Miracle-dz/UniFAR-FTUs huggingface dataset:
Computergestützte Strukturbestimmung biochemischer Komplexe durch einen Fuzzy Logic-basierten Algorithmus

Die spezifische Erkennung zweier Molekule und die anschliesende Ausbildung eines Komplexes spielen eine Schlusselrolle in vielen biochemischen Prozessen. Die mathematische Behandlung der molekularen Erkennung in biochemischen Komplexen kann deswegen einen grosen Beitrag in Untersuchungen der katalytischen Wirkung von Enzymen und der Entwicklung neuer Wirkstoffe (de novo-Design) liefern. Daher wurde in der Literatur eine Vielzahl von Algorithmen zur Bestimmung der Rezeptor-Ligand-Wechselwirkungen (Docking-Algorithmen) vorgestellt. Viele dieser Algorithmen setzen voraus, das die Bindungsstelle des Rezeptors, das aktive Zentrum, bekannt ist. Die Liganden werden bei diesen Ansatzen dann moglichst optimal in dieses aktive Zentrum eingepast. Ist das aktive Zentrum jedoch nicht bekannt, sind diese Algorithmen wegen der grosen Anzahl zu berucksichtigenden Freiheitsgrade sehr rechenzeitaufwendig. In der hier vorgestellten Arbeit wird deswegen ein Docking-Algorithmus entwickelt, der ausgehend von den dreidimensionalen Strukturdaten biochemischer Komplexpartner das aktive Zentrum eines Rezeptors identifiziert und Vorschlage fur mogliche Bindungsmodi eines Liganden in diesem aktive Zentrum macht. Dazu wird versucht, die menschliche Fahigkeit der Formerkennung und Problemoptimierung in mathematischen Algorithmen abzubilden. Die Grundlage dazu bildet die von Zadeh vorgestellte Fuzzy Set Theory, die eine Beschreibung verbaler Begriffe in mathematisch zuganglicher Form, den linguistischen Variablen, ermoglicht. Der Algorithmus beruht auf dem Modell einer molekularen Oberflache. Jeder Punkt dieser Oberflache wird durch die topographischen Eigenschaften, das elektrostatische Potential, die Lipophilie und die Fahigkeit, Wasserstoffbruckenbindungen auszubilden, charakterisiert. Anhand dieser Eigenschaften konnen die Oberflachen mit Hilfe der Fuzzy Set Theory miteinander verglichen werden und so komplementare Oberflachenbereiche identifiziert werden. Diese werden dann mit dem Geometric Hashing-Algorithmus von Schwartz und Sharir aufeinander projiziert und somit mogliche Komplexstrukturen bestimmt. Der Algorithmus wurde an 35 biochemischen Komplexen aus der Protein Data Bank getestet. Fur alle diese Komplexe konnte eine Komplexstruktur ermittelt werden, die nach einer Energieoptimierung mit einer einfachen Zielfunktion nur einen rms-Abstand (root mean squares deviation) von maximal 2.5 A zur kristallographischen Struktur aufweist.
Assessment of Acute Cardiac Function via Post-Resuscitation Triple-Rule-Out Computed Tomography

Background: In patients with return of spontaneous circulation (ROSC) after resuscitation, the current gold standard for assessing acute cardiac function is cardiac echocardiography. However, its use may be limited in acute critically ill patients by delays, interobserver discrepancies or the varying priorities of radiographic examinations. We now report that standardised acute cardiac function in these patients can be assessed with triple rule out thoracic (TRO) computed tomography. Methods and patients: We retrospectively analysed cardiac function in all patients with ROSC after resuscitation and who underwent acute computed tomography between 01/2013 and 01/2015 with a new post processing software client after TRO- computed tomography angiography (n=15). The syngo-CT-cardiac-function-client (syngo.via VA 20, Siemens, Erlangen, Germany) was used to measure ejection fraction, myocardial mass, stroke volume, end systolic and end-diastolic volumes, as well as coronary morphology. Multivariate regression modelling and ROC analysis were used to control the independent associations between these parameters. Results: ROC curve analysis showed that right cardiac end systolic volume and left cardiac end systolic volume were associated with ROSC (AUC: 0.74 and AUC: 0.74, respectively). In these patients, we defined thresholds for right cardiac end systolic volume of 119 ml and for left cardiac end systolic volume of 48 ml. Conclusion: In combination with TRO computed tomography, the syngo-CT-cardiac-function-client provides a valuable, standardised tool to assess acute cardiac function in patients with ROSC after resuscitation.
Subconscious man: The basal ganglia as a target for intervention in emotional disorders

Why the Subconscious? Why is it that when I am driving my car in the Paris traffic jams I manage not to hit other cars or run down my fellow citizens? Although I am thinking of other things, I am able to turn the steering wheel as I should, brake in time, and declutch efficiently. My ability to do this is surprising, given that I am unaware of what I am doing. I am not paying attention to the task. It seems as if these actions happen all by themselves, automatically, with a sort of autonomous intelligence, which means that I adapt perfectly to my environment. There is nothing special about these movements except that they are learned, or even overlearned. In this sort of situation, which we could label as I do not think I am doing something, perceiving, or thinking, but I do, I perceive, and I think automatically, I do things subconsciously. However, I can modify this behavior at will. All I have to do is make the decision. My thoughts can be interrupted to imagine a novel situation or to adapt to a changing environment. This time, I do not think I am doing something, but I do it nonautomatically. This is what we might call preconsciousness. Whether or not my behavior is automatic, I can now think about what I am doing. I can say to myself, “Hey, I am driving without thinking about it. ” In this case I can reflect on what I am doing; I think I am doing something (or I have a feeling or I am thinking, even that I exist). We are in the realm of consciousness. But what is the basis of these mental abilities, which are vital to our existence? Our brains continuously receive a vast amount of information over both time and space. Some of this information is stored in the brain: a rapid short-term storage when I am conscious, a long-term process in a preconscious state, and a permanent storage in the state of subconsciousness. The subconscious is therefore in a position to sort through the mass of information we continuously receive, working as a sort of autopilot—but a living autopilot. This subconscious behavior is obviously more limited in lower vertebrates such as reptiles and birds, but is nevertheless sufficient to ensure their survival. In humans, an understanding of subconscious behaviors is particularly informative, because despite their complexity, they are expressed as observable motor behavior. But this motor behavior is the reflection of our intellect and emotion. Because these behaviors are natural and irrepressible, it is difficult or even impossible to hide them, meaning that they are an excellent reflection of personality. Thus, every doctor knows that the best way of examining a patient is to observe the way he walks, look at his gestures, the way he speaks (expression of speech processed by buccolingual and laryngeal motor function), and especially facial expressions. Much can be read from someone’s face, even untruths. Why? Because subconscious behavior is a faithful reflection of what is happening in the brain.
ASSISTED REPRODUCTION TECHNOLOGIES Differences in pregnancy outcomes in donor egg frozen embryo transfer ( FET ) cycles following preimplantation genetic screening ( PGS ) : a single center retrospective study

Purpose This study aims to test the hypothesis, in a singlecenter retrospective analysis, that live birth rates are significantly different when utilizing preimplantation genetic screening (PGS) compared to not utilizing PGS in frozen–thawed embryo transfers in our patients that use eggs from young, anonymous donors. The question therefore arises of whether PGS is an appropriate intervention for donor egg cycles. Methods Live birth rates per cycle and live birth rates per embryo transferred after 398 frozen embryo transfer (FET) cycles were examined frompatientswho elected to have PGS compared to those who did not. Blastocysts derived from donor eggs underwent trophectoderm biopsy and were tested for aneuploidy using array comparative genomic hybridization (aCGH) or nextgeneration sequencing (NGS), then vitrified for future use (test) or were vitrified untested (control). Embryos were subsequently warmed and transferred into a recipient or gestational carrier uterus. Data was analyzed separately for single embryo transfer (SET), double embryo transfer (DET), and for own recipient uterus and gestational carrier (GC) uterus recipients. Results Rates of implantation of embryos leading to a live birth were significantly higher in the PGS groups transferring two embryos (DET) compared to the no PGS group (GC, 72 vs. 56%; own uterus, 60 vs. 36%). The live birth implantation rate in the own uterus group for SET was higher in the PGS group compared to the control (58 vs. 36 %), and this almost reached significance but the live birth implantation rate for the SETGC group remained the same for both tested and untested embryos. Live births per cycle were nominally higher in the PGSGCDETand own uterus SETand DET groups compared to the non-PGS embryo transfers. These differences almost reached significance. The live birth rate per cycle in the SET GC group was almost identical. Conclusions Significant differences were noted only for DET; however, benefits need to be balanced against risks associated with multiple pregnancies. Results observed for SET need to be confirmed on larger series and with randomized cohorts.
Identification for wiener system with discontinuous piece-wise linear function via sparse optimization

This paper presents a new approach to the identification of Wiener system consisted of an ARX subsystem followed by a static discontinuous piece-wise linear subsystem. We show this problem can be transformed into an ℓ<sub>0</sub>-norm optimization problem, which is intractable(NP hard). To overcome this difficulty, we consider ℓ<sub>1</sub>-norm convex relaxation inspired by compressed sensing. In the noise-free case, sufficient conditions are provided for recovering unknown parameters via ℓ<sub>0</sub>-norm and ℓ<sub>1</sub>-norm minimization programs. Numerical experiments demonstrate our novel algorithms perform well in noisy measurements case.
Assessment of antifungal activity of six popular toothpastes against clinical isolates of Candida albicans

Introduction The oral cavity is a habitat for a large number of microorganisms which coexist with one another as normal microbiota. Candida species are ovoid budding yeast like fungi. The organism is a normal commensal of humans found on skin and throughout gastrointestinal tract. Poor oral hygiene, high carbohydrate diet, nutritional deficiencies, diabetes mellitus, dental prostheses, heavy cigarette smoking, immunosuppression and HIV infection are associated with increased incidence of oral thrush. Oral candidiasis may present as oral thrush, acute atrophic candidiasis, chronic atrophic candidiasis/denture sore mouth, angular cheilitis and Candida leukoplakia. Different toothpaste brands have their own composition and concentration of ingredients. Many toothpastes claim to have antimicrobial properties. More research is needed to evaluate these claims. Objectives The study aims to determine the antifungal activity of six different toothpastes commonly used in the locality. Materials & Methods Six brands of toothpastes were selected to determine the antifungal activity against 10 clinical isolates of Candida albicans by standard agar well diffusion method. Antifungal activity of toothpastes was determined in both undiluted and diluted forms on antimycotic sensitivity media by measuring the zone of inhibition. Results All toothpastes showed antifungal activity in undiluted forms. Brand-1 and brand-3 showed antifungal activity even in diluted solutions. Conclusion All six toothpastes have antifungal activity in undiluted forms, but brand-1 & 3 have activity in diluted forms also. There is a need to create a standardized method to evaluate antifungal activity of different brands of toothpastes.
Opsonization Modulates Rac-1 Activation during Cell Entry by Leishmania amazonensis

ABSTRACT Lesions caused by Leishmania amazonensis normally heal, but relapses occur due to parasite persistence in host tissues. It has been proposed that infection of fibroblasts plays an important role in this process by providing the parasites with a safe haven in which to replicate. However, most previous studies have focused on the entry of Leishmania into macrophages, a process mediated by serum opsonins. To gain insight into a possible role of nonopsonic entry in the intracellular persistence of amastigotes, we examined the invasion of Chinese hamster ovary (CHO) cells. Amastigotes entered CHO cells by a cytochalasin D, genistein, wortmannin, and 2,3-butanedione monoxime-sensitive pathway and replicated within phagolysosomes. However, unlike most phagocytic processes described to date, amastigote internalization in CHO cells involved activation of the GTPases Rho and Cdc42 but not Rac-1. When uptake was mediated by fibronectin or when amastigotes were opsonized with immunoglobulin G and internalized by Fc receptor-expressing CHO cells, Rac-1 activation was restored and found to be required for parasite internalization. Given the essential role of Rac in assembly of the respiratory burst oxidase, invasion through this nonopsonic, Rac-1-independent pathway may play a central role in the intracellular survival of Leishmania in immune hosts.
Why Do We Like the iPhone? The Role of Evaluative Conditioning in Attitude Formation

Evaluative conditioning (EC) is the change in liking due to the paring of an affectively meaningful and a neutral stimulus. Starting with the exemplary question of why we like the iPhone, this article provides an overview of past and present research and gives an outlook to future research on this topic. We outline four different theoretical EC accounts and discuss how each account is consistent with current empirical evidence.
Segmentation de surfaces représentées par des nuages de points non organisés

L'objectif de la reconstruction tridimensionnelle des surfaces consiste a produire un modele geometrique a partir d'informations discretes. Afin d'arriver a un minimum de precision en respectant la forme de l'objet, une etape de segmentation s'impose. Nous disposons initialement de nuages de points pouvant etre non structures, issus de la fusion de plusieurs vues, le but est de subdiviser ces nuages en sous ensembles homogenes au sens geometriques. Pour aborder le probleme de maniere generale, nous proposons, d'une part une methode de calcul de voisinage, qui s'adapte avec la variation de la densite des points, et d'autre part une methode iterative, basee sur l'analyse en composantes principales, pour le calcul precis des proprietes differentielles : courbures, repere de darboux et les lignes de courbures, qui sont les outils necessaire a nos approches de segmentation. Pour realiser la segmentation, nous introduisons une notion de contour flou que nous appellerons zone frontaliere. En se basant sur les proprietes intrinseques de surfaces, nous detectons les trois types de contours qui peuvent se presenter dans les images de profondeurs (aretes vives, contours d'occlusion et contours lisses). A partir de ces zones frontalieres nous presentons deux methodes de segmentation ; la premiere consiste a affiner ces zones frontalieres pour obtenir les contours filiformes, en utilisant un algorithme de cooperation entre courbures et directions qui permet le suivi en 3d. La deuxieme methode permet l'extraction des regions homogenes, en utilisant un processus de propagation d'ondes. En outre, une approche de suivi de contour exterieur a ete proposee. Tout au long de notre travail, la robustesse et la precision des resultats etaient au centre de nos preoccupations ; nous presentons une etude de complexite des algorithmes ainsi qu'une analyse des erreurs commises qui valident nos approches de segmentation.
Resonant cantilevers with nanoparticles-spaced functional graphene-oxide sheets for high-performance sensing to ppt-level explosive vapor

To high-performance detection of ultra-low concentration explosive vapor, we develop resonant microcantilever sensors by using a nano sensing material of functionalized GO/Au-NPs (gold-nanoparticles in situ grown on graphene-oxide sheet). To achieve specific-modification for fine selectivity and enlarge graphene surface-area for fast capturing the gas-molecules, surface-modified graphene-oxide sheets are stacked into porous-layered nanostructure by using Au-NPs as the nano-gap supporting pillars. Ultra-sensitive detection of TNT vapor is experimentally implemented, resulting in finer detection limit than 20 ppt and very high selectivity to ppm-level interfering gases.
Thermodynamics of the daunomycin–DNA interaction: Ionic strength dependence of the enthalpy and entropy

Fluorescence and absorbance methods were used to study the interaction of daunomycin with calf‐thymus DNA over a wide range of temperatures and NaCl concentrations. van't Hoff analysis provided estimates for the enthalpy of the binding reaction over the NaCl range of 0.05–1.0 M. Daunomycin binding is exothermic over this entire range, and the favorable binding free energy arises primarily from the large, negative enthalpy. Both the enthalpy change and entropy change are strong functions of ionic strength. Possible molecular contributions to the enthalpy and entropy are discussed, leading to the tentative conclusion that hydrogen‐bonding interactions at the interacalation site are the primary contributors to the observed thermodynamic parameters. The dependence of the enthalpy on the ionic strength is well beyond the predictions of current polyelectrolyte theory and cannot be fully accounted for. The enthalpy and entropy changes observed compensate one another to produce relatively small free‐energy changes over the range of solution conditions studied.
Insights into the Effect of Soil pH on N2O and N2 Emissions and Denitrifier Community Size and Activity

ABSTRACT The objective of this study was to investigate how changes in soil pH affect the N2O and N2 emissions, denitrification activity, and size of a denitrifier community. We established a field experiment, situated in a grassland area, which consisted of three treatments which were repeatedly amended with a KOH solution (alkaline soil), an H2SO4 solution (acidic soil), or water (natural pH soil) over 10 months. At the site, we determined field N2O and N2 emissions using the 15N gas flux method and collected soil samples for the measurement of potential denitrification activity and quantification of the size of the denitrifying community by quantitative PCR of the narG, napA, nirS, nirK, and nosZ denitrification genes. Overall, our results indicate that soil pH is of importance in determining the nature of denitrification end products. Thus, we found that the N2O/(N2O + N2) ratio increased with decreasing pH due to changes in the total denitrification activity, while no changes in N2O production were observed. Denitrification activity and N2O emissions measured under laboratory conditions were correlated with N fluxes in situ and therefore reflected treatment differences in the field. The size of the denitrifying community was uncoupled from in situ N fluxes, but potential denitrification was correlated with the count of NirS denitrifiers. Significant relationships were observed between nirS, napA, and narG gene copy numbers and the N2O/(N2O + N2) ratio, which are difficult to explain. However, this highlights the need for further studies combining analysis of denitrifier ecology and quantification of denitrification end products for a comprehensive understanding of the regulation of N fluxes by denitrification.
Modulation of Cytokine and Chemokine Secretions in Rhesus Monkey Trophoblast Co‐Culture With Decidual but not Peripheral Blood Monocyte–Derived Macrophages

Citation Rozner AE, Dambaeva SV, Drenzek JG, Durning M, Golos TG. Modulation of cytokine and chemokine secretions in rhesus monkey trophoblast co‐culture with decidual but not peripheral blood monocyte–derived macrophages. Am J Reprod Immunol 2011; 66: 115–127
Kinetics of internalization and degradation of asialo-glycoproteins in isolated rat hepatocytes.

The rate constants for internalization of surface-bound asialo-orosomucoid by hepatocytes were 0.040 min-1 at 20 degrees C, 0.18 min-1 at 30 degrees C and 0.28 min-1 at 40 degrees C. At 40 degrees C, internalization accounted for most of the increase in cell-associated radioactivity. The activation energy over the temperature range 20 to 40 degrees C was 68 +/- 7 (S.D.) kJ/mol. At 10 degrees C, most of the cell-associated asialo-orosomucoid was bound to the cell surface in a reaction which followed ordinary chemical kinetics. Pre-incubation of hepatocytes with a large concentration of unlabelled asialo-orosomucoid did not influence the uptake of subsequently added 125I-asialofetuin; neither was degradation of 125I-asialo-fetuin affected in this experiment. The fractional rate of degradation (the fraction of cell-associated asialo-fetuin which was degraded per unit time) was constant over a twelve-fold range of intracellular asialo-fetuin concentrations. Increasing the temperature from 20 to 30 degrees C produced approximately a ten-fold increase in the rate of degradation of either asialo-fetuin or asialo-orosomucoid. The average activation energies of degradation over the range 20 to 40 degrees C were 125 kJ/mol for asialo-fetuin and 149 kJ/mol for asialo-orosomucoid; however, the Arrhenius plots were not straight lines over this temperature range.
Catechol-O-methyltransferase Val158Met genotype moderates the effect of disorganized attachment on social development in young children

Abstract Children with histories of disorganized attachment exhibit diverse problems, possibly because disorganization takes at least two distinctive forms as children age: controlling–punitive and controlling–caregiving. This variation in the developmental legacy of disorganization has been attributed primarily to variations in children's rearing experiences. Here an alternative explanation of these divergent sequelae of disorganization is evaluated: one focused on genotype. Structural equation modeling was applied to data on 704 Norwegian children to test whether the catechol-O-methyltransferase Val158Met genotype moderates the effect of disorganized attachment, which was measured dimensionally at 4 years of age using the Manchester Child Attachment Story Task, on changes in aggressive behavior and social competence from ages 4 to 6. Children who scored high on disorganization and were homozygous for the valine allele displayed significantly greater increases in aggression and decreases in self-oriented social skills (e.g., self-regulation and assertiveness) over time than did their disorganized counterparts carrying the methionine allele, whereas disorganized children carrying the methionine allele increased their other-oriented social skill (e.g., cooperation and responsibility) scores more than did valine-homozygous children. These results are consistent with the controlling–punitive and controlling–caregiving behaviors observed in disorganized children, suggesting that the children's genotype contributed to variations in the social development of disorganized children.