Miracle-dz/UniFAR-FTUs huggingface dataset:
Thermodynamics of denaturation of staphylococcal nuclease mutants: an intermediate state in protein folding

A valuable approach lo understanding the forces that maintain protein structure is to analyze the thermodynamic effects of mutations on protein folding. The folding process is most often described using an energetic model that assumes a two‐state transition between the native and denatured states. However, some results obtained using this approach for mutants of the protein staphylococcal nuclease have contradicted expectations from our current understanding of protein energetics. The application of differential scanning calorimetry to a set of mutant nuclease proteins allowed us to measure directly the effects of mutations on the enthalpy and heat capacity changes of unfolding, as well as on the cooperativity. We found that most of these effects can be understood with a three‐state model of folding including a distinct intermediate, but not with the two‐state model. Use of a three‐state instead of a two‐state model leads to large differences in conclusions about the stability effects of some mutations, suggesting that réévaluation of the effects of mutations on this and other proteins may be necessary to achieve an accurate description of folding energetics. The two‐state assumption commonly used in protein stability studies may be an oversimplification in many cases. —Carra, J. H. , Privalov, P. L. Thermodynamics of denaturationof staphylococcal nuclease mutants: an intermediate state in protein folding. FASEB J. 10, 67‐74 (1996)
Discrete-Time Sliding Mode Control With Time-Varying Surface for Hard Disk Drives

A time optimal-based discrete-time sliding mode control (DSMC) scheme with application to hard disk drives (HDDs) is developed in this study. In this approach, an approximate time optimal switching curve is adopted for the time-varying sliding mode design and the controller, which consists of an equivalent part and a discontinuous one, is designed such that the trajectory from any initial point is driven into a sliding region in the vicinity of the switching surface without chattering and thereafter remains inside it. By using the time-varying switching surface, one unified framework for both track seeking and following control is provided and smooth transition from seeking control to track following control is achieved as well. Simulation and experimental studies on the design of controller in HDDs were conducted to illustrate its feasibility and effectiveness. The simulation/experimental results demonstrate that the proposed scheme provides better performance during track seeking than the commonly used discrete-time proximate time-optimal servomechanism (PTOS) and sliding mode proximate time optimal servomechanism (SMPTOS). Moreover, the unified controller achieves better disturbance suppression in track-following than the proportional-integral-differential (PID) control.
Floating–Harbor syndrome and polycystic kidneys associated with SRCAP mutation

Floating–Harbor syndrome (FHS) is a rare genetic disorder recently shown to be caused by mutations in the Snf2‐related CREB‐binding protein activator protein gene (SRCAP). It comprises three key clinical features of characteristic facies, expressive and receptive speech impairment and short stature. We report on a patient with this syndrome associated with early adult‐onset hypertension and bilateral polycystic kidneys. Family screening for polycystic kidney disease was negative and mutations in polycystic kidney disease 1 and 2 genes (PKD1 and PKD2) were absent. Sequencing of the SRCAP gene demonstrated a de novo mutation matching one of the known FHS‐associated mutations. The patient required treatment with anti‐hypertensives and will require lifelong renal monitoring. We suggest this patient's presentation may be due to the pleiotropic effects of SRCAP mutations. Further, the protein encoded by SRCAP is known to interact with CREB‐binding protein, the product of the gene mutated in Rubinstein–Taybi syndrome, which is associated with renal abnormalities. A literature review of the renal findings in patients with Floating–Harbor syndrome identified another patient with possible polycystic kidneys, two patients with early onset hypertension, and a young patient with a ruptured intracranial aneurysm, which can be a feature of classic adult polycystic kidney disease. Collectively, these findings suggest that all patients with Floating–Harbor syndrome should undergo regular blood pressure monitoring and screening for polycystic kidneys by ultrasound at the time of the FHS diagnosis with imaging to be repeated during adulthood if a childhood ultrasound was negative. © 2012 Wiley Periodicals, Inc.
Object-related Attention: An Event-related Potential Study

In two experiments reaction time (RT) and event-related potentials (ERPs) were measured to visual stimuli consisting of two objects (Duncan, 1984; Vecera & Farah, 1994). Target stimuli were defined by two features, which either were distributed between the two objects or belonged to a single object. In Experiment 1 the two objects appeared in spatial overlap, whereas in Experiment 2 the two objects were spatially separated. In both experiments RT was shorter in the single-object condition. The late positive component of the ERP (P3) emerged, peaked, and declined earlier in the single-object condition. It is suggested that object-related attention may facilitate the earlier onset of search for the relevant features.
Changing River Ice Seasonality and Impacts on Interior Alaskan Communities

Subsistence harvesters in high latitudes rely on frozen rivers for winter access to local resources. During recent decades, interior Alaskan residents have observed changes in river ice regimes that are significant hindrances to travel and subsistence practices. We used remote sensing in combination with local observations to examine changes in seasonality of river breakup and freeze-up and to assess the implications on travel for subsistence harvesters. Spring and autumn air temperatures, respectively, were found to impact timing of breakup (−2.0 days °C−1) and freeze-up (+2.0 days °C−1). Spring air temperatures have increased by 0.2°–0.6°C decade−1 over the last 62–93 years, depending on study area and time period. Local observations indicate that the breakup season has advanced by about 6 days over the last century. Autumn air temperatures have not changed over the long term, but have been generally warmer over the last 15 years. Over various time periods throughout the last century, we found no change in freeze-up timing for some communities, whereas other communities showed delays of 1.0–2.1 days decade−1. The length of time the river was unsafe for travel during the freeze-up season was 2 to 3 times greater than during breakup. The duration of river ice cover for safe travel has declined over the last century and is expected to decline further as the climate continues to warm, thereby presenting new challenges to accessing subsistence resources and necessitating community adaptation.
Handwriting Recognition with Multigrams

We introduce a novel handwriting recognition approach based on sub-lexical units known as multigrams of characters, that are variable lengths characters sequences. A Hidden Semi Markov model is used to model the multigrams occurrences within the target language corpus. Decoding the training language corpus with this model provides an optimized multigram lexicon of reduced size with high coverage rate of OOV compared to the traditional word modeling approach. The handwriting recognition system is composed of two components: the optical model and the statistical n-grams of multigrams language model. The two models are combined together during the recognition process using a decoding technique based on Weighted Finite State Transducers (WFST). We experiment the approach on two Latin language datasets (the French RIMES and English IAM datasets) and we show that it outperforms words and character models language models for high Out Of Vocabulary (OOV) words rates, and that it performs similarly to these traditional models for low OOV rates, with the advantage of a reduced complexity.
Improving sparse organic WiFi localization with inertial sensors

Personal location discovery and navigation within buildings has become an important research topic in the last years. One method to determine one's current position based on mobile-devices is to compare the set of available WiFi access points (APs), i.e. the fingerprint of a given space, to a previously collected database. In this context, this paper addresses the inherent problem of such systems that this fingerprint database needs to be established beforehand. Thus, situations can occur where a building is only partially represented in the database and localization can only be provided in a subset of the spaces of the building. This problem occurs especially in crowd-sourcing (organic) approaches where users consecutively contribute location-binds. In these situations an additional system is needed to provide localization. We present a first study on the fusion of pedestrian dead reckoning (PDR) from inertial sensors with position estimates from a WiFi localization system. We outline a possible design of particle filter and analyze its behavior on experimental data. We conclude that the outlined method can help to improve WiFi localization and is especially useful within crowd-sourcing environments.
Colima y Manila: dos ciudades hermanadas por la historia

Durante dos siglos y medio, las ciudades de Colima y Manila mantuvieron una estrecha relacion sociocultural como resultado de los viajes transpacificos del “Galeon” de Manila. En su travesia hacia el puerto de Acapulco esta embarcacion encallaba con regularidad en el puerto de Salagua (Manzanillo, Colima) para abastecerse de viveres, asi como para enviar al virrey de la Nueva Espana el pliego oficial con los pormenores del “Galeon”. Fue asi como numerosos asiaticos (conocidos en la Nueva Espana como “indios chinos”) desembarcaron en territorio colimense y se establecieron en las haciendas de palmas (Machuca, 2009a), muy familiares para ellos por tratarse de una planta de origen asiatico. Los filipinos ensenaron diversos usos del cocotero (Cocos nucifera L), desde bebidas, comidas, utensilios y casas habitacion conocidas como palapas; esta herencia pervive actualmente y es parte de la vida cotidiana de los colimenses. Rememorar los lazos historicos entre Colima y Manila servira de fundamento para proponer el hermanamiento oficial entre ambas ciudades; por ello, este articulo presenta diez argumentos historicos que evidencian las relaciones e intercambios culturales entre ambas municipalidades, desde sus inicios a mediados del siglo xvi hasta la epoca de la Independencia
Metabolic Profiling of Human Long-Term Liver Models and Hepatic Clearance Predictions from In Vitro Data Using Nonlinear Mixed-Effects Modeling

Early prediction of human clearance is often challenging, in particular for the growing number of low-clearance compounds. Long-term in vitro models have been developed which enable sophisticated hepatic drug disposition studies and improved clearance predictions. Here, the cell line HepG2, iPSC-derived hepatocytes (iCell®), the hepatic stem cell line HepaRG™, and human hepatocyte co-cultures (HμREL™ and HepatoPac®) were compared to primary hepatocyte suspension cultures with respect to their key metabolic activities. Similar metabolic activities were found for the long-term models HepaRG™, HμREL™, and HepatoPac® and the short-term suspension cultures when averaged across all 11 enzyme markers, although differences were seen in the activities of CYP2D6 and non-CYP enzymes. For iCell® and HepG2, the metabolic activity was more than tenfold lower. The micropatterned HepatoPac® model was further evaluated with respect to clearance prediction. To assess the in vitro parameters, pharmacokinetic modeling was applied. The determination of intrinsic clearance by nonlinear mixed-effects modeling in a long-term model significantly increased the confidence in the parameter estimation and extended the sensitive range towards 3% of liver blood flow, i.e., >10-fold lower as compared to suspension cultures. For in vitro to in vivo extrapolation, the well-stirred model was used. The micropatterned model gave rise to clearance prediction in man within a twofold error for the majority of low-clearance compounds. Further research is needed to understand whether transporter activity and drug metabolism by non-CYP enzymes, such as UGTs, SULTs, AO, and FMO, is comparable to the in vivo situation in these long-term culture models.
ADH modulates plasma membrane lipid order of living MDCK cells via a cAMP-dependent process.

Using 1-[4-(trimethylamino)phenyl]-6-phenyl-hexa-1,3,5-triene, a fluorescent probe that specifically labels the external leaflet of the plasma membrane of living cells, we examined the effects of antidiuretic hormone (ADH) and various agents known to raise intracellular adenosine 3',5'-cyclic monophosphate (cAMP) on the physical state of the plasma membrane of Madin-Darby canine kidney (MDCK) cells. In polarized cells grown as a monolayer, [desamino-Cys1, DArg8]-vasopressin (V2-agonist) elicited a biphasic decrease in the lipid order as estimated from the decrease in fluorescence anisotropy (from r = 0.317 to r = 0.304, 37 degrees C) of the apical domain of the plasma membrane, equivalent at the peak response (t = 5 min) to that produced by an upward shift in temperature of 5-6 degrees C. A similar response was obtained by adding dibutyryl cAMP to the monolayers. Experiments on cell suspensions further indicated that the biphasic decrease in lipid order could also be evoked by forskolin, prostaglandin E2, and bradykinin but not by bradykinin plus indomethacin and was inhibitable by the protein kinases inhibitor compound H7. These data demonstrate that the lipid order of the plasma membrane of MDCK cells can be modulated in situ by cAMP-dependent processes probably involving protein kinase A activity, i.e., that membrane "fluidity" might act in the regulation of the cellular function of living epithelial cells. They provide a rationale for the changes in lipophilic solute permeability that accompany the increase in water permeability of target cells on ADH administration.
Politics, partisanship and the power to veto: does gubernatorial line-item veto power affect state budgets?

ABSTRACT How does line-item veto (LIV) power affect a governor’s ability to structure the state budget? Is LIV power only relevant as a partisan tool? Is it still relevant when the state legislature can override the veto? We use a rich disaggregated data set to test the effect of the gubernatorial LIV on state budgets, controlling for political factors such as party affiliation of the governor and legislature, minority status of the governor, and the legislature’s ability to override a LIV. Our results suggest that LIV power has very weak influence, if any, on governors’ ability to influence state budgets.
Economic Sustainability of the Australian Grain Supply Chain Post Market Deregulation

From a grain supply chain once supported by a statutory market scheme, poised to stabilise market fluctuations and protect primary producer financial returns, the Australian grain market has now been significantly altered through the process of market deregulation. The deregulation of the Australian grain statutory market scheme created free market conditions in order to increase competition and industry growth; however removed much of the stabilisation mechanisms for primary producers and the greater grain supply chain. In opposition to the intent of the market deregulation, productivity growth within the primary production portion of the Australian grain supply chain has been notably diminished, since the deregulation of the statutory market scheme. Through understanding the impact of deregulation on the social systems, within the primary production environment of the Australian grain supply chain, it is evident that deregulation has had a significant effect on the capacity and desire of primary producers to innovate and the subsequent ability of the supply chain and grain industry to ensure economic sustainability. Keywords: Economic sustainability, supply chain, deregulation, grain production, risk, decision making
Sleep issues in Parkinson’s disease

Sleep disturbances in patients with Parkinson’s disease (PD) are common, are often severe, and are typically underrecognized and ineffectively treated. After the recognition that some patients with PD could fall asleep unexpectedly when driving, with resulting dangerous consequences, it became evident not only that PD medications might be partly responsible but that there were many additional factors contributing to sleep disturbance in these patients. This review discusses the myriad sleep disorders seen in patients with PD, presents their diagnostic features, and gives recommendations on their management. Effective management of sleep disturbances and excessive daytime sleepiness can greatly improve the quality of life for patients with PD.
Goldmann tonometry tear film error and partial correction with a shaped applanation surface

Purpose The aim of the study was to quantify the isolated tear film adhesion error in a Goldmann applanation tonometer (GAT) prism and in a correcting applanation tonometry surface (CATS) prism. Methods The separation force of a tonometer prism adhered by a tear film to a simulated cornea was measured to quantify an isolated tear film adhesion force. Acrylic hemispheres (7.8 mm radius) used as corneas were lathed over the apical 3.06 mm diameter to simulate full applanation contact with the prism surface for both GAT and CATS prisms. Tear film separation measurements were completed with both an artificial tear and fluorescein solutions as a fluid bridge. The applanation mire thicknesses were measured and correlated with the tear film separation measurements. Human cadaver eyes were used to validate simulated cornea tear film separation measurement differences between the GAT and CATS prisms. Results The CATS prism tear film adhesion error (2.74±0.21 mmHg) was significantly less than the GAT prism (4.57±0.18 mmHg, p<0.001). Tear film adhesion error was independent of applanation mire thickness (R2=0.09, p=0.04). Fluorescein produces more tear film error than artificial tears (+0.51±0.04 mmHg; p<0.001). Cadaver eye validation indicated the CATS prism’s tear film adhesion error (1.40±0.51 mmHg) was significantly less than that of the GAT prism (3.30±0.38 mmHg; p=0.002). Conclusion Measured GAT tear film adhesion error is more than previously predicted. A CATS prism significantly reduced tear film adhesion error bŷ41%. Fluorescein solution increases the tear film adhesion compared to artificial tears, while mire thickness has a negligible effect.
The effect of perceived psychological stress on the immunogenicity of the quadrivalent human papillomavirus vaccine in males

ABSTRACT Background: The human papillomavirus (HPV) vaccine is recommended for male and female recipients aged 9–26 years, and is effective in preventing HPV infection and cancer precursors. However, there is variability in immunogenicity among recipients as measured by anti-HPV geometric mean titers. In this study, we explored the effect of stress level on the immunogenicity of the HPV vaccine among college age males. Methods: 220 males aged 18–25 y were randomly assigned to 6-month (0, 2, and 6) and 12-month (0, 2, and 12) dosing schedules. Antibody titers were measured before the first dose and 2–6 weeks following the final dose. We recorded participants' age and stress level, based on a 4-item Perceived Stress Scale (PSS-4) questionnaire. Results: The average age of participants was 21.3 y old. Inspection of titers by quartile on the stress scale generally showed highest titers with highest stress. Spearman correlation coefficients revealed significant correlation between stress and titers for HPV-6, 16, and 18 but not for HPV-16 in the group of 6-month dosing schedule; no associations were found for the 12-month dosing schedule. For most strains, linear regression revealed significant (P > 0.05) associations on antibody titer for categorical age and dosing schedule but not stress. Conclusion: The evidence is mixed for an association between stress and HPV vaccine response for the 6-month dosing schedule, but no association was found for stress for the 12-month dosing schedule. Further investigations with larger and more diverse population groups are needed to explore the association between stress level and vaccine immunogenicity.
Selecting new artists – A qualitative study on the roles of various forms of capital in the selection system within the popular music industry

The academic (and popular) literature on the various forms of capital gives a clear message: it requires a combination of cultural, social and symbolic capital to make it through as a new artist in the music industry. However, it remains unclear how these capitals relate to each other in everyday life: the precise reasons why or the circumstances under which the various forms of capital influence career development are still unclear. Besides this, the role of positive psychological capital has been largely ignored. This leads to the following research question: How do the various forms of capital of popular music artists influence the decision-making process of intermediaries in selecting new artists in the Netherlands? Subsequently, this research is a qualitative study in which the process of selection, the decision-making process of industry professionals, has been explored. In-depth, semi-structured interviews with intermediaries active inside the popular music sector in the Netherlands, including booking agencies, artist managers, and record labels, have been conducted to formulate an answer to the research question. To get in touch with these intermediaries, the ‘snowballing’ method has been used to get in contact with these informants who possess specific and relevant information on selection systems within the music industry. The recorded interviews have been transcribed and then a thematic content analysis has been conducted following the central themes – the various forms of capital – through coding and categorisation of the excerpts according to the various themes. When coming across, evaluating and eventually selecting new artists by industry professionals, cultural capital, social capital, and symbolic capital came out to be the most essential assets for an artist during the interviews. (Positive) psychological capital can be regarded as a plus, not as a necessity during the selection process, due to the changing nature of the corresponding states. Including this latter largely ignored capital, this research adds volume to tighten the research gap on the mobilisation and conversion of alternative capitals, the roles and functions of intermediaries in the music industry, and their effects on career development of new popular music artists in the Netherlands. Besides this, this research sheds light on the precise reasons why and the circumstances under which the various forms of capital influence the decision-making process of selecting. In this manner, this research adds volume onto qualitative systematic studies on the demand for artists.
Design of a low latency spectrum analyzer using the Goertzel Algorithm with a Network on Chip

This paper presents the design of a Low latency spectrum analyzer targeted for Systems on Chip applications to perform real time multiband control. The discrete Fourier transforms are computed with the Goertzel Algorithm which performs better than the traditional FFT in our application case. The application is mapped on a Network on Chip. The complete design includes the scheduling, the mapping and the fine tuning of the NoC, which was performed with our Matlab NoC Simulation environment. The Goertzel algorithm dataflow makes it possible to use a broadcast type routing algorithm to reduce the traffic in the NoC. The results present the details of the design and reveal the parameters that can be adjusted to fine tune the Performance/Consumption tradeoff of the application.