Miracle-dz/UniFAR-FTUs huggingface dataset:
A PECULIAR CODON USAGE PATTERN REVEALED AFTER REMOVING THE EFFECT OF DNA METHYLATION

DNA methylation and deamination increases the C→T mutation rate in CpG dinucleotides, especially in vertebrate genomes. This has profound effect on codon usage in heavily vertebrate genomes, and may obscure the effect of other factors on codon usage bias. We have classified the sense codons into three groups: those decreased by DNA methylation (i.e., CpG-containing codons), those increased by DNA methylation (i.e., TpGand CpAcontaining codons), and those not directly affected by DNA methylation, and studied the codon usage of the last group. RRR and YYY codons are used significantly more frequently than the rest of the codons. This pattern is much stronger in vertebrate genomes than in other genomes and can be used as a content sensor in gene finding.
Soil suction and cracking from the onset to the end of desaturation: micro-scale evidence and model

A multi-scale, multi-physics sequence of processes is discussed as developing during drying of non-clayey soils. Two variables are believed to be central in drying: suction resulting from the evaporation and effective stress associated with external constraints imposed on drying shrinkage. These two variables are tracked across the scales, both in experiments and simulations. The effective stress is critical as leading eventually to soil drying-cracking. Cracking is a most unwanted development in soil undergoing dewatering. Drying cracks often arise in the apparent absence of external forces. Hence, a tensile eigen-stress pattern resulting from stiff inclusions, or tensile stress produced by reaction forces at the boundary constraints need to be contemplated to reach cracking criteria. An earlier tubular micro-scale model of porous drying medium indicates that transport of water toward evaporating surface during saturation phase induces a high suction. A critical suction value is reached at which water body boundary is penetrated in an unstable manner by air. At the meso-scale such air penetration constitutes a surface imperfection, inducing a total stress concentration near its tip, and in the presence of significant pore suction, a rapid increase in local tensile effective stress and crack propagation. Recent experimental results from a configuration of a cluster of grains provide geometrical data suggesting that an imperfection resulting from of air entry penetrates deep into the granular medium over 4 - 8 radii of the typical pore. Further evolution entails separation of grain clusters by funicular bridge instabilities, and in the last stage formation of two-grain pendular capillary bridges. The final phase is associated with a gradual decrease of the micro-scale suction within these elementary bridges, which eventually evolve into a positive pressure before the bridge rupture.
Metronomic Chemotherapy: A Systematic Review of the Literature and Clinical Experience

Metronomic chemotherapy, continuous and dose-dense administration of chemotherapeutic drugs with lowered doses, is being evaluated for substituting, augmenting, or appending conventional maximum tolerated dose regimens, with preclinical and clinical studies for the past few decades. To date, the principle mechanisms of its action include impeding tumoral angiogenesis and modulation of hosts' immune system, affecting directly tumor cells, their progenitors, and neighboring stromal cells. Its better toxicity profile, lower cost, and easier use are main advantages over conventional therapies. The evidence of metronomic chemotherapy for personalized medicine is growing, starting with unfit elderly patients and also for palliative treatment. The literature reviewed in this article mainly demonstrates that metronomic chemotherapy is advantageous for selected patients and for certain types of malignancies, which make it a promising therapeutic approach for filling in the gaps. More clinical studies are needed to establish a solidified role for metronomic chemotherapy with other treatment models in modern cancer management.
Chemical Bond-Based Representation of Materials

This paper introduces a new representation method that is mainly based on chemical bonds among atoms in materials. Each chemical bond and its surrounded atoms are considered as a unified unit or a local structure that is expected to reflect a part of materials' nature. First, a material is separated into local structures; and then represented as matrices, each of which is computed by using information about the corresponding chemical bond as well as orbital-field matrices of two related atoms. After that, all local structures of the material are utilized by using the statistics point of view. In the experiment, the new method was applied into a materials informatics application that aims at predicting atomization energies using QM7 data set. The results of the experiment show that the new method is more effective than two state-of-the-art representation methods in most of the cases.
Assessment of First Comer Advantages and Network Effects; the Case of Turkish GSM Market

First comer advantages and network effects are frequently stated as among the most important determinants of market structures and this is particularly relevant for network economies including telecommunications markets. Connected to this, regulatory tools such as number portability have frequently been used to reduce market imperfections resulting from these effects. Within this context, this paper aims to analyze the role of these factors in creating the current market structure of Turkish GSM sector. By examining relevant data such as development of market shares in a historical perspective and by making use of consumer surveys, it is concluded that the dominant operator has benefited from being first comer in the market and established a stable market share (power) due to network effects that are used by this firm deliberately to entrench its position especially in the form of switching costs, scale economies, brand image and tariff (on-net vs. off-net pricing) differentiation; however, it is also observed that introduction of number portability lead to reduction in switching costs, increasing market competition.
Market Power and Innovation in the Intangible Economy

This paper offers a unified explanation for the slowdown of productivity growth, the decline in business dynamism, and the rise of market power. Using a quantitative framework, I show that the rise of intangible inputs, such as software, can explain these trends. Intangibles reduce marginal costs and raise fixed costs, which gives firms with high-intangible adoption a competitive advantage, in turn deterring other firms from entering. I structurally estimate the model on French and US micro data. After initially boosting productivity, the rise of intangibles causes a decline in productivity growth, consistent with the empirical trends observed since the mid-1990s. (JEL D22, D24, E23, L11, O31, O47)
DeepSignals: Predicting Intent of Drivers Through Visual Signals

Detecting the intention of drivers is an essential task in self-driving, necessary to anticipate sudden events like lane changes and stops. Turn signals and emergency flashers communicate such intentions, providing seconds of potentially critical reaction time. In this paper, we propose to detect these signals in video sequences by using a deep neural network that reasons about both spatial and temporal information. Our experiments on more than a million frames show high per-frame accuracy in very challenging scenarios.
The Hsp 70 homolog Ssb and the 14-3-3 protein Bmh 1 jointly regulate transcription of glucose repressed genes in Saccharomyces cerevisiae

Chaperones of the Hsp70 family interact with a multitude of newly synthesized polypeptides and prevent their aggregation. Saccharomyces cerevisiae cells lacking the Hsp70 homolog Ssb suffer from pleiotropic defects, among others a defect in glucose-repression. The highly conserved heterotrimeric kinase SNF1/AMPK (AMP-activated protein kinase) is required for the release from glucoserepression in yeast and is a key regulator of energy balance also in mammalian cells. When glucose is available the phosphatase Glc7 keeps SNF1 in its inactive, dephosphorylated state. Dephosphorylation depends on Reg1, which mediates targeting of Glc7 to its substrate SNF1. Here we show that the defect in glucose-repression in the absence of Ssb is due to the ability of the chaperone to bridge between the SNF1 and Glc7 complexes. Ssb performs this post-translational function in concert with the 14-33 protein Bmh, to which Ssb binds via its very Cterminus. Raising the intracellular concentration of Ssb or Bmh enabled Glc7 to dephosphorylate SNF1 even in the absence of Reg1. By that Ssb and Bmh efficiently suppressed transcriptional deregulation of reg1 cells. The findings reveal that Ssb and Bmh comprise a new chaperone module, which is involved in the fine tuning of a phosphorylation-dependent switch between respiration and fermentation.
Transfer printing of semiconductor nanowire lasers

The authors review their work on the accurate positioning of semiconductor nanowire (NW) lasers by means of nanoscale Transfer Printing (nano-TP). Using this hybrid nanofabrication technique, indium phosphide NWs are successfully integrated at selected locations onto heterogeneous surfaces with high positioning accuracy. Moreover, they show that NW lasers can also be organised to form bespoke spatial patterns, including (one-dimensional) 1D or 2D arrays, or complex configurations with a defined number of NWs and controlled separation between them. Besides, their nano-TP technique also permits the integration of NWs with different dimensions in a single system. Notably, the nano-TP fabrication protocols do not affect the optical or structural properties of the NWs and they retain their room-temperature lasing emission after their positioning onto all investigated receiving surfaces. This developed nano-TP technique offers therefore new exciting prospects for the fabrication of hybrid bespoke nanophotonic systems using NW lasers as building blocks.
Likelihood Ratio-based Forensic Voice Comparison with the Cantonese Triphthong / iau /

This paper describes a likelihood ratio-based forensic voice comparison using the Cantonese triphthong /iau/. The features for comparison are both the formant pattern and tonal F0 of /iau/ contained in 15 native speakers’ non-contemporaneous natural speech. Kernel density multivariate likelihood ratios are calculated based on polynomial coefficients converted from raw frequency values of F1, F2, F3 and F0. A loglikelihood-ratio cost (Cllr) value for the F-pattern of 0.6 is obtained, showing that comparisons with /iau/ F-pattern have reasonable validity, and also reasonable strength of evidence can be achieved. Likelihood ratios calculated based on tonal F0 do not show good performance (Cllr=0.95), and are therefore not fused with the F-pattern LRs.
Control of Movement Automatic and intentional influences on saccade landing X

Aagten-Murphy D, Bays PM. Automatic and intentional influences on saccade landing. J Neurophysiol 118: 1105–1122, 2017. First published May 24, 2017; doi:10.1152/jn.00141. 2017. —Saccadic eye movements enable us to rapidly direct our high-resolution fovea onto relevant parts of the visual world. However, while we can intentionally select a location as a saccade target, the wider visual scene also influences our executed movements. In the presence of multiple objects, eye movements may be “captured” to the location of a distractor object, or be biased toward the intermediate position between objects (the “global effect”). Here we examined how the relative strengths of the global effect and visual object capture changed with saccade latency, the separation between visual items and stimulus contrast. Importantly, while many previous studies have omitted giving observers explicit instructions, we instructed participants to either saccade to a specified target object or to the midpoint between two stimuli. This allowed us to examine how their explicit movement goal influenced the likelihood that their saccades terminated at either the target, distractor, or intermediate locations. Using a probabilistic mixture model, we found evidence that both visual object capture and the global effect co-occurred at short latencies and declined as latency increased. As object separation increased, capture came to dominate the landing positions of fast saccades, with reduced global effect. Using the mixture model fits, we dissociated the proportion of unavoidably captured saccades to each location from those intentionally directed to the task goal. From this we could extract the time course of competition between automatic capture and intentional targeting. We show that task instructions substantially altered the distribution of saccade landing points, even at the shortest latencies.
Characterization of the double stranded DNA stain SYTOX orange

Disclaimer This document contains a student thesis (bachelor's or master's), as authored by a student at Eindhoven University of Technology. Student theses are made available in the TU/e repository upon obtaining the required degree. The grade received is not published on the document as presented in the repository. The required complexity or quality of research of student theses may vary by program, and the required minimum study period may vary in duration.
PURIFICATION OF YEAST GLUCOSE TOLERANCE FACTOR AND ITS EFFECT ON INTRACORPORAL GLUCOSE CONVERSION IN PHYSICAL ACTIVITY

Article history: Received: 2 February 2016 Accepted in revised form: 18 March 2016 ABSTRACT Objective: this paper was aimed to study the separation and purification of yeast glucose tolerance factor (GTF) and its effect on intracorporal glucose conversion of body builders. Methods: Yeast high-yield GTF was adopted in order to improve the detection sensitivity of chromium; in separation and purification process, the method high performance liquid chromatographyinductively coupled plasmamass spectrometry/ atomic emission spectrometry (HPLC-ICPMS/AES) was applied in microanalysis of the distribution of GTF; according to the analysis results, appropriate separation technique was selected for batch separation and purification; by comparing the blood indexes of fed mice, intracorporal glucose conversion of body builders could be deduced. Results: Chromium/ protein ratio of Peak 1 was much lower than that of Peak 2; Peak1 was micromolecular chromium-binding protein, while Peak 2 was micromolecular chromium-binding protein. N-terminal amino acid sequence analysis results of peak PP1 showed that amino acids in peak PP1 were probably connected with chromium by coordination bonds instead of peptide bonds. In addition, triglyceride and cholesterol level in blood decreased. Conclusion: Chromium-enriched yeast has an improvement effect on diabetes to some degree.
H 2 S and NH 3 Detection with Langmuir-Schaefer Monolayer Organic Field-Effect Transistors †

In this work gas sensing properties of Langmuir-Schaefer monolayer organic field-effect transistors (LS OFETs) prepared from organosilicon derivative of [1]benzothieno[3,2-b][1]benzothiophene (BTBT) have been investigated. The monolayer has been deposited using Langmuir-Schaefer method, which results in a uniform low-defect monolayer with excellent electrical performance, hole mobility up to 7 × 10−2 cm2 V−1 s−1, the threshold voltage around 0 V and on-off ratio of 104. Developed sensors demonstrate a long-term stability of a half-year storage under ambient conditions. Preliminary investigations demonstrated that the LS OFETs give instantaneous response on ammonia and hydrogen sulfide at low concentrations. The results reported open new perspectives for the OFET-based gas-sensing technology.
Maryna Charnyshova. Masters Thesis. Development Studies with Psychology Major

My primary objective in this study was to investiga e the impact of the upbringing environment on the development of children’s effort ul control and achievement motivation. Twenty-five SOS Children’s Villageand 33 family-r aised children reported on achievement motivation, whereas SOS Village and family mothers as essed children’s effortful control along with emotion regulation as an additional vari able. Consistent with predictions, SOS Village children were characterized by lower levels of emotion regulation than children from conventional families. The data on SOS Village chil dren’s lower levels of effortful control were marginally significant. As opposed to the expe ctations, SOS Village children had higher achievement motivation than their family-reared cou nterparts. Moreover, relations existed between effortful control and some of the achieveme nt motivation components, namely, effortful control was positively related to hope of success and negatively related to active fear of failure. A number of associations were also foun d between achievement motivation components and emotion regulation. Finally, there w as an interaction between children’s upbringing environment and effortful control such t hat there was a significant difference in the effect of a rearing condition on achievement mo ivation of children with different levels of effortful control. Implications include a focus on developing self-regulation abilities of institutionally-reared children when designing inte rventions to improve their behavior.
Kalman Filtering of Earth Orientation Changes

The orientation of the earth in space changes unpredictably in a rapid and irregular manner, in addition to the uniform rotation of the earth. Observations of extra-terrestrial objects from the surface of the earth are affected by these variations, and knowledge of these changes is required for a variety of geodetic and astrometric purposes as well as being of interest in its own right. The orientation of the earth (specified by a three dimensional rotation vector) is measured by a variety of techniques; combination of these data sets is complicated by irregular changes in the spacing and accuracy of the various time series, and also by the existence of lower dimensional measurements of different linear combinations of the rotation vector components. A Kaiman filter has been developed at JPL to smooth and predict earth orientation changes for application to spacecraft navigation by the NASA Deep Space Network. The filter, which provides estimates of the earth orientation changes (and of the excitation of these changes) based on whatever measurements are available, has been used for a number of research applications, both in the reduction of geodetic and astrometric data, and in research into the geophysical causes of earth orientation changes. The JPL Kaiman filter uses stochastic models to account statistically for otherwise unpredictable changes in earth orientation; these models make it possible to provide reasonable estimates of the error in the smoothed time series, and to automatically vary the amount of smoothing according to the accuracy and density of the data. The derivation of the stochastic models used by the filter, the implementation of the models into the filter, a statistical description of what the filter does, and the results of filtering specific data sets will be discussed.
Envorinmental Exposure Assessment in Premature Thelarche Cases in the Well-Child Outpatient Poliklinic.

Sekiz yasindan kucuk kiz cocuklarinda cinsel olgunlasma belirtisi olmadan meme gelisimi, neredeyse evrensel olarak prematur telars (PT) olarak kabul edilir. Prevelans ve etiyoloji acikca bilinmemektedir. Calismamizda, unilateral veya bilateral PT olan kiz cocuklarini izlemini yapmak ve bakim urunlerini kullanmayi biraktiklarindaki gerilemeyi gostermeyi amacladik. Calisma retrospektif planlandi. Eylul 2016 ile Şubat 2017 tarihleri arasinda izlemde olan prematur telars tanisi almis cocuklar ve ebeveynleri calismaya dahil edildi. Saglam cocuk izleminde olan pubik veya aksiller killanma, vajinal kanama veya diger cinsel olgunlasma bulgusu ile iliskisi olmayan unilateral veya bilateral meme gelisimi olan tum cocuklarin tek semptomu vardi. Organik bir neden saptanmayan bu cocuklarda, bakim urunleri kesildikten sonra izleme alindi. 28 kiz cocugu degerlendirildi ve ortalama yas 2,3 (± 0,3) yil idi. Cocuklarin kronik hastaligi yoktu. Tum vakalar Tanner evre 2 olarak tanimlandi ve erken meme gelisimi nedeniyle takibe alindi. 18 (%64,2) kiz cocugun unilateral meme gelisimi vardi. Bakim urunleri kullanmayi kestikten sonra, unilateral ve bilateral meme gelisimi olan cocuklarda 6 ay icinde gerileme oldu. Gunumuzde, PT ve Puberte prekoks veya erken meme gelisimi riskini gosteren herhangi bir ongorucu test yoktur. Cocuklarin, bakim urun kullanimi nedeniyle bircok teste maruz kalabilir. Klinisyenler bu turlu urunler yonunden dikkatli olmalidirlar. Aileler cocuklari icin bakim urunlerinin kullanim miktarini asgari duzeyde tutabilirler.
SFB 649 Discussion Paper 2008-001 Testing Monotonicity of Pricing Kernels

The behaviour of market agents has always been extensively covered in the literature. Risk averse behaviour, described by von Neumann and Morgenstern (1944) via a concave utility function, is considered to be a cornerstone of classical economics. Agents prefer a fixed profit over uncertain choice with the same expected value, however lately there has been a lot of discussion about the reliability of this approach. Some authors have shown that there is a reference point where market utility functions are convex. In this paper we have constructed a test to verify uncertainty about the concavity of agents’ utility function by testing the monotonicity of empirical pricing kernels (EPKs). A monotone decreasing EPK corresponds to a concave utility function while non-monotone decreasing EPK means non-averse pattern on one or more intervals of the utility function. We investigated the EPK for German DAX data for years 2000, 2002 and 2004 and found the evidence of non-concave utility functions: H0 hypothesis of monotone decreasing pricing kernel was rejected at 5% and 10% significance level in 2002 and at 10% significance level in 2000. JEL classification codes: G12, C12
Impact of phosphate solubilizer fertilizer on phosphorus availability and potato yield in Andisols of Indonesia

Andisols are soil types formed in volcanic ash characterised by high adsorbed phosphate unavailable to plants. Farmers use manures to increase the availability of phosphorus in Andisols although this seems less than effective. The purpose of the research was to formulate a phosphate solubilizer fertilizer (PSF) to increase P solubility and enhance Andisols potato yields. PSF was made from chicken manure enriched with phosphate bacteria, Humic-fulvic (HF) acids and N-Acyl Homoserine Lactone. PSF effectiveness was tested in Pikovskaya and in Andisols to increase P solubility and enhance potato yield. The best of PSF formula based on P solubility was for chicken manure enriched with 4% HF acids and at 2% dose. The PSF P solubility efficiency in Pikovskaya was 51% and 80% in Andisols. Andisols potato yield at the same dose of PSF 20 Mg·ha‒1 compared to chicken manure enhanced with the some dose by up to 2 Mg·ha‒1.
The second variation of nonorientable minimal submanifolds

Suppose M is a complete nonorientable minimal submanifold of a Riemannian manifold N. We derive a second variation formula for the area of M with respect to certain perturbations, giving a sufficient condition for the instability of M. Some simple applications are given: we show that the totally geodesic IRip2 is the only stable surface in IRiP3, and we show the non-existence of stable nonorientable cones in R . We reproduce and marginally extend some known results in the truly non-compact setting.