Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular dynamics of folding of secondary structures in Go-type models of proteins

We consider six different secondary structures of proteins and construct two types of Go-type off-lattice models: with the steric constraints and without. The basic amino acid–amino acid potential is Lennard–Jones for the native contacts and a soft repulsion for the non-native contacts. The interactions are chosen to make the target secondary structure be the native state of the system. We provide a thorough equilibrium and kinetic characterization of the sequences through the molecular dynamics simulations with the Langevin noise. Models with the steric constraints are found to be better folders and to be more stable, especially in the case of the β structures. Phononic spectra for vibrations around the native states have low frequency gaps that correlate with the thermodynamic stability. Folding of the secondary structures proceeds through a well-defined sequence of events. For instance, α helices fold from the ends first. The closer to the native state, the faster establishment of the contacts. Increas.
The Random Projection Method for Stiff Multispecies Detonation Capturing

In this paper we extend the random projection method, proposed for general hyperbolic systems with stiff reaction terms, for underresolved numerical simulation of stiff, inviscid, multispecies detonation waves. The key idea in this method is to randomize the ignition temperatures in suitable domains. Several numerical experiments, in both one and two dimensions, demonstrate the reliability and robustness of this novel method.
Osteopenia in alcoholics: effect of alcohol abstinence.

AIMS The aims of this study were to assess bone mineral density (BMD) and content (BMC), osteocalcin, serum telopeptide, PTH and vitamin D in alcoholics, and to determine if a 6-month period of abstinence leads to changes in these parameters. METHODS Serum osteocalcin, insulin-like growth factor 1 (IGF-1), telopeptide (40 patients) and 1,25 dihydroxyvitamin D, were measured in 28 controls and 77 alcoholic patients, 48 of whom were evaluated again 6 months later. All patients underwent whole-body assessment of BMD by a Hologic QDR-2000 (Waltham, MA, USA) bone densitometer, at the beginning of the study and 6 months later. RESULTS Patients showed higher serum telopeptide levels (0.59 +/- 0.40 versus 0.19 +/- 0.10 nmol/100 ml, P < 0.001), lower IGF-1 [median = 49, interquartile range (IQR) = 31-121 ng/ml versus 135, IQR = 116-237 ng/ml, P < 0.001], vitamin D [26.5, IQR = 17.0-37.8 pg/ml versus 82.4 (IQR = 60.9-107.4 pg/ml, P < 0.001] and osteocalcin (2.1, IQR = 1.1-3.6 ng/ml versus 6.65, IQR = 4.9-8.8 ng/ml, P < 0.001) than those in controls. Patients also showed lower BMD values, Z- and T-scores at many levels of the skeleton and reduced total BMC. After 6 months, those who continued drinking showed a loss of bone mass, whereas those who abstained showed either no change or increase, differences being especially marked at pelvis, right arm and total BMD and BMC. Simultaneously, abstainers showed a significant increase in osteocalcin (versus a decrease among those who continued drinking). Serum telopeptide increased in both groups. CONCLUSION Ethanol consumption leads to osteopenia, and decreased serum osteocalcin, which improve with abstinence, whereas those who continue drinking show a worsening of both parameters.
Reactive Oxygen Species in the Regulation of Stomatal Movements1[OPEN]

Reactive oxygen species play an important role in guard cell signaling leading to stomatal closure and regulate signal amplification and specificity. Guard cells form stomatal pores that optimize photosynthetic carbon dioxide uptake with minimal water loss. Stomatal movements are controlled by complex signaling networks that respond to environmental and endogenous signals. Regulation of stomatal aperture requires coordinated activity of reactive oxygen species (ROS)-generating enzymes, signaling proteins, and downstream executors such as ion pumps, transporters, and plasma membrane channels that control guard cell turgor pressure. Accumulation of ROS in the apoplast and chloroplasts is among the earliest hallmarks of stomatal closure. Subsequent increase in cytoplasmic Ca2+ concentration governs the activity of multiple kinases that regulate the activity of ROS-producing enzymes and ion channels. In parallel, ROS directly regulate the activity of multiple proteins via oxidative posttranslational modifications to fine-tune guard cell signaling. In this review, we summarize recent advances in the role of ROS in stomatal closure and discuss the importance of ROS in regulation of signal amplification and specificity in guard cells.
HIV-1 Dynamics in Vivo: Virion Clearance Rate, Infected Cell Life-Span, and Viral Generation Time

A new mathematical model was used to analyze a detailed set of human immunodeficiency virus-type 1 (HIV-1) viral load data collected from five infected individuals after the administration of a potent inhibitor of HIV-1 protease. Productively infected cells were estimated to have, on average, a life-span of 2.2 days (half-life t1/2 = 1.6 days), and plasma virions were estimated to have a mean life-span of 0.3 days (t1/2 = 0.24 days). The estimated average total HIV-1 production was 10.3 × 109 virions per day, which is substantially greater than previous minimum estimates. The results also suggest that the minimum duration of the HIV-1 life cycle in vivo is 1.2 days on average, and that the average HIV-1 generation time—defined as the time from release of a virion until it infects another cell and causes the release of a new generation of viral particles—is 2.6 days. These findings on viral dynamics provide not only a kinetic picture of HIV-1 pathogenesis, but also theoretical principles to guide the development of treatment strategies.
Receiver performance evaluation on IEEE 802.15.6 based WBAN for monitoring Parkinson's disease

Advantages of remote health monitoring are incontestable: prolonging the patient's possibility to stay at home by monitoring the health condition remotely, the quality of patient's life is improved as well as healthcare costs are significantly reduced. Parkinson's disease is one example, for which some wireless monitoring systems have been presented recently. However, concrete performance evaluations for the IEEE 802.15. 6 standard based communication in the realistic use scenarios have not been presented yet in the literature. The aim of this paper is to evaluate performance of ultra wideband energy detector receivers on the physical layer of the IEEE 802.15. 6 standard. The monitoring system and node locations are designed for monitoring Parkinson's disease symptoms. Measurement based radio channel models were used in the evaluations. Two modulation methods, on-off keying and pulse position modulation, are evaluated and compared using two different antennas suitable for body area network communication. Pulse position modulation based system is found to outperform on-off keying based system, which on the other hand, is simpler to implement. Furthermore, it is shown how antenna placement, position, and properties are impacting on the channel characteristics of the radio link, and hence, on the bit error rate performance.
A Rigorous Analysis of Least Squares Sine Fitting Using Quantized Data: The Random Phase Case

This paper considers least square (LS) based estimation of the amplitude and square amplitude of a quantized sine wave, done by considering random initial record phase. Using amplitude- and frequency-domain modeling techniques, it is shown that the estimator is inconsistent, biased, and has a variance that may be underestimated if the simple model of quantization is applied. The effects of both sine wave offset values and additive Gaussian noise are considered. General estimator properties are derived, without making simplifying assumptions on the role of the quantization process, to allow assessment of measurement uncertainty, when this LS procedure is used.
Gadopentetate Dimeglumine as an Intradiscal Contrast Agent

Study Design. Magnetic resonance discography using gadolinium as an intradiscal contrast agent was investigated in a prospective study. Objective. To evaluate the utility of magnetic resonance discography using gadolinium as an intradiscal contrast agent, as compared with the current standard of computed tomographic discography using intradiscal iodinated contrast agent. Summary of Background Data. Magnetic resonance arthrography with gadolinium has been used to evaluate shoulder, elbow, wrist, hip, knee, and other joints. Gadolinium has not been used as an intradiscal contrast agent. The authors’ preliminary results using gadolinium as an intradiscal contrast agent for magnetic resonance discography were reported previously. They report the results of their completed study. Methods. For this study, 42 disc levels were studied in 13 patients. Water-soluble iodinated contrast and gadopentetate dimeglumine were injected at each disc level. After discography, anteroposterior and lateral radiographs, computed tomography scans, and T1-weighted magnetic resonance imaging were performed. Six physicians interpreted the results from each disc level in a blinded fashion. Interscan and interobserver interpretation variability was determined for magnetic resonance discography and computed tomographic discography using the Pearson correlation-coefficient (r) test. Results. Interscan variability was highly correlated between computed tomographic discography and magnetic resonance discography when used to determine disc normality (r = 0.87), general degeneration (r = 0.87), anular fissure (r = 0.89), disc herniation (r = 0.92), and contrast leakage (r = 0.77). Interscan variability was assessed by the Pearson test, and all values of r for all the readers were noted to be statistically significant at P values less than 0.01. Interobserver variability was significantly correlated among the four more experienced readers (neuroradiologists and spine surgeons), but not among the spine fellows. Interobserver variability was also significantly correlated by computed tomographic (CT) and magnetic resonance imaging (MRI) discography for disc normality (CT r = 0.60; MRI r = 0.56), general degeneration (CT r = 0.76; MRI r = 0.71), anular fissure (CT r = 0.79; MRI r = 0.84), and disc herniation (CT r = 0.63; MRI r = 0.64). The readings for contrast leakage did not reach statistical significance for computed tomographic or magnetic resonance discography. Conclusions. The high interscan and interobserver correlation rates obtained for magnetic resonance discography using gadolinium, as compared with the standard computed tomographic discography technique, indicate that magnetic resonance discography may be an acceptable substitute for the imaging of disc pathology. Magnetic resonance discography with gadolinium can be recommended for patients allergic to iodinated contrast agents and for patients who wish to limit their radiation exposure.
Circumnavigating the cost of support

Although social support is typically associated with a number of health benefits, for some individuals support worsens outcomes, likely because receiving support can undermine feelings of competence. Some have argued that invisible support (i.e., support that recipients do not recognize as help) can reduce negative support-related health consequences (Bolger, Zuckerman, & Kessler, 2000); still, the physiological benefits of invisible support have yet to be established and likely differ as a function of self-efficacy. The purpose of this study was to investigate how visibility of support and self-efficacy interact to affect the cortisol reactivity of a support recipient. In a 2 (self-efficacy: high vs. low) × 2 (support visibility: visible vs. invisible) between-subjects, experimental design, 74 undergraduate students were primed for either high or low self-efficacy using false feedback. Participants then received either visible or invisible support from a confederate while preparing a speech as part of the Trier Social Stress Task (Kirschbaum, Pirke, & Hellhammer, 1993). A series of repeated measures analyses of variance revealed that individuals primed to have high self-efficacy experienced cortisol increases in response to the speech task when they received visible support but not invisible support. By contrast, individuals primed to have low self-efficacy experienced increased cortisol when they received invisible support but not visible support. This research suggests that although invisible support can effectively buffer stress, it is not always the best support strategy.
Semantic-Preserving Transformations for Stream Program Orchestration on Multicore Architectures

Because the demand for high performance with big data processing and distributed computing is increasing, the stream programming paradigm has been revisited for its abundance of parallelism in virtue of independent actors that communicate via data channels. The synchronous data-flow (SDF) programming model is frequently adopted with stream programming languages for its convenience to express stream programs as a set of nodes connected by data channels. Unlike general data-flow graphs, SDF requires the specification of the number of data items produced and consumed by a node already at compile-time. Static data-rates enable program transformations that greatly improve the performance of SDF programs on multicore architectures. The major application domain is for SDF programs are digital signal processing, audio, video, graphics kernels, networking, and security. The major optimization objective with stream programs is data throughput. Stream program orchestration is a term that denotes compiler optimizations and run-time techniques that aim at performance improvements of stream programs on multicore architectures. A large body of research has already been devoted to stream program orchestration. Nevertheless, current compilers and run-time systems for stream programming languages are not able yet to harvest the raw computing power of contemporary parallel architectures. We identify data channels as the dominating roadblock for achieving high performance of SDF programs. Data channels between communicating nodes, i.e., between a producer and a consumer, employ FIFO-queue semantics. Funneling a data item (token) from a producer to a consumer through a FIFO queue incurs non-negligible overhead. The producer is required to perform an enqueue-operation, followed by a dequeue operation in the consumer. The enqueue and dequeue operations induce the
Frequency-Doubling OEO Using the Polarization Property of LiNbO3 Modulator

A frequency-doubling optoelectronic oscillator (OEO) has been proposed. In the proposed device, several passive components are introduced into the traditional OEO to handle the polarization state of the laser in the feedback loop. Making use of the polarization dependence of the LiNbO3 intensity modulator, a special double sidebands modulation is implemented where the polarization direction of the optical carrier is orthogonal with that of the first-order sidebands. Two polarizers are used to choose the specific optical components from the modulated light, which ensures that a microwave signal at the second-harmonic frequency outputs from the OEO when the fundamental frequency signal is self-oscillating in the loop. In the experiment, a 20-GHz frequency-doubled signal was generated, whose phase noise performance and immunity to the polarization drift were measured and evaluated.
Working Paper No . 5 18 Entry Costs Rise with Development By

Looking at manufacturing industries over time and across countries, the number of firms and establishments is closely tied to employment. Relative to employment, the number of businesses is at best weakly increasing in output per worker. In many models of firm dynamics, trade and growth, these facts imply that the cost of creating a new firm or plant increases sharply with productivity. This increase in entry costs can stem from rising cost of labor used in entry, as well as higher output costs of setting up a business to use more sophisticated technologies. How entry costs vary with development matters for welfare in many settings, such as in love of variety models and in span-of-control models. Our findings suggest that the welfare impact of productivity-enhancing policies is not significantly amplified through an increase in the number of firms or plants. ∗Department of Economics, Stanford Institute for Economic Policy Research (SIEPR), and NBER. †Huiyu Li is grateful to SIEPR for the Shultz Graduate Student Fellowship in Economic Policy, and Shorenstein APARC at Stanford for the Shorenstein Predoctoral Fellowship in Contemporary Asia. 2 BOLLARD, KLENOW, LI
Reduced expression of Raf-1 kinase inhibitory protein in renal cell carcinoma: a significant prognostic marker

Aims: Renal cell carcinoma (RCC) is the third most common urological malignancy. Raf-1 kinase inhibitor protein (RKIP) has emerged as a significant metastatic suppressor and useful prognostic marker for a variety of human cancers. The aims of this study were to evaluate RKIP expression in RCC patients, and to determine the association of this protein with metastasis and its prognostic significance. Methods: Immunohistochemical staining for RKIP was performed for 310 cases of various types of RCC. We investigated whether RKIP expression correlated with clinicopathological parameters and patient outcomes. Results: The tubules of normal kidney showed consistently strong cytoplasmic and membranous RKIP immunoreactivity. RKIP expression was significantly reduced in 42.2% of RCC cases (negative 24.5%, weakly positive 17.7%). Reduced RKIP expression was significantly related to presence of distant metastasis (p < 0.001), higher disease stage (p = 0.004), larger tumour size (p = 0.005), and sarcomatoid subtype (p = 0.001). Univariate analysis showed that reduced RKIP expression was significantly associated with poor overall survival and disease-free survival (p = 0.0014 and 0.0001, respectively). The multivariate analysis revealed that reduced RKIP expression was an independent predictor of poor prognosis for overall patient survival (p = 0.035). Conclusion: Our results strongly suggested that reduced RKIP expression is associated with tumour progression and metastasis. Therefore, we concluded that RKIP expression is a significant prognostic marker for patients with RCC.
Rape Stem Weevil (Ceutorhynchus napi Gyll. 1837) and Cabbage Stem Weevil (Ceutorhynchus pallidactylus Marsh. 1802) (Coleoptera: Curculionidae) – Important Oilseed Rape Pests

Stem mining weevils, rape stem weevil (Ceutorhynchus napi Gyll. 1837) and cabbage stem weevil (Ceutorhynchus pallidactylus Marsh. 1802) have become more important oliseed rape pests. Rape stem weevil is present in middle and west European countries and cabbage stem weevil is present in almost all European countries. The most important morphological difference between adults is colour of their legs. Biological and ecological characteristics of these two pests are similar, stem mining weevils are observed as pest complex. Differences in biology cause different approach in pest control. Both species have single generation annually. Larvae feed inside the petioles and stems of oilseed rape. Phyrethroids are used for adult control of stem mining weevils.
Association of Hepatitis C Virus Infection With CD4/CD8 Ratio in HIV-Positive Women

Background: Recent studies reported that the CD4/CD8 T-cell ratio is inversely associated with biomarkers traditionally used to measure immune activation and systemic inflammation in highly active antiretroviral therapy–treated HIV-infected (HIV+) patients. The relation of hepatitis C virus (HCV) coinfection with the CD4/CD8 ratio in HIV+ patients is unknown. Methods: We examined 50,201 CD4/CD8 ratios measured over 20 years in 3 groups of HIV+ women enrolled in the Women's Interagency HIV Study: HCV antibody negative (n = 1734), cleared HCV (n = 231), and chronic HCV (n = 751) in multivariate models. IFNL4-&Dgr;G genotype and HCV viral load were also considered. Results: Compared with HCV antibody negative status, chronic HCV infection was associated with lower CD4/CD8 ratios when HIV viral load was suppressed to the lower limit of quantification (&bgr; = −0.08; P = 0.002). Cleared HCV (&bgr; = −0.10; P = 0.0009), but not IFNL4-&Dgr;G genotype or HCV viral load, was also associated with lower CD4/CD8 ratios when HIV viral load was suppressed to the lower limit of quantification. Conclusions: The association of HCV coinfection with CD4/CD8 ratio is consistent with previously observed associations of HCV coinfection with biomarkers traditionally used to measure immune activation and systemic inflammation in HIV+ patients. These data provide additional support for the use of CD4/CD8 ratio for routine monitoring of immune activation and inflammation in HIV+ patients, including those with HIV/HCV coinfection; however, the unexpected association between cleared HCV and lower CD4/CD8 ratio requires additional study.
The Emergence of Regional Immigrant Concentrations in USA and Australia: A Spatial Relatedness Approach

This paper examines the patterns of the US and Australian immigration geography and the process of regional population diversification and the emergence of new immigrant concentrations at the regional level. It presents a new approach in the context of human migration studies, focusing on spatial relatedness between individual foreign-born groups as revealed from the analysis of their joint spatial concentrations. The approach employs a simple assumption that the more frequently the members of two population groups concentrate in the same locations the higher is the probability that these two groups can be related. Based on detailed data on the spatial distribution of foreign-born groups in US counties (2000–2010) and Australian postal areas (2006–2011) we firstly quantify the spatial relatedness between all pairs of foreign-born groups and model the aggregate patterns of US and Australian immigration systems conceptualized as the undirected networks of foreign-born groups linked by their spatial relatedness. Secondly, adopting a more dynamic perspective, we assume that immigrant groups with higher spatial relatedness to those groups already concentrated in a region are also more likely to settle in this region in future. As the ultimate goal of the paper, we examine the power of spatial relatedness measures in projecting the emergence of new immigrant concentrations in the US and Australian regions. The results corroborate that the spatial relatedness measures can serve as useful instruments in the analysis of the patterns of population structure and prediction of regional population change. More generally, this paper demonstrates that information contained in spatial patterns (relatedness in space) of population composition has yet to be fully utilized in population forecasting.
Sex-Related Differential Item Functioning (DIF) Analysis of TIMSS

The purpose of this study was to analyze items that exhibited sex-related Differential Item Functioning (DIF) from the mathematics tests of TIMSS 1999 using the Jordanian data. The analysis included determining the prevalence and the content of the DIF items for each sex. Data used were the responses of 5299 eighth grade students (2470 females and 2829 males) to a total of 124 multiple-choice math items. Mantel-Haenszel (MH) DIF procedure was applied on the eight test booklets. Results showed that, on average, more than 20% of the items on each test booklet exhibited sex-related DIF, and the DIF items were evenly distributed between males and females. Math content of DIF items was analyzed and the content preferred by each sex was determined. Implications of the results and recommendations were discussed.