gebhart/patrepeval huggingface dataset:
A New Coarse-Grained Model for E. coli Cytoplasm: Accurate Calculation of the Diffusion Coefficient of Proteins and Observation of Anomalous Diffusion (2014)

A new coarse-grained model of the E. coli cytoplasm is developed by describing the proteins of the cytoplasm as flexible units consisting of one or more spheres that follow Brownian dynamics (BD), with hydrodynamic interactions (HI) accounted for by a mean-field approach. Extensive BD simulations were performed to calculate the diffusion coefficients of three different proteins in the cellular environment. The results are in close agreement with experimental or previously simulated values, where available. Control simulations without HI showed that use of HI is essential to obtain accurate diffusion coefficients. Anomalous diffusion inside the crowded cellular medium was investigated with Fractional Brownian motion analysis, and found to be present in this model. By running a series of control simulations in which various forces were removed systematically, it was found that repulsive interactions (volume exclusion) are the main cause for anomalous diffusion, with a secondary contribution from HI.
Differential Expression of FosB Proteins and Potential Target Genes in Select Brain Regions of Addiction and Depression Patients (2016)

Chronic exposure to stress or drugs of abuse has been linked to altered gene expression throughout the body, and changes in gene expression in discrete brain regions are thought to underlie many psychiatric diseases, including major depressive disorder and drug addiction. Preclinical models of these disorders have provided evidence for mechanisms of this altered gene expression, including transcription factors, but evidence supporting a role for these factors in human patients has been slow to emerge. The transcription factor ΔFosB is induced in the prefrontal cortex (PFC) and hippocampus (HPC) of rodents in response to stress or cocaine, and its expression in these regions is thought to regulate their "top down" control of reward circuitry, including the nucleus accumbens (NAc). Here, we use biochemistry to examine the expression of the FosB family of transcription factors and their potential gene targets in PFC and HPC postmortem samples from depressed patients and cocaine addicts. We demonstrate that ΔFosB and other FosB isoforms are downregulated in the HPC but not the PFC in the brains of both depressed and addicted individuals. Further, we show that potential ΔFosB transcriptional targets, including GluA2, are also downregulated in the HPC but not PFC of cocaine addicts. Thus, we provide the first evidence of FosB gene expression in human HPC and PFC in these psychiatric disorders, and in light of recent findings demonstrating the critical role of HPC ΔFosB in rodent models of learning and memory, these data suggest that reduced ΔFosB in HPC could potentially underlie cognitive deficits accompanying chronic cocaine abuse or depression.
Terceiro setor: a organização das políticas sociais e a nova esfera pública (2004)

A forma como vem se configurando o "Terceiro Setor", no Brasil, indica a presença de agentes políticos, culturais, econômicos e sociais, com ações nem sempre convergentes para a criação de modelos dinâmicos de organização. No campo das políticas sociais, visualiza-se hiato entre o conjunto de carências e a emergência de novo papel da sociedade civil, com base em pesquisas do autor no Vale do Paraíba.
Assessment of Ingestion by Chewing and Swallowing Sensors (2017)

This section provides a review of the methods and sensor systems used for characterization of food intake using chewing and swallowing. The chewing sensors have been monitored using a variety of sensor modalities for the detection of swallowing, including acoustical, electromechanical, magnetic, bioelectric, and other sensors. Chewing and swallowing can be measured by a variety of different sensors that rely on capturing various manifestations of the ingestion process such as sounds, muscle activity, motion, and others. The first and most fundamental task that is accomplished by the chewing sensors is measurement of the physical and/or physiological phenomena that accompany the chewing process. The chapter introduces the various sensor modalities for chewing detection. During chewing, the mandible movement is controlled by the temporalis, masseter, and pterygoid muscles. Jaw motion during chewing can also be monitored by placing accelerometer on the temporalis muscle or accelerometer attached to the temple of the glasses.
Higher Physical Fitness Regulates In Vitro Tumor Cell Growth in Older Adults with Treatment Naïve Chronic Lymphocytic Leukemia (CLL) (2021)

Abstract Chronic lymphocytic leukemia (CLL) is associated with physical dysfunction and low overall fitness that predicts poor survival following commencement of treatment. However, it remains unknown whether higher fitness in CLL patients provides anti-oncogenic effects. We identified ten fit (CLL-FIT) and ten less fit (CLL-UNFIT) treatment-naïve CLL patients from 144 CLL patients who completed a set of physical fitness and performance tests. Patient plasma was used to determine its effects on in vitro 5-day growth/viability of three B-cell cell lines (OSU-CLL, Daudi and Farage). Plasma exosomal miRNA profiles, circulating lipids, lipoproteins, inflammation levels, and immune cell phenotypes were also assessed. CLL-FIT was associated with fewer viable OSU-CLL cells at Day 1 ( p= 0.003), Day 4 ( p= 0.001) and Day 5 ( p= 0.009). No differences between groups were observed for Daudi and Farage cells. Of 455 distinct exosomal miRNAs identified, 32 miRNAs were significantly different between groups. Of these, 14 miRNAs had ≤-1 or ≥1 log2 fold differences. CLL-FIT patients had 5 exosomal miRNAs with lower expression and 9 miRNAs with higher expression. CLL-FIT patients had higher HDL cholesterol, lower inflammation, and lower levels of triglyceride components (all p &lt;0.05). CLL-FIT patients had lower frequencies of low-differentiated NKG2+/CD158a/b neg ( p= 0.015 and p =0.014) and higher frequencies of NKG2A neg /CD158b+ mature NK-cells ( p= 0.047). Absolute numbers of lymphocytes including CD19+/CD5+ CLL-cells were similar between groups ( p =0.359). Higher physical fitness in CLL patients is associated with altered CLL-like cell line growth in vitro , and with altered circulating and cellular factors indicative of better immune functions and tumor control.
Injection efficiency of CHISEL gate currents in short MOS devices: physical mechanisms, device implications, and sensitivity to technological parameters (2000)

This paper analyzes MOSFET gate currents in the so-called channel initiated secondary electron injection regime (CHISEL). A Monte Carlo model of the phenomenon is validated and then extensively used to explore CHISEL scaling laws. Results indicate that, compared to conventional channel hot electron injection (CHE), CHISEL exhibits a weaker dependence on channel length and a larger sensitivity to short channel effects. These results are confirmed experimentally and exhaustively explained with the help of simulations; furthermore, some of their possible detrimental consequences on the programming efficiency of CHISEL based flash cells are analyzed. Finally, the impact of channel doping, oxide thickness, and junction depth on CHISEL efficiency has been explored, and guidelines to maintain high injection efficiency in short devices are derived.
Endothelin-1 mediates attenuated carotid baroreceptor activity by intermittent hypoxia (2011)

The objectives of the present study were to examine the effects of intermittent hypoxia (IH) on arterial baroreflex function and assess the underlying mechanism(s). Experiments were performed on adult male rats treated with 14 days of IH (15 s of hypoxia, 5 min of normoxia; 8 h/day) or normoxia (control). Arterial blood pressures were elevated in IH-treated rats, and this effect was associated with attenuated heart rate and splanchnic sympathetic nerve responses to arterial baroreflex activation. In IH-treated rats, carotid baroreceptor responses to elevated sinus pressures were attenuated. Endothelin-1 (ET-1) levels were elevated in the carotid sinus region of IH-treated rats, and this effect was associated with increased endothelin converting enzyme (ECE) activity, which generates biologically active ET-1. ET(A) receptor antagonist prevented the effects of IH on carotid baroreceptor activity. In IH-treated rats, reactive oxygen species (ROS) levels were elevated in the carotid sinus region, and antioxidant treatment prevented the effects of IH on ET-1 levels, ECE activity, carotid baroreceptor activity, and baroreflex function. These results demonstrate that 1) IH attenuates arterial baroreflex function, which is in part due to reduced carotid baroreceptor responses to elevated carotid sinus pressure, and 2) IH-induced carotid baroreceptor dysfunction involves reactive oxygen species-dependent upregulation of ET-1 signaling in the carotid sinus region.
Emphysema diagnosis using X-ray dark-field imaging at a laser-driven compact synchrotron light source (2012)

In early stages of various pulmonary diseases, such as emphysema and fibrosis, the change in X-ray attenuation is not detectable with absorption-based radiography. To monitor the morphological changes that the alveoli network undergoes in the progression of these diseases, we propose using the dark-field signal, which is related to small-angle scattering in the sample. Combined with the absorption-based image, the dark-field signal enables better discrimination between healthy and emphysematous lung tissue in a mouse model. All measurements have been performed at 36 keV using a monochromatic laser-driven miniature synchrotron X-ray source (Compact Light Source). In this paper we present grating-based dark-field images of emphysematous vs. healthy lung tissue, where the strong dependence of the dark-field signal on mean alveolar size leads to improved diagnosis of emphysema in lung radiographs.
Large quantity, high speed pressure data acquisition (1976)

Approaches used for conducting in-flight pressure surveys for aircraft are examined, taking into account difficulties related to a use of scanivalves which are employed only in cases in which there is not sufficient space for the mounting of individual transducers. In connection with attempts to eliminate these difficulties a new pressure survey module was manufactured. The dimensions of the new module make it possible to mount it in places in which the old scanivalve module could be mounted. One of the difficulties related to the use of the old scanivalve module has been the risk of data loss in flight in connection with the migration of foreign matter within the tubing. In the new module an electrical sampling method is employed to eliminate this risk. Attention is also given to an engine ground test and preflight system and the development of a calibration module.
The Lateral Range and Energy Deposition of Fast Secondary Electrons (2004)

Extended abstract of a paper presented at Microscopy and Microanalysis 2004 in Savannah, Georgia, USA, August 1–5, 2004.
Multi-Constriction Microfluidic Sensors for Single-Cell Biophysical Characterization (2017)

Cancer is a major health issue that has been associated with over 80 million deaths worldwide in the last decade. Recently, significant improvements have been made in terms of treatment and diagnosis. However, despite these advancements there is still a demand for low-cost, high-accuracy, and easy-to-use technologies capable of classifying cells. Analysis of cell behavior in microfluidic deformability assays provides a label-free method of observing cell response to physical and chemical stimuli. This body of work shows advancements made toward reaching our goal of a robust and cost-effective biosensing device that allows for the identification of normal and cancer cells. These devices can also monitor cell responses to physical and chemical stimuli in the form of mechanical deformation and chemotherapeutic drugs, respectively. Our initial design was a microfluidic device that consisted of three channels with varying deformation and relaxation regions. Cell velocities from the deformations regions allowed us to distinguish between normal and cancer cells at the single-cell level. The next design used a singular deformation channel that was embedded with an array of electrodes in order to measure entry time, transit time and velocities as a single cell passes through the channel. These factors were found to reveal information about the biomechanical properties of single cells. Embedded electrodes were implemented in order to reduce post processing times of the data analysis and provide more insight into the bioelectrical information of cells. Finally, we report a microfluidic device with parallel deformation channels and a single electrode pair to improve throughput and automate data collection of deformability assays. This thesis demonstrates how microfluidic deformability assays, with and without embedded electrodes, show promising capabilities to classify different cells based on their biophysical traits which can be utilized as a valuable tool for testing responses to physical and chemical stimuli.
Effects of different target sites on antisense RNA-mediated regulation of gene expression (2014)

Antisense RNA is a type of noncoding RNA (ncRNA) that binds to complementary mRNA sequences and induces gene repression by inhibiting translation or degrading mRNA. Recently, several small ncRNAs (sRNAs) have been identified in Escherichia coli that act as antisense RNA mainly via base pairing with mRNA. The base pairing predominantly leads to gene repression, and in some cases, gene activation. In the current study, we examined how the location of target sites affects sRNA-mediated gene regulation. An efficient antisense RNA expression system was developed, and the effects of antisense RNAs on various target sites in a model mRNA were examined. The target sites of antisense RNAs suppressing gene expression were identified, not only in the translation initiation region (TIR) of mRNA, but also at the junction between the coding region and 3' untranslated region. Surprisingly, an antisense RNA recognizing the upstream region of TIR enhanced gene expression through increasing mRNA stability.
Gate-defined Two-dimensional Hole and Electron Systems in an Undoped InSb Quantum Well (2022)

Quantum transport measurements are performed in gate-defined, high-quality, two-dimensional hole and electron systems in an undoped InSb quantum well. For both polarities, the carrier systems show tunable spin-orbit interaction as extracted from weak anti-localization measurements. The effective mass of InSb holes strongly increases with carrier density as determined from the temperature dependence of Shubnikov-de Haas oscillations. Coincidence measurements in a tilted magnetic field are performed to estimate the spin susceptibility of the InSb two-dimensional hole system. The g-factor of the two-dimensional hole system decreases rapidly with increasing carrier density.
PO-522 Biological layers identified two independent classifications in melanoma tumours (2018)

Introduction Melanoma is the most lethal malignancy of the skin. The Cancer Genome Atlas (TCGA) Network proposed a molecular classification of melanoma, consisting in three subtypes: keratin-high, immune-high and membrane-low. However, this classification has not been translated into therapeutic advances yet. The aim of this study is to characterise molecular differences of melanoma at biological and molecular levels and propose a novel molecular classification with clinical impact. Material and methods A novel approach based on the existence of different molecular informative layers was used in this study to establish independent sets of information. A probabilistic graphical model, followed by successive sparse k-means and consensus cluster analyses were used to classify melanoma tumour samples from the TCGA cohort. Then, molecular classification was validated in another public cohort: GSE65904. Results and discussions We established that there were at least two different kinds of molecular information: an immune layer and a histological layer. Immune high and immune low groups were established based on immune layer information. Keratin low-proliferation low, melanogenesis high-membrane low, melanogenesis low-membrane high and keratin high groups were established based on molecular layer information. This suggests that the information related to the immune system is independent from other molecular features and is distributed among the groups established by the TCGA classification. Besides, the immune and histological assignments showed different clinical outcomes in another dataset, identifying two immune groups with prognostic value. Conclusion In this work we proposed a novel analytical approach based on informative molecular layers. In this way, two independent classifications, an immune-based and a histological-based classification, were established. Immune classification showed prognostic value in an independent cohort. Besides, the histological and the immune layers may deserve additional research for define new potential targeted therapies.
Landmark matching via large deformation diffeomorphisms (2000)

This paper describes the generation of large deformation diffeomorphisms phi:Omega=[0,1]3<-->Omega for landmark matching generated as solutions to the transport equation dphi(x,t)/dt=nu(phi(x,t),t),epsilon[0,1] and phi(x,0)=x, with the image map defined as phi(.,1) and therefore controlled via the velocity field nu(.,t),epsilon[0,1]. Imagery are assumed characterized via sets of landmarks {xn, yn, n=1, 2, ..., N}. The optimal diffeomorphic match is constructed to minimize a running smoothness cost parallelLnu parallel2 associated with a linear differential operator L on the velocity field generating the diffeomorphism while simultaneously minimizing the matching end point condition of the landmarks. Both inexact and exact landmark matching is studied here. Given noisy landmarks xn matched to yn measured with error covariances Sigman, then the matching problem is solved generating the optimal diffeomorphism phi;(x,1)=integral0(1)nu(phi(x,t),t)dt+x where nu(.)=argmin(nu.)integral1(0) integralOmega parallelLnu(x,t) parallel2dxdt +Sigman=1N[yn-phi(xn,1)] TSigman(-1)[yn-phi(xn,1)]. Conditions for the existence of solutions in the space of diffeomorphisms are established, with a gradient algorithm provided for generating the optimal flow solving the minimum problem. Results on matching two-dimensional (2-D) and three-dimensional (3-D) imagery are presented in the macaque monkey.
Mistake in the Formation and Performance of Contracts: Remedial Options under Australian Law (2009)

Dr Nick Seddon writing in the Australian Law Journal said of the contemporary law: 'The law relating to mistake in contract is old, arcane, uncertain in application, complex and controversial.' Newnes M in Errichetti Nominees Pty Ltd v Paterson Group Architects Pty Ltd [2007] WASC 77 strongly endorsed Dr Seddon's views. 'There is little doubt that the subject of mistake in Australian law is both difficult and confusing.' The High Court has considered the applicable principles in three cases, namely, McRae v Commonwealth Disposals Commission (1950) 84 CLR 377; Svanosio v McNamara (1956) 96 CLR 186; and Taylor v Johnson (1983) 151 CLR 422. The first two cases were concerned with common mistake, that is, a mistake shared by both contracting parties and Taylor concerned unilateral mistake.
Transition-Metal Silyl Derivatives (2004)

This chapter contains sections titled: Introduction The Formation of Compounds Containing Transition-metal–Silicon Bonds Late Transition-metal Derivatives Methods Involving Oxidative Addition of SiH Bonds Methods Involving Oxidative Addition of Other SiX Bonds Methods Employing Transition-metal Anions Methods Employing Main-group Metal Silyl Compounds Miscellaneous Methods Transition-metal Silicon Clusters Early Transition-metal Derivatives Methods Employing Main-group Metal Silyl Compounds Methods Involving Cleavage of SiH Bonds Related F-element Derivatives Transition-metal Silylene Complexes Indirect Evidence for Coordinated Silylenes Attempted Preparations Transition-metal Silene Complexes Structure and Bonding Structural Information Metal–silicon Bond Distances Other Structural Features Information from NMR Studies Information from Infrared and Raman Studies Information from Mass Spectrometric Studies Reactions Involving MSi Bonds Cleavage of MSi Bonds by Nucleophiles Cleavage of MSi Bonds by Electrophiles Cleavage of MSi Bonds by Other Reagents Insertion Reactions Insertion of Alkenes Insertion of Alkynes Insertion of Nitriles Insertion of Organic Carbonyl Compounds Insertion of Carbon Monoxide and Isocyanides Catalytic Reactions Hydrosilylation Dehydrogenative Coupling Reactions Involving Hydrosilanes Redistribution on Silicon Other SiC Bond-forming Reactions Catalytic Reactions with Hydrosilanes and Carbon Monoxide References
Late Rehabilitation After Stroke (2011)

Physiotherapy is usually provided in the first months after a stroke; its effectiveness in the chronic phase is uncertain. The authors of this article conducted a systematic review and meta-analysis of randomized clinical trials to evaluate motor and functional recovery outcomes when physiotherapy is provided late after stroke. They identified …
ENCYCLOPEDIA WALKABOUTS WITH VISNOMAD - A New Visualization Tool Designed as an Aid for Textual Exploration (2010)

We present an original visualizer that allows users to travel through the network of pages of an early encyclopedia of computer science. The purpose of this tool is to better understand the relationship between concepts of computer science at an early stage in the development of the eld. The visualizer is written in Java, interfaces to a database server, and sports two dierent graphical representations, a tree and a graph that are logically connected. We present our design goals, our choices of implementations and the challenges encountered.
Persistence of Gene Expression Profile in CD200 Transgenic Skin Allografts Is Associated With Graft Survival on Retransplantation to Normal Recipients (2012)

Adoptive transfer of tolerance in MLC to BL/6 grafts was most evident when both skin and splenocytes were transferred from primary BALB/c recipients, although there was an attenuation of MLC responses after graft transfer alone. Adoptive transfer of tolerance occurred concomitant with persistent overexpression of genes encoding Foxp3, transforming growth factor β, interleukin 10, and PD-1 (and PD-L1/PD-L2) in tolerant skin grafts and increased expression of mRNAs for indoleamine 2,3-dioxygenase and the subunits encoding interleukin 35. Infusion of anti-CD4 or anti-transforming growth factor β to secondary recipients on retransplantation abolished increased graft survival, suggesting the importance of each to the final outcome.
Thomas Wolfe's Civil War (2002)

Two mythic achievements in the novel form have eluded the creative powers of both the greatest northern and southern writers: the Great American Novel and the Great Civil War Novel. I am convinced that the Great American Novel must also be the Great Civil War Novel. Thomas Wolfe, who wrote "Chickama....