the acoustic samples from the region of interest have a distinct geometrical structure. In this paper, we show that the high-dimensional acoustic samples indeed lie on a low-dimensional manifold and can be embedded into a low-dimensional space. Motivated by this result, we propose a semi-supervised source localization algorithm based on two-microphone measurements, which recovers the inverse mapping between the acoustic samples and their corresponding locations. The idea is to use an optimization framework based on manifold regularization, that involves smoothness constraints of possible solutions with respect to the manifold. The proposed algorithm, termed manifold regularization for localization, is adapted while new unlabelled measurements (from unknown source locations) are accumulated during runtime. Experimental results show superior localization performance when compared with a recently presented algorithm based on a manifold learning approach and with the generalized cross-correlation algorithm as a baseline. The algorithm achieves 2° accuracy in typical noisy and reverberant environments (reverberation time between 200 and 800 ms and SNR between 5 and 20 dB).
Effects of feeding pistachio by-products silage on growth performance, serum metabolites and urine characteristics in Holstein male calves.

This study investigated physiological effects of pistachio by-products silage (PBPS) substituted in Holstein male calves diets and its effects on the growth performance. Twenty-four Holstein male calves (4-5 months of age and 155.6 ± 13.5 kg BW) were randomly assigned to one of four experimental diets (n = 6); contained 0%, 6%, 12% and 18% of PBPS (DM basis) respectively. During a 6-month experiment, dry matter intake (DMI) and weight gain were recorded and blood and urine samples were collected at different times. Results showed that mean DMI was not affected by different levels of PBPS in diets. But the calves fed 6% PBPS had the highest average daily gain (p < 0.05) and the lowest feed conversion ratio (p < 0.05). The calves fed 12% and 18% PBPS had lower albumin, white blood cell, haemoglobin and packed cell volume (p < 0.05) than those fed other diets. However, other serum metabolites, complete blood count (CBC), insulin and liver enzymes were not affected by the experimental diets. The long-term feeding of PBPS at different levels had no significant effect (p > 0.05) on pH, specific gravity, the number of white and red blood cells and epithelial cells count in urine. The animals did not show any symptom of illness or toxicity during the experimental period and all of the blood and urine parameters were in a normal range. It was concluded that substitution of PBPS up to 18% of the total diet that provide up to 18.2 g/kg DM total tannin had no adverse effects for Holstein male calves.
The active cochlea

Peter Dallas Auditory Physiology Laboratory (The Hugh Knowles Center) and Department of Neurobiology and Physiology, Northwestern University, Evanston, Illinois 60208 The cochlea is a hydromechanical frequency analyzer located in the inner ear (Fig. 1 a). Its principal role is to perform a real- time spectral decomposition of the acoustic signal in producing a spatial frequency map. The frequency analysis may be un- derstood with the aid of Figure 1 b, which shows a straightened cochlea with a snapshot of its basilar membrane displaced in response to a single-frequency sound (pure tone). Upon delivery of an acoustic signal into the fluid-filled cochlea, the basilar membrane undergoes an oscillatory motion at the frequency of the sound, resulting in a wave traveling toward its distal end. The drawing shows an instantaneous view ofthis traveling wave. The wave is spatially confined along the length of the basilar membrane, and the location of its maximum amplitude is re- lated to the frequency of the sound. The higher the frequency, the more restricted the disturbance to the proximal end. The vibrating membrane supports the sense organ of hearing, the spiral organ of Corti (Fig. 2) which is deformed maximally in the region of the peak of the traveling wave. In this location, the sensory receptor cells of the organ of Corti receive maximal mechanical stimulation, transduce it into maximal electrical signals, and thus produce maximal afferent sensory outflow from the cochlea. Thus, mechanical frequency analysis is performed by matching particular frequencies with particular groups of auditory receptor cells and their nerve fibers. Understanding of frequency analysis in the inner ear pro- gressed through three main epochs. The first was dominated by Helmholtz’s suggestions that lightly damped, spatially ordered, mechanically resonant elements in the cochlea perform the spec- tral analysis (this period was reviewed by Wever, 1949). The second epoch, lasting from the late 1940s to the early 1970s was dominated by von Bekesy’s description of the traveling wave (von BtkCsy, 1960). We are now in the third epoch (an overview of its evolution is given in Dallos, 1988) during which a fundamentally different paradigm has emerged. According to this paradigm, von Btktsy’s traveling wave is boosted by a local electromechanical amplification process in which one of the mammalian ear’s sensory cell groups, outer hair cells, function as both sensors and mechanical feedback elements. The ideas that the operation of a sense organ is dependent upon local mechanical feedback modification by what resembles a sensory receptor cell, that such mechanical feedback may operate at audio frequencies utilizing some novel cellular motor, and that
In vitro activity of essential oils of free and nanostructured Melaleuca alternifolia and of terpinen-4-ol on eggs and larvae of Haemonchus contortus

Abstract Haemonchus contortus is one of the major gastrointestinal nematodes responsible for significant economic and production losses of sheep. Diseases caused by this species lack effective anthelmintic products, and the search for new compounds to replace synthetic anthelmintics has been extensive. The present investigation assesses the in vitro activity of the essential oil of melaleuca (Melaleuca alternifolia), both free (TTO) and nanostructured (nanoTTO), and terpinen-4-ol (terp-4-ol) on eggs and larvae of H. contortus. Tests of egg hatching (EHT) and inhibition of larval migration (LMIT) were used to assess the in vitro efficacy of TTO, nanoTTO and terp-4-ol. Using EHT, at a concentration of 3.5 mg/ml, 100% inhibition occurred using TTO and terp-4-ol, with LC50 values of 0.43 and 0.63 mg/ml, and LC90 values of 1.75 mg/ml and 3.12 mg/ml, respectively. NanoTTO had lower activity, with 82.6% inhibition at the same concentration. Using LMIT, TTO and nanoTTO had a similar activity with 88.0% and 84.8% inhibition, respectively, at a concentration of 56 mg/ml. Terp-4-ol had a greater effect on larvae, with 85.7% inhibition at a concentration of 56 mg/ml and 82.4% at 3.5 mg/ml, demonstrating high activity at the lowest concentration tested. Therefore, the results indicate that all substances tested showed ovicidal and larvicidal activity against H. contortus. TTO, terp-4-ol and, mainly, nanoTTO may be targeted in in vivo studies, besides being a promising line of research into the control and treatment of veterinary important helminths.
Timing performance of 4×4mm2 SiPMs with different cell layout coupled to LYSO scintillator

In this paper we investigate the impact of the single-cell signal response on the timing resolution capabilities of a silicon photomultiplier coupled to a slow scintillator such as LYSO. At FBK, we produced SiPMs featuring different layout configurations and, as a consequence, different values of the parameters composing the equivalent circuit. All the devices were coupled to Teflon-wrapped LYSO crystals and both energy and timing properties were analyzed. The study evidences that it is possible to strongly enhance the timing performance by a careful optimization of the sensor layout.
Communicating uncertainty in seasonal and interannual climate forecasts in Europe

Across Europe, organizations in different sectors are sensitive to climate variability and change, at a range of temporal scales from the seasonal to the interannual to the multi-decadal. Climate forecast providers face the challenge of communicating the uncertainty inherent in these forecasts to these decision-makers in a way that is transparent, understandable and does not lead to a false sense of certainty. This article reports the findings of a user-needs survey, conducted with 50 representatives of organizations in Europe from a variety of sectors (e.g. water management, forestry, energy, tourism, health) interested in seasonal and interannual climate forecasts. We find that while many participating organizations perform their own ‘in house’ risk analysis most require some form of processing and interpretation by forecast providers. However, we also find that while users tend to perceive seasonal and interannual forecasts to be useful, they often find them difficult to understand, highlighting the need for communication formats suitable for both expert and non-expert users. In addition, our results show that people tend to prefer familiar formats for receiving information about uncertainty. The implications of these findings for both the providers and users of climate information are discussed.
Insertional Inactivation of Branched-Chain α-Keto Acid Dehydrogenase in Staphylococcus aureus Leads to Decreased Branched-Chain Membrane Fatty Acid Content and Increased Susceptibility to Certain Stresses

ABSTRACT Staphylococcus aureus is a major community and nosocomial pathogen. Its ability to withstand multiple stress conditions and quickly develop resistance to antibiotics complicates the control of staphylococcal infections. Adaptation to lower temperatures is a key for the survival of bacterial species outside the host. Branched-chain α-keto acid dehydrogenase (BKD) is an enzyme complex that catalyzes the early stages of branched-chain fatty acid (BCFA) production. In this study, BKD was inactivated, resulting in reduced levels of BCFAs in the membrane of S. aureus. Growth of the BKD-inactivated mutant was progressively more impaired than that of wild-type S. aureus with decreasing temperature, to the point that the mutant could not grow at 12°C. The growth of the mutant was markedly stimulated by the inclusion of 2-methylbutyrate in the growth medium at all temperatures tested. 2-Methylbutyrate is a precursor of odd-numbered anteiso fatty acids and bypasses BKD. Interestingly, growth of wild-type S. aureus was also stimulated by including 2-methylbutyrate in the medium, especially at lower temperatures. The anteiso fatty acid content of the BKD-inactivated mutant was restored by the inclusion of 2-methylbutyrate in the medium. Fluorescence polarization measurements indicated that the membrane of the BKD-inactivated mutant was significantly less fluid than that of wild-type S. aureus. Consistent with this result, the mutant showed decreased toluene tolerance that could be increased by the inclusion of 2-methylbutyrate in the medium. The BKD-inactivated mutant was more susceptible to alkaline pH and oxidative stress conditions. Inactivation of the BKD enzyme complex in S. aureus also led to a reduction in adherence of the mutant to eukaryotic cells and its survival in a mouse host. In addition, the mutant offers a tool to study the role of membrane fluidity in the interaction of S. aureus with antimicrobial substances.
Hybrid Radiosity/Monte Carlo Methods

Monte Carlo methods refer to any method that uses random numbers to get an approximate answer to a problem. In computer graphics Monte Carlo techniques can be used to perform radiosity calculations and can be used in distribution ray tracing for effects such as soft shadows and motion blur. Although these notes are for a course on radiosity, they have a great deal of material from a previous Siggraph 93 global illumination course notes that also dealt with distribution ray tracing, although the radiosity material has been expanded. In these notes I will cover the basics of both Monte Carlo simulation, where a physical system is modeled, Monte Carlo integration, where random numbers are used to approximate integrals, and Quasi-Monte Carlo integration, where non-random numbers are used. This discussion will cover the general techniques, and will use global illumination problems as examples. One appeal of using Monte Carlo methods is that they are easy to design and use. However, it is not so easy to design a good Monte Carlo method, where the computation can be completed to the desired accuracy relatively quickly. Here both cleverness and some analytic skills are required. Fortunately, the analytic skills are fairly narrow in scope, so many of them can be covered in this short tutorial. A more formal discussion of Monte Carlo simulation can be found in the neutron transport literature (e.g. [47]) and an extremely current survey of Monte Carlo integration for practical applications can be found in the survey article by Spanier and Maize[48].
Learning to Explain Entity Relationships in Knowledge Graphs

We study the problem of explaining relationships between pairs of knowledge graph entities with human-readable descriptions. Our method extracts and enriches sentences that refer to an entity pair from a corpus and ranks the sentences according to how well they describe the relationship between the entities. We model this task as a learning to rank problem for sentences and employ a rich set of features. When evaluated on a large set of manually annotated sentences, we find that our method significantly improves over state-of-the-art baseline models.
CENP-B box, a nucleotide motif involved in centromere formation, occurs in a New World monkey

Centromere protein B (CENP-B) is one of the major proteins involved in centromere formation, binding to centromeric repetitive DNA by recognizing a 17 bp motif called the CENP-B box. Hominids (humans and great apes) carry large numbers of CENP-B boxes in alpha satellite DNA (AS, the major centromeric repetitive DNA of simian primates). Only negative results have been reported regarding the presence of the CENP-B box in other primate taxa. Consequently, it is widely believed that the CENP-B box is confined, within primates, to the hominids. We report here that the common marmoset, a New World monkey, contains an abundance of CENP-B boxes in its AS. First, in a long contig sequence we constructed and analysed, we identified the motif in 17 of the 38 alpha satellite repeat units. We then sequenced terminal regions of additional clones and found the motif in many of them. Immunostaining of marmoset cells demonstrated that CENP-B binds to DNA in the centromeric regions of chromosomes. Therefore, functional CENP-B boxes are not confined to hominids. Our results indicate that the efficiency of identification of the CENP-B box may depend largely on the sequencing methods used, and that the CENP-B box in centromeric repetitive DNA may be more common than researchers previously thought.