Miracle-dz/UniFAR-FTUs huggingface dataset:
Global absolute quantification reveals tight regulation of protein expression in single Xenopus eggs

While recent developments in genomic sequencing technology have enabled comprehensive transcriptome analyses of single cells, single cell proteomics has thus far been restricted to targeted studies. Here, we perform global absolute protein quantification of fertilized Xenopus laevis eggs using mass spectrometry-based proteomics, quantifying over 5800 proteins in the largest single cell proteome characterized to date. Absolute protein amounts in single eggs are highly consistent, thus indicating a tight regulation of global protein abundance. Protein copy numbers in single eggs range from tens of thousands to ten trillion copies per cell. Comparison between the single-cell proteome and transcriptome reveal poor expression correlation. Finally, we identify 439 proteins that significantly change in abundance during early embryogenesis. Downregulated proteins include ribosomal proteins and upregulated proteins include basal transcription factors, among others. Many of these proteins do not show regulation at the transcript level. Altogether, our data reveal that the transcriptome is a poor indicator of the proteome and that protein levels are tightly controlled in X. laevis eggs.
Interval-valued fuzzy cognitive maps for supporting business decisions

Fuzzy cognitive maps (FCMs) are used to model uncertainty in complex causal relationships among concepts. This is an important issue for supporting business decisions. However, determining the precise values of these relationships is difficult in the domain of business decision-making. To overcome this problem, we introduce interval-valued FCMs representing a generalization of FCMs. Interval-valued FCMs provide desirable additional freedom in the design of concepts and their causal relationships. This feature enables decision makers to model highly complex business decision-making problems. We demonstrate this for two case studies: (1) a supplier-selection task, and (2) business-performance modelling.
Non-destructive determination of thickness of the dielectric layers using EDX

In this work a non-destructive method for measuring the thickness of the dielectric layers consisting of silicon dioxide and silicon nitride has been developed using a scanning electron microscope (SEM) equipped with energy dispersive X-ray spectrometer (EDS). Rising in accelerating voltage of electron beam leads to increasing in the depth of generation of the characteristic X-ray. If the ratio of the signal intensity of one of the substrate’s elements to the noise equal to 3 suggests that the generation’s depth of the characteristic X-ray coincides with the thickness of the overlying film. Dependence of the overlying film's thickness on the accelerating voltage can be plotted. Validation of the results was carried out by using the equation of Anderson-Hassler. The generation’s volume of the characteristic X-Ray was simulated by CASINO program. The simulations results are in good agreement with experimental results for small thicknesses.
An optimal filter for the detection of galaxy clusters through weak lensing

We construct a linear filter optimised for detecting dark-matter halos in weak-lensing data. The filter assumes a mean radial profile of the halo hear pattern and modifies that shape by the noise power spectrum. Aiming at separating dark-matter halos from spurious peaks caused by large-scale structure lensing, we model the noise as being composed of weak lensing by large-scale structures and Poisson noise from random galaxy positions and intrinsic ellipticities. Optimal filtering against the noise requires the optimal filter scale to be smaller than typical halo sies. Although a perfect separation of halos from spurious large-scale structure peaks is strictly impossible, we use numerical simulations to demonstrate that our filter produces substantially more sensitive, reliable and stable results than the conventionally used aperture-mass statistic.
Computational Tools for Interpreting Ion Channel pH-Dependence

Activity in many biological systems is mediated by pH, involving proton titratable groups with pKas in the relevant pH range. Experimental analysis of pH-dependence in proteins focusses on particular sidechains, often with mutagenesis of histidine, due to its pKa near to neutral pH. The key question for algorithms that predict pKas is whether they are sufficiently accurate to effectively narrow the search for molecular determinants of pH-dependence. Through analysis of inwardly rectifying potassium (Kir) channels and acid-sensing ion channels (ASICs), mutational effects on pH-dependence are probed, distinguishing between groups described as pH-coupled or pH-sensor. Whereas mutation can lead to a shift in transition pH between open and closed forms for either type of group, only for pH-sensor groups does mutation modulate the amplitude of the transition. It is shown that a hybrid Finite Difference Poisson-Boltzmann (FDPB) – Debye-Hückel continuum electrostatic model can filter mutation candidates, providing enrichment for key pH-coupled and pH-sensor residues in both ASICs and Kir channels, in comparison with application of FDPB alone.
The financial cost of hamstring strain injuries in the Australian Football League

Background Hamstring strain injuries (HSIs) have remained the most prevalent injury in the Australian Football League (AFL) over the past 21 regular seasons. The effect of HSIs in sports is often expressed as regular season games missed due to injury. However, the financial cost of athletes missing games due to injury has not been investigated. The aim of this report is to estimate the financial cost of games missed due to HSIs in the AFL. Method Data were collected using publicly available information from the AFL's injury report and the official AFL annual report for the past 10 competitive AFL seasons. Average athlete salary and injury epidemiology data were used to determine the average yearly financial cost of HSIs for AFL clubs and the average financial cost of a single HSI over this time period. Results Across the observed period, average yearly financial cost of HSIs per club increased by 71% compared with a 43% increase in average yearly athlete salary. Over the same time period the average financial cost of a single HSI increased by 56% from $A25 603 in 2003 to $A40 021 in 2012, despite little change in the HSI rates during the period. Conclusions The observed increased financial cost of HSIs was ultimately explained by the failure of teams to decrease HSI rates, but coupled with increases in athlete salaries over the past 10 season. The information presented in this report highlights the financial cost of HSIs and other sporting injuries, raising greater awareness and the need for further funding for research into injury prevention strategies to maximise economical return for investment in athletes.
STING Report: convenient web-based application for graphic and tabular presentations of protein sequence, structure and function descriptors from the STING database

The Sting Report is a versatile web-based application for extraction and presentation of detailed information about any individual amino acid of a protein structure stored in the STING Database. The extracted information is presented as a series of GIF images and tables, containing the values of up to 125 sequence/structure/function descriptors/parameters. The GIF images are generated by the Gold STING modules. The HTML page resulting from the STING Report query can be printed and, most importantly, it can be composed and visualized on a computer platform with an elementary configuration. Using the STING Report, a user can generate a collection of customized reports for amino acids of specific interest. Such a collection comes as an ideal match for a demand for the rapid and detailed consultation and documentation of data about structure/function. The inclusion of information generated with STING Report in a research report or even a textbook, allows for the increased density of its contents. STING Report is freely accessible within the Gold STING Suite at http://www.cbi. cnptia.embrapa. br, http://www.es. embnet.org/SMS/, http://gibk26.bse. kyutech.ac. jp/SMS/ and http://trantor.bioc. columbia.edu/SMS (option: STING Report).
Computational Shape Models Characterize Shape Change of the Left Atrium in Atrial Fibrillation

Shape change of the left atrium (LA) and LA appendage in atrial fibrillation (AF) patients is hypothesized to be linked to AF pathology and to play a role in thrombogenesis; however, many aspects of shape variation in the heart are poorly understood. To date, studies of the LA shape in AF have been limited to empirical observation and summary metrics, such as volume and its likeness to a sphere. This paper describes a more comprehensive approach to the study of the LA shape through the use of computationally derived statistical shape models. We describe practical approaches that we have developed to extract shape parameters automatically from the three-dimensional MR images of the patient. From these images and our techniques, we can produce a more comprehensive description of LA geometric variability than that has been previously possible. We present the methodology and results from two examples of specific analyses using shape models: (1) we describe statistically significant group differences between the normal control and AF patient populations (n = 137) and (2) we describe characteristic shapes of the LA appendage that are associated with the risk of thrombogenesis determined by transesophageal echocardiography (n = 203).
Different respiratory phenotypes are associated with isocyanate exposure in spray painters

Associations have been observed between exposure to isocyanates, consisting mainly of oligomers, and respiratory symptoms and isocyanate specific sensitisation in spray painters. The aim of the present study was to assess associations between isocyanate exposure and more objective respiratory effect measures such as bronchial hyperresponsiveness (BHR), baseline spirometry and exhaled nitric oxide (eNO) in a subset of spray painters. Methacholine challenge and eNO measurements were performed in 229 workers. Questionnaires and blood samples were obtained. Specific immunoglobulin (Ig)E and IgG to hexamethylene di-isocyanate were assessed in serum using various assays. Personal exposure was estimated by combining personal task-based inhalatory exposure measurements and time-activity information. Workers with higher isocyanate exposure were more often hyperresponsive (prevalence ratio comparing the 75th versus 25th percentile of exposure 1.8). In addition, significant exposure-related decreased forced expiratory volume in one second (FEV1), FEV1/forced vital capacity ratio and flow–volume parameters independent of BHR were found. BHR was more prevalent among sensitised workers. This was statistically significant for only IgG-ImmunoCAP (Phadia, Uppsala, Sweden) positive workers. eNO was not associated with exposure although slightly elevated eNO levels in specific IgG positive subjects were found. The current study provides evidence that exposure to isocyanate oligomers is related to asthma with bronchial hyperresponsiveness as a hallmark, but also shows independent chronic obstructive respiratory effects resulting from isocyanate exposure.
Incidence and Prognostic Significance of Thrombocytopenia Developed During Acute Coronary Syndrome in Contemporary Clinical Practice

Background— Prior studies examining thrombocytopenia among patients with acute coronary syndromes (ACS) evaluated highly selected patients in a clinical trial setting using varying definitions of thrombocytopenia. The incidence, severity, and prognostic significance of acquired thrombocytopenia during ACS in community practice have not been well defined. Methods and Results— We examined 36 182 patients with non–ST-segment elevation ACS enrolled at 379 US hospitals participating in the Can Rapid Risk Stratification of Unstable Angina Patients Suppress Adverse Outcomes With Early Implementation of the American College of Cardiology/American Heart Association Guidelines (CRUSADE) quality improvement initiative between June 2004 and December 2006. Patients with baseline platelet counts <150×109/L were excluded. Overall, 4697 patients (13%) developed new thrombocytopenia, defined as nadir platelet count <150×109/L (referenced lower limit of normal), during their ACS hospitalization. Risks of in-hospital mortality and bleeding correlated directly with severity of thrombocytopenia; even mild thrombocytopenia (nadir 100 to 149×109/L) was associated with increased risks of mortality (adjusted odds ratio [OR], 2.01; 95% CI, 1.69 to 2.38) and bleeding (adjusted OR, 3.76; 95% CI, 3.43 to 4.12). Each 10% drop in platelet count was associated with increased mortality and bleeding risks (adjusted ORs, 1.39 [95% CI, 1.33 to 1.46] and 1.89 [95% CI, 1.83 to 1.95], respectively). A ≥50% drop in platelet count was associated with higher risk of adverse outcomes regardless of the nadir count. A novel combined definition of acquired thrombocytopenia—nadir <150×109/L or platelet count drop ≥50%—identifies a population of ACS patients at higher risk of mortality and major bleeding (adjusted ORs, 2.58 [95% CI, 2.23 to 2.98] and 4.32 [95% CI, 3.97 to 4.70], respectively). Conclusions— Thrombocytopenia, a common complication of ACS, is associated with increased mortality and bleeding risks. Even mild thrombocytopenia or a platelet count drop ≥50% in the setting of normal nadir values is clinically significant. Application of a combined definition for thrombocytopenia using both absolute and relative thresholds permits increased sensitivity for patients at high risk of adverse outcomes.
The Role of the Basal Ganglia in Beat Perception

Perception of musical rhythms is culturally universal. Despite this special status, relatively little is known about the neurobiology of rhythm perception, particularly with respect to beat processing. Findings are presented here from a series of studies that have specifically examined the neural basis of beat perception, using functional magnetic resonance imaging (fMRI) and studying patients with Parkinson's disease. fMRI data indicate that novel beat‐based sequences robustly activate the basal ganglia when compared to irregular, nonbeat sequences. Furthermore, although most healthy participants find it much easier to discriminate changes in beat‐based sequences compared to irregular sequences, Parkinson's disease patients fail to show the same degree of benefit. Taken together, these data suggest that the basal ganglia are performing a crucial function in beat processing. The results of an additional fMRI study indicate that the role of the basal ganglia is strongly linked to internal generation of the beat. Basal ganglia activity is greater when participants listen to rhythms in which internal generation of the beat is required, as opposed to rhythms with strongly externally cued beats. Functional connectivity between part of the basal ganglia (the putamen) and cortical motor areas (premotor and supplementary motor areas) is also higher during perception of beat rhythms compared to nonbeat rhythms. Increased connectivity between cortical motor and auditory areas is found in those with musical training. The findings from these converging methods strongly implicate the basal ganglia in processing a regular beat, particularly when internal generation of the beat is required.
Empirical verification of a controllable angle of a single-wheel mobile robot

The ultimate goal of a single-wheel mobile robot is to maintain balance and to navigate on its terrain autonomously. To become an autonomous vehicle, it is required to stand up and drive by itself. In this paper, a controllable balancing angle of the single-wheel mobile robot, GYROBO developed previously, is found by empirical studies. A dynamic equation of the gyroscopic effect between a gimbal and a body is verified by experimental studies. The physical relationship between the gimbal and the body system is studied. PWM(Pulse Width Modulation) characteristic of the control system, a maximum slew rate of gimbal and body, and the falling phenomenon of the robot are numerically analyzed by extensive experimental studies.
Sequence analysis Estimation of an in vivo fitness landscape experienced by HIV-1 under drug selective pressure useful for prediction of drug resistance evolution during treatment

Motivation: HIV-1 antiviral resistance is a major cause of antiviral treatment failure. The in vivo fitness landscape experienced by the virus in presence of treatment could in principle be used to determine both the susceptibility of the virus to the treatment and the genetic barrier to resistance. We propose a method to estimate this fitness landscape from cross-sectional clinical genetic sequence data of different subtypes, by reverse engineering the required selective pressure for HIV-1 sequences obtained from treatment naive patients, to evolve towards sequences obtained from treated patients. The method was evaluated for recovering 10 random fictive selective pressures in simulation experiments, and for modeling the selective pressure under treatment with the protease inhibitor nelfinavir. Results: The estimated fitness function under nelfinavir treatment considered fitness contributions of 114 mutations at 48 sites. Estimated fitness correlated significantly with the in vitro resistance phenotype in 519 matched genotype-phenotype pairs (R1⁄40.47 (0.41 0.54)) and variation in predicted evolution under nelfinavir selective pressure correlated significantly with observed in vivo evolution during nelfinavir treatment for 39 mutations (with FDR 1⁄4 0.05). Availability: The software is available on request from the authors, and data sets are available from http://jose.med.kuleuven.be/ kdforc0/nfv-fitness-data/. Contact: annemie.vandamme@uz.kuleuven.be Supplementary information: Supplementary data are available at Bioinformatics online.
Survival of parents and siblings of supercentenarians.

BACKGROUND Given previous evidence of familial predisposition for longevity, we hypothesized that siblings and parents of supercentenarians (age >or= 110 years) were predisposed to survival to very old age and that, relative to their birth cohorts, their relative survival probabilities (RSPs) are even higher than what has been observed for the siblings of centenarians. METHODS Mean age at death conditional upon survival to ages 20 and 50 and survival probabilities from ages 20 and 50 to higher ages were determined for 50 male and 56 female siblings and 54 parents of 29 supercentenarians. These estimates were contrasted with comparable estimates based on birth cohort-specific mortality experience for the United States and Sweden. RESULTS Conditional on survival to age 20 years, mean age at death of supercentenarians' siblings was approximately 81 years for men and women. Compared with respective Swedish and U.S. birth cohorts, these estimates were 17%-20% (12-14 years) higher for the brothers and 11%-14% (8-10 years) higher for the sisters. Sisters had a 2.9 times greater probability and brothers had a 4.3 times greater probability of survival from age 20 to age 90. Mothers of supercentenarians had a 5.8 times greater probability of surviving from age 50 to age 90. Fathers also experienced an increased survival probability from age 50 to age 90 of 2.7, but it failed to attain statistical significance. CONCLUSIONS The RSPs of siblings and mothers of supercentenarians revealed a substantial survival advantage and were most pronounced at the oldest ages. The RSP to age 90 for siblings of supercentenarians was approximately the same as that reported for siblings of centenarians. It is possible that greater RSPs are observed for reaching even higher ages such as 100 years, but a larger sample of supercentenarians and their siblings and parents is needed to investigate this possibility.
Modélisation, déformation et reconnaissance d'objets tridimensionnels à l'aide de maillages simplexes

Dans cette these, une representation originale d'objets tridimensionnels est introduite: les maillages simplexes. un k-maillage simplexe est un maillage ou chaque sommet est connecte a k + 1 sommets voisins. Ainsi un contour est represente par un 1-maillage simplexe et une surface tridimensionnelle par un 2-maillage simplexe. La structure d'un maillage simplexe est duale de celle des triangulations. Plusieurs proprietes topologiques et geometriques originales rendent l'utilisation des maillages simplexes particulierement bien adaptee a la representation de surfaces deformables. Nous introduisons la notion d'angle simplexe, de courbure moyenne discrete et de parametre metrique a chaque sommet du maillage. La propriete geometrique essentielle des maillages simplexes est la possibilite de representer localement la forme d'un k-maillage en un sommet a l'aide de (k + 1) quantites adimensionnees. Les maillages simplexes deformables sont alors utilises dans un systeme de modelisation d'objets tridimensionnels. En presence d'images volumiques ou de profondeur, un maillage simplexe est deforme sous l'action de forces regularisantes et de forces externes. Les maillages simplexes sont adaptatifs a plusieurs titres. D'une part, les sommets se concentrent aux endroits de fortes courbure et d'autre part, le maillage peut etre raffine ou decime en fonction de la proximite des sommets aux donnees. Enfin, l'utilisation de maillages simplexes spheriques quasi-reguliers permet la reconnaissance de forme d'objets tridimensionnels, meme en presence d'occultations. La forme d'un objet est alors representee par l'ensemble des valeurs des angles simplexes du maillage simplexe deforme, projete sur le maillage spherique originel. La forme de deux objets est comparee par l'intermediaire de leur image simplexe (simplex angle image)
A Case Report of Surgical Resections with Local and Systemic Chemotherapy for Three Recurrences of Colon Cancer Occurring Ten Years after Colectomy

A 56-year-old Japanese woman who underwent a curative resection of ascending colon cancer at 43 years of age was found to have a tumor in her lower left abdominal cavity by computed tomography at 53 years of age. The tumor in the omentum was resected and identified as an adenocarcinoma compatible with metastasis from the primary ascending colon cancer. Although the patient received adjuvant chemotherapy with tegafur uracil and calcium folinate, liver metastasis was detected 9 months after the first recurrence. A segmentectomy and hepatectomy was performed, and histopathological findings indicated metastasis from the primary colon cancer. A third recurrence was detected in the right abdominal cavity 7 months after the second surgery. The patient received 5 cycles of combination chemotherapy consisting of folinic acid, fluorouracil and irinotecan before the third operation. The metastatic tumor resection together with intraperitoneal chemotherapy was performed, and histopathological findings indicated metastasis from the primary colon cancer. After the third surgery, the patient received adjuvant chemotherapy consisting of 5 cycles of folinic acid, fluorouracil and oxaliplatin. The patient is well with no evidence of recurrence 12 months after the third recurrence. This case suggests that colon cancer can be dormant for over 10 years and that long-term follow-up is required after curative resection. Aggressive local as well as systemic chemotherapy may be required for the management of colon cancer recurrence.