Miracle-dz/UniFAR-FTUs huggingface dataset:
Mathematical modelling of profiled haemodialysis

In healthy individuals, the removal of fluid and toxic catabolic waste products is a continuous 24 hour process. When the kidneys fail, fluid is retained and the accumulation of some important ions, such as those of potassium and hydrogen, may become life threatening. For many patients with severe loss of kidney function dialysis is the only means of preventing excessive fluid gain and the accumulation of toxic chemicals in the blood (see, for example, [3] for an introduction to treatment of Chronic Renal Failure). Haemodialysis is the transport of water, ions and middle molecules (up to the size of albumin) across the artificial membrane separating the patient plasma volume and the dialysis machine fluid (the dialysate) using both passive diffusion and pressure-driven ultrafiltration. In contrast to healthy kidney function, haemodialysis is an intermittent treatment: patients typically dialyse for 4-6 hours, 3 times a week. During each session, 3-4 litres of fluid is removed along with catabolic end-products, and osmotically active solutes. The short duration and intermittent nature of haemodialysis means that most patients experience large and acute swings in body fluid volume, ion and solute composition not normally encountered in health. These changes can result in significant intraand interdialytic morbidity. Indeed, intradialytic morbidity is recorded in around 30% of all haemodialysis treatments. In a significant number of patients, the underlying problem is the rapid removal of water and osmotically active sodium chloride which can lead to severe hypotension or the overhydration and swelling of brain cells. While this is an age-wide problem, it is particularly prevalent in the growing population of elderly haemodialysis patients, many of whom also have impaired cardiac function. One practice aimed at reducing the incidence of volume-related interdialytic morbidity is profiled haemodialysis in which the rate of water removal and/or the dialysis machine sodium concentration are varied with time according to a predetermined profile designed to prevent the wide fluctuations in
Eubacterium callanderi Bacteremia: Report of the First Case

ABSTRACT Eubacterium callanderi is an environmental anaerobic rod-shaped bacterium first isolated in 1998 from an industrial anaerobic digester. We report on the first clinical isolate of E. callanderi, which was recovered from the blood of a patient with a bladder carcinoma. Identification of the organism was made by cell fatty acid chromatographic analysis and 16S rRNA gene sequencing.
Isometric scaling of maxillary sinus volume in hominoids.

Previous hypotheses of maxillary sinus size evolution have proposed one or more changes in the volume of the structure across hominoid phylogeny. These hypotheses have been used subsequently to support the phylogenetic placement of fossil taxa relative to the living Hominoidea. The null hypothesis, that no change in sinus volume independent of size has occurred in ape evolution, is evaluated here by scaling analysis. Mixed sex samples of adult dry crania for the extant ape genera were examined by computer tomography imaging and the volume of the maxillary sinus was obtained. Sinus volume was then regressed, using both least squares and reduced major axis models, against cranial size variables. The results clearly demonstrate that the null hypothesis of no change in relative sinus volume cannot be rejected; thus, there is no support for hypotheses that maxillary sinus volume, independent of cranial size, has changed in the course of hominoid evolution. This result, in turn, has implications for the phylogenetic placement of fossil taxa and highlights the need for the careful delineation of character states in studies of hominoid systematics.
Recovery of Background Structures in Nanoscale Helium Ion Microscope Imaging

This paper discusses a two step enhancement technique applicable to noisy Helium Ion Microscope images in which background structures are not easily discernible due to a weak signal. The method is based on a preliminary adaptive histogram equalization, followed by ‘slow motion’ low-exponent Lévy fractional diffusion smoothing. This combined approach is unexpectedly effective, resulting in a companion enhanced image in which background structures are rendered much more visible, and noise is significantly reduced, all with minimal loss of image sharpness. The method also provides useful enhancements of scanning charged-particle microscopy images obtained by composing multiple drift-corrected ‘fast scan’ frames. The paper includes software routines, written in Interactive Data Language (IDL),1 that can perform the above image processing tasks.
Apoptosis and Fas expression in human fetal membranes.

Apoptosis (i.e. programmed cell death) plays a key role in maintaining reproductive function in the ovary, mammary and prostate glands, uterus, and testis. The purpose of the present report was to determine, based on biochemical and morphological parameters, whether cells in human fetal membranes undergo apoptosis and express Fas (CD95), a cell surface receptor that mediates apoptosis. Using the terminal deoxynucleotidyl transferase deoxy-UTP-nick end labeling immunohistochemical technique, apoptotic nuclei were identified in amnion epithelial, chorionic trophoblast, and decidua parietalis cell layers of human fetal membranes at term. Electron microscopy of fetal membranes revealed ultrastructural characteristics in amnion epithelium and chorion trophoblast cell layers consistent with apoptosis, including condensation of chromatin along the periphery of the nucleus and nuclear shrinkage. The apoptotic index (percentage of terminal deoxynucleotidyl transferase deoxy-UTP-nick end labeling-positive nuclei of the total nuclei) ranged from 8-29% in amnion epithelial, chorionic trophoblast, and decidual cell layers from women at 23-30, 31-36, and 37-42 weeks gestation. The apoptotic index was statistically greater in the 37-42 week group than in the 23-30 week group in chorionic trophoblast (P < 0.05) and decidual cell (P < 0.01) layers. In contrast, the apoptotic index in the amnion epithelial cell layer was statistically greater (P < 0.05) in the 23-30 week group than in the 31-36 week group, suggesting that apoptosis may be independently regulated in amnion epithelial, chorionic trophoblast, and decidual cell types. Based on the importance of Fas in mediating apoptosis, we investigated whether Fas was expressed by human fetal membrane cells. Immunohistochemical staining of fetal membranes with anti-Fas antibody localized Fas in amnion epithelial, chorionic trophoblast, and decidua parietalis cell layers. A 266-bp band corresponding to the cytoplasmic domain of Fas was detected in samples of amnion, chorion, decidua, and placenta by RT-PCR. Northern blotting revealed a molecular weight of approximately 1.9 kilobases for Fas messenger ribonucleic acid in amniotic tissue. These data suggest that apoptosis and Fas signaling may play a role in remodeling of fetal membrane architecture across gestation.
Mutations produced by DNA polymerase III holoenzyme of Escherichia coli after in vitro synthesis in the absence of single‐strand binding protein

Single‐stranded plasmid DNA, containing the mnt gene, was replicated in vitro with DNA polymerase III holoenzyme. Escherichia colimutH bacteria, defective in mismatch repair, were transformed with the products of in vitro synthesis. Mutations in mnt were readily identified and 33 out of 65 isolates were single base changes including transition, transversion and frameshift mutations. The remaining 32 isolates were deletions of apparently random length and substitutions (deletion/insertions). The intergenic deletions as well as the transition and frameshift mutations were identical to those previously isolated from mismatch repair‐defective cells in vivo.
The effect of APOA 5 and APOC 3 variants on lipid parameters in European Whites , Indian Asians and Afro-Caribbeans with type 2 diabetes

HAL is a multi-disciplinary open access archive for the deposit and dissemination of scientific research documents, whether they are published or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers. L’archive ouverte pluridisciplinaire HAL, est destinée au dépôt et à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d’enseignement et de recherche français ou étrangers, des laboratoires publics ou privés. The effect of and variants on lipid parameters in European Whites, Indian Asians and Afro-Caribbeans with type 2 diabetes Birgit Dorfmeister, Jackie A. Cooper, Jeffrey W. Stephens, Helen Ireland, Steven J. Hurel, Steve E. Humphries, Philippa J. Talmud
The Sequence and Structure Determine the Function of Mature Human miRNAs

Micro RNAs (miRNAs) (19–25 nucleotides in length) belong to the group of non-coding RNAs are the most abundant group of posttranscriptional regulators in multicellular organisms. They affect a gene expression by binding of fully or partially complementary sequences to the 3’-UTR of target mRNA. Furthermore, miRNAs present a mechanism by which genes with diverse functions on multiple pathways can be simultaneously regulated at the post-transcriptional level. However, little is known about the specific pathways through which miRNAs with specific sequence or structural motifs regulate the cellular processes. In this paper we showed the broad and deep characteristics of mature miRNAs according to their sequence and structural motifs. We investigated a distinct group of miRNAs characterized by the presence of specific sequence motifs, such as UGUGU, GU-repeats and purine/pyrimidine contents. Using computational function and pathway analysis of their targeted genes, we were able to observe the relevance of sequence and the type of targeted mRNAs. As the consequence of the sequence analysis we finally provide the comprehensive description of pathways, biological processes and proteins associated with the distinct group of characterized miRNAs. Here, we found that the specific group of miRNAs with UGUGU can activate the targets associated to the interferon induction pathway or pathways prominently observed during carcinogenesis. GU-rich miRNAs are prone to regulate mostly processes in neurogenesis, whereas purine/pyrimidine rich miRNAs could be involved rather in transport and/or degradation of RNAs. Additionally, we have also analyzed the simple sequence repeats (SSRs). Their variation within mature miRNAs might be critical for normal miRNA regular activity. Expansion or contraction of SSRs in mature miRNA might directly affect its mRNA interaction or even change the function of that distinct miRNA. Our results prove that due to the specific sequence features, these molecules can also be involved in well-defined cellular processes depending on their sequence contents. The pathway mapping and theoretical gene target identification allowed us to create a biological framework to show the relevance of the specific miRNAs in regulation the distinct type of targets.
Detecting intonation phrase boundaries in German laboratory speech by means of H tone upstep

This paper proposes a linguistically informed method for automated detection of Intonation Phrase (IP) boundaries in German lab speech. The method makes use of H tone upstep, a phenomenon that applies to the nuclear pitch accent or boundary tone of a non-final IP. The H tone of these events is considerably higher in f0 scaling than the H tone of the immediately preceding pitch accent. This is made use of in order to test for the presence of IP boundaries at certain positions in an utterance: The scaling of the f0 peaks of two adjacent intonational events are extracted and compared in regard to their relative height. If the second value is not lower than the first one, H tone upstep can be assumed, which points to the presence of an upcoming IP boundary. The method is tested on a data set of 216 lab speech utterances and performs with an accuracy of 94%. It is meant to provide a tool for linguists from any background who are working on IP formation in German with data gained in elicited production studies.
Disabled persons as lead users in the domestic environment

The paper describes the results of a user study conducted to probe the user experience and preferences of disabled persons in their domestic environments in order to challenge and improve the current state of accessible design. The study indicates that current accessible products and environments fail to take into account the holistic user experience, particularly the emotional and aesthetic aspects. The study introduced innovative users who personalise their accessible products and environments in order to reflect their identity and lifestyle, thereby avoiding stigmatisation, and to integrate them into society, thereby averting alienation. This leads to nearly luxurious solutions, whose value for users rests beyond pure use. Innovative disabled users could act as lead users who inform and inspire designers.
Oxidative activation of acylguanidine prodrugs: intestinal presystemic activation in rats limits absorption and can be inhibited by co-administration of ketoconazole

1 The disposition of acyl prodrugs was studied to improve the delivery of a guanidine-containing parent compound with poor membrane permeability and poor absorption. 2. The prodrugs were evaluated in vitro and in vivo for conversion to drug. Prodrugs were evaluated for hydrolytic or oxidative bioactivation in intestinal homogenate and rat liver S9 or microsomes. The disposition of the prodrugs in vivo was monitored in bile duct-cannulated rats. 3. Compounds with n -alkylacyl groups were efficiently bioactivated, but were hydrolysed before absorption. 4. Hydrolytic bioactivation could be blocked in vitro by branching in the alkyl chain. These compounds showed modest improvements in absorption, despite favourable permeability. Experiments with liver microsomes demonstrated efficient NADPH-dependent oxidative bioactivation, which was proposed to occur through a CYP-mediated side chain oxidation followed by cyclization and release of parent compound. Ketoconazole co-administration yielded approximately a twofold increase in absorption. 5. The hydrolytically stable prodrugs were successful in increasing absorption of parent drug and were efficiently bioactivated, but they did not yield increased systemic levels of drug.
Stimulation of nitric oxide mechanotransduction in single osteoblasts using atomic force microscopy

Nitric oxide (NO) released from mechanosensitive bone cells plays a key role in the adaptation of bone structure to its mechanical usage. Despite its importance in bone, the mechanisms involved in NO mechanotransduction at the cellular level remain unknown. Using combined atomic force microscopy and fluorescence microscopy, we report both stimulation and real‐time monitoring of NO responses in single osteoblasts induced by application of quantified periodic indenting forces to the osteoblast membrane. Peak forces ranging from 17 to 50 nN stimulated three distinct NO responses in the indented osteoblasts: (1) a rapid and sustained diffusion of NO from the perinuclear region, (2) diffusion of NO from localized pools throughout the osteoblast, and (3) an initial increase and subsequent drop in intracellular NO. Force‐indentation characteristics showed considerable interosteoblast variation in elasticity. NO responses were associated with application of force to more rigid membrane sites, suggesting cytoskeletal involvement in mechanotransduction. © 2007 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 26:513–521, 2008
Influence of microvascular resistance on fractional flow reserve after successful percutaneous coronary intervention

Increased microvascular resistance may impair hyperemic coronary flow by limiting the maximal and constant vasodilation, resulting in increased fractional flow reserve (FFR) due to the underestimation of the translesional pressure gradient. We examined whether microvascular resistance affects FFR after successful percutaneous coronary intervention (PCI). Methods and Results: We measured FFR and the index of microcirculatory resistance (IMR) in 104 coronary arteries of 98 patients after successful elective stenting. FFR values were compared according to the quartiles of the IMR values. Coronary flow was assessed using the hyperemic mean transit time (Tmn). The IMR values for the interquartile ranges of 8.5–11.3, 13.9–16.3, 20.9–24.5, and 34.2–61.6 were 10.2, 15.1, 22.8, and 38.2, respectively. Both FFR and Tmn values differed significantly across the IMR quartiles (P < 0.001). The angiographic and intravascular ultrasound findings and post‐PCI cardiac troponin levels showed no significant difference across the IMR quartiles. Multivariate logistic regression analysis revealed that the left anterior descending artery lesion location (odds ratio [OR] 0.17, 95% confidence interval [CI] 0.06–0.49, P = 0.001), IMR (OR 1.05, 95% CI 1.01–1.09, P = 0.012), and minimal cross‐sectional lumen area (OR 1.49, 95% CI 1.03–2.17, P = 0.036) were independent predictors of increased FFR. Conclusions: Increased microvascular resistance may reduce coronary flow and increase FFR after successful elective PCI. © 2014 Wiley Periodicals, Inc. © 2014 Wiley Periodicals, Inc.
Organisation-based co-ordination of wireless sensor networks

Esta tesis presenta el Coalition Oriented Sensing Algorithm (COSA) como un mecanismo de auto-organizacion para redes de sensores inalambricos (WSN). El objetivo del algoritmo es extender la vida util de la red, al mismo tiempo que la funcionalidad basica de la misma – la monitorizacion fiel del entorno– tambien es garantizada. La evaluacion del funcionamiento del algoritmo se apoya en una plataforma de simulacion novedosa, RepastSNS. La implementacion de COSA y la preparacion de la plataforma para el desarrollo de los experimentos dan lugar a una estructura software reutilizable. Esta estructura favorece la implementacion de futuras ampliaciones del algoritmo, asi como su exportacion a otros entornos. El uso de las WSNs se ha popularizado en los ultimos anos. Sus particulares caracteristicas han favorecido la aplicacion de las mismas a multiples areas. No obstante, la gestion energetica de las WSNs sigue siendo objeto de estudio para los investigadores, que tratan de aliviar las fuertes restricciones que estas presentan en cuanto a disponibilidad de energia se refiere. En esta linea, se han propuesto diversas tecnicas para conservacion de la energia. La restriccion energetica es especialmente acusada cuando las WSNs se despliegan en entornos que no permiten la conexion de los nodos a la red ni la recarga de sus baterias. Este es el tipo de entorno considerado para la evaluacion de COSA. El caso de uso estudiado considera una WSN desplegada a lo largo de un rio navegable con el objetivo de monitorizar el estado del agua y detectar la presencia de polucion en ella. La definicion de COSA se inspira en el paradigma de los Sistemas Multiagente (MAS) mediante la identificacion de los nodos de la WSN con agentes del MAS. COSA define un algoritmo para formacion de coaliciones basado en dialogos por parejas de agentes (nodos). El algoritmo esta completamente embebido en el comportamiento del agente. Los agentes que implementan COSA se comunican con sus vecinos para intercambiar informacion sobre su percepcion del entorno y su estado. Como resultado de esta comunicacion local, los agentes eligen su rol en la organizacion y establecen relaciones leader-follower. La definicion de este tipo de relaciones se basa en dos funciones relacionales y un protocolo de negociacion que establece las normas de coordinacion. Los agentes se juntan en grupos para compensar la calidad de los datos recogidos y el consumo de energia asociado. Esta habilidad permite adaptar el consumo energetico de la red a cambios en el entorno, al mismo tiempo que se satisfacen los objetivos de muestreo en cuanto a calidad de la informacion enviada al sink se refiere. Los resultados experimentales obtenidos apoyan las hipotesis preliminares en cuanto al comportamiento de COSA. A partir de estos resultados tambien se pone de manifiesto la relacion existente entre la coordinacion local y las ganancias obtenidas por el uso de COSA.
The Cholestanol-Conjugated Sulfated Oligosaccharide PG545 Disrupts the Lipid Envelope of Herpes Simplex Virus Particles

ABSTRACT Herpes simplex virus (HSV) and many other viruses, including HIV, initiate infection of host cells by binding to glycosaminoglycan (GAG) chains of cell surface proteoglycans. Although GAG mimetics, such as sulfated oligo- and polysaccharides, exhibit potent antiviral activities in cultured cells, the prophylactic application of these inhibitors as vaginal microbicides failed to protect women upon their exposure to HIV. A possible explanation for this failure is that sulfated oligo- and polysaccharides exhibit no typical virucidal activity, as their interaction with viral particles is largely electrostatic and reversible and thereby vulnerable to competition with GAG-binding proteins of the genital tract. Here we report that the cholestanol-conjugated sulfated oligosaccharide PG545, but not several other sulfated oligosaccharides lacking this modification, exhibited virucidal activity manifested as disruption of the lipid envelope of HSV-2 particles. The significance of the virus particle-disrupting activity of PG545 was also demonstrated in experimental animals, as this compound, in contrast to unmodified sulfated oligosaccharide, protected mice against genital infection with HSV-2. Thus, PG545 offers a novel prophylaxis option against infections caused by GAG-binding viruses.
Thought Experiments and Experimental Philosophy

Much of the recent movement organized under the heading “Experimental Philosophy” has been concerned with the empirical study of responses to thought experiments drawn from the literature on philosophical analysis. I consider what bearing these studies have on the traditional projects in which thought experiments have been used in philosophy. This will help to answer the question what the relation is between Experimental Philosophy and philosophy, whether it is an “exciting new style of [philosophical] research”, “a new interdisciplinary field that uses methods normally associated with psychology to investigate questions normally associated with philosophy” (Knobe et al. 2012), or whether its relation to philosophy consists, as some have suggested, in no more than the word ‘philosophy’ appearing in its title, or whether the truth lies somewhere in between these two views.