gebhart/patrepeval huggingface dataset:
Towards the rational design of synthetic cells with prescribed population dynamics (2012)

The rational design of synthetic cell populations with prescribed behaviours is a long-standing goal of synthetic biology, with the potential to greatly accelerate the development of biotechnological applications in areas ranging from medical research to energy production. Achieving this goal requires well-characterized components, modular implementation strategies, simulation across temporal and spatial scales and automatic compilation of high-level designs to low-level genetic parts that function reliably inside cells. Many of these steps are incomplete or only partially understood, and methods for integrating them within a common design framework have yet to be developed. Here, we address these challenges by developing a prototype framework for designing synthetic cells with prescribed population dynamics. We extend the genetic engineering of cells (GEC) language, originally developed for programming intracellular dynamics, with cell population factors such as cell growth, division and dormancy, together with spatio-temporal simulation methods. As a case study, we use our framework to design synthetic cells with predator-prey interactions that, when simulated, produce complex spatio-temporal behaviours such as travelling waves and spatio-temporal chaos. An analysis of our design reveals that environmental factors such as density-dependent dormancy and reduced extracellular space destabilize the population dynamics and increase the range of genetic variants for which complex spatio-temporal behaviours are possible. Our findings highlight the importance of considering such factors during the design process. We then use our analysis of population dynamics to inform the selection of genetic parts, which could be used to obtain the desired spatio-temporal behaviours. By identifying, integrating and automating key stages of the design process, we provide a computational framework for designing synthetic systems, which could be tested in future laboratory studies.
Cognitive Assistants for Evidence-Based Reasoning Tasks (2011)

Evidence-based reasoning is at the core of many problem solving and decision making tasks in a wide variety of domains. This paper introduces a computational theory of evidence-based reasoning, the architecture of a learning agent shell which incorporates general knowledge for evidence-based reasoning, a methodology that uses the shell to rapidly develop cognitive assistants in a specific domain, and a sample cognitive assistant for intelligence analysis.
Supplementary Table S1 from Neuroendocrine Transdifferentiation in Human Prostate Cancer Cells: An Integrated Approach (2023)

&lt;p&gt;Supplementary Table S1. Topology-based pathway analysis.&lt;/p&gt;
Large-area OLED lightings and their applications (2011)

In this paper, we review the key issues related to the fabrication of large-area organic light-emitting devices (OLEDs) for lighting applications. We discuss the origin of a short-circuit problem, luminance non-uniformity, hot spot, efficiency reduction (power loss), and heat generation and present the way of suppressing them. We also introduce three different application areas of large-area OLED lighting panels. They can be integrated with a solar cell for power recycling or inorganic LEDs for emotional lightings. The feasibility of using OLEDs for the application of visible-light communications is also reviewed.
Antibodies to endogenous and recombinant erythropoietin (2006)

Owing to the very few cases of anti-erythropoietin (EPO) antibodies arising in patients treated with recombinant human EPO (rHuEPO) before 1998, it was generally believed that EPO is weakly immunogenic. Several recent reports, however, suggest that this theory may be wrong. Indeed, low amounts of rHuEPO are immunogenic in animals such as the mouse, rat, rabbit, or horse, despite the high degree of sequence identity of the mammalian EPO molecules. Interestingly, in most cases injection of rHuEPO to these animals not only leads to production of antibodies that recognize the injected rHuEPO but also cross react with the endogenous EPO molecule and neutralize it, leading to pronounced anemia in rHuEPO-treated animals [1, and our own unpublished data]. A hybrid molecule linking recombinant human granulocytemacrophage colony-stimulating factor (rHuGM-CSF) and EPO has been administrated to rhesus monkeys. This treatment induced a neutralizing immune response to EPO, whereas no antibodies against GM-CSF were detected. Again, the anti-EPO antibodies cross reacted with monkey EPO and induced a pronounced anemia [2]. Thus, the low incidence of neutralizing antiEPO antibodies among rHuEPO-treated patients is most likely due to the good quality of the available rHuEPO preparations rather than to a low antigenic property of the molecule itself. rHuEPO appears to differ from endogenous human EPO only at the level of glycosylation. This high similarity explains why rHuEPO treatment exhibits a high degree of both efficiency and safety. During the last four years, however, a large number of cases of pure red cell aplasia due to neutralizing anti-EPO antibodies have been reported in patients treated with rHuEPO for anemia associated with renal failure of various etiologies [3]. In this review, we address several questions:
Circuit Aware Approximate System Design With Case Studies in Image Processing and Neural Networks (2018)

This paper aims to exploit approximate computing units in image processing systems and artificial neural networks. For this purpose, a general design methodology is introduced, and approximation-oriented architectures are developed for different applications. This paper proposes a method to compromise power/area efficiency of circuit-level design with accuracy supervision of system-level design. The proposed method selects approximate computational units that minimize the total computation cost, yet maintaining the ultimate performance. This is accomplished by formulating a linear programming problem, which can be solved by conventional linear programming solvers. Approximate computing units, such as multipliers, neurons, and convolution kernels, which are proposed by this paper, are suitable for power/area reduction through accuracy scaling. The formulation is demonstrated on applications in image processing, digital filters, and artificial neural networks. This way, the proposed technique and architectures are tested with different approximate computing units, as well as system-level requirement metrics, such as PSNR and classification performance.
Transfer of the Lower Trapezius as a Surgical Treatment for Combined Injuries to the Suprascapular and Axillary Nerves: A Case Report. (2019)

Early recovery after surgery was achieved, with excellent improvement of the range of shoulder motion. We report the transfer of the lower trapezius to the infraspinatus might provide a useful salvage procedure for patients with poor functional prognosis of a chronic suprascapular nerve injury.
The prion dilemma confounding science educators (2013)

In this paper, the issue of the prion hypothesis, a simmering controversy within the scientific community, is addressed. We inquire into the appropriateness of the use of certain augmentations and rhetoric approaches used during scientific debates, as well as the aptness of unequivocal statements in textbooks that indicate “abnormal prions” as a primary cause of Transmissible Spongiform Encephalopathies.
Figures S1-S6 from Rhabdoid Tumors Are Sensitive to the Protein-Translation Inhibitor Homoharringtonine (2023)

&lt;p&gt;Combined supplementary figures with accompanying legends.&lt;/p&gt;
Noncontact acousto-thermal evaluation of evolving fatigue damage in polycrystalline Ti-6Al-4V (2014)

Non-Contact Acousto-Thermal Signature (NCATS) analysis uses conversion of acoustic energy to heat to characterize evolving damage in materials. In the past, the observed temperature changes were interpreted using phenomenological approaches. This paper presents details of the mechanisms and the theoretical models to predict the temperature change due to conversion of acoustic energy to heat. NCATS experimental measurements performed using 20 kHz high amplitude acoustic waves on as received and fatigued polycrystalline Ti-6Al-4V are compared with theoretical calculations based on the mechanisms of transverse thermal currents, inter-crystalline thermal currents, and dislocation density changes. In the as received samples, the transverse thermal currents contribution has been found to be negligible compared with inter-crystalline thermal currents contribution. The experimentally measured maximum temperature change in the as received sample has been found to be 0.5 °C, and the theoretical prediction based on inter-crystalline thermal currents is 0.08 °C. In the fatigue damaged samples, the maximum temperature change increases with increasing damage that can be attributed to the increasing dislocation density. The theoretical prediction of the maximum temperature attained by a sample that is near failure based on dislocation contribution is 2.0 °C, while the experimental measurements have been found to be 0.95 °C. The differences between the theoretical and the experimental measurements are discussed in the context of the uncertainties in several physical parameters used in the theoretical calculations.
0433 Quality Of Life And Depressive Symptoms In Midlife Women With And Without Insomnia (2018)

Insomnia affects upwards of 40% of midlife women. Insomnia disorder, as well as associated symptoms like depression, may produce significant impairment in daily functioning. In this study, we compared quality of life and impact of menopausal symptoms on quality of life domains between women, all in the menopausal transition, with (n=54) and without (n=46) insomnia disorder. We also investigated the association of depressive symptoms with quality of life within each group. One hundred women (49.3 ± 3.25 years) underwent a clinical structured interview including a sleep history module to establish the presence of insomnia disorder. Women also completed clinical measures assessing depressive symptoms (Beck Depression Inventory-II, BDI), quality of life, and impairment associated with menopausal symptoms (Menopause-Specific Quality of Life, and Work and Social Adjustment Scale). Women with insomnia compared with good sleepers had a poorer quality of life (p = 0.002) and greater impairment associated with vasomotor (hot flashes), psychological, and physical symptoms (p<0.05). They also reported more impairment in work, social leisure activities, and functioning in relationships, attributed to their menopausal symptoms, compared to controls (p<0.001). BDI scores were higher in the insomnia (7.52 ± 5.43, median=7) than control (3.48 ± 3.77, median=2) group, although none of the women met DSM-IV criteria for mood disorders. Within the insomnia (r= -0.48, p<0.01) and control (r = -0.48, p<0.01) groups, higher BDI scores were associated with a poorer quality of life. Menopausal women with insomnia disorder have a poorer quality of life and more impairment across several domains. Over and above the impact of insomnia, symptoms of depression are associated with poorer quality of life enjoyment and satisfaction in midlife women. It is critical to recognize and treat menopausal insomnia and depressive symptoms to improve overall quality of life. This study was supported by the HL088088 grant (FCB).
Photodynamic Therapy in Organ Transplant Recipients (2008)

Clinical applications of photodynamic therapy (PDT) have expanded over the last several years due to new light sources and FDA approved photosensitizers. Compared to surgery and radiation therapy for nonmelanoma skin cancers, PDT has many potential advantages. A single, noninvasive session can treat simultaneously multiple areas as well as extensive superficial lesions. Repeated sessions can be performed without total dose limitations. PDT is generally associated with good patient tolerance, relatively short healing time, and overall good cosmesis. It can be carried out in nonsurgical candidates and can occasionally be combined with other therapeutic modalities (Table 45.1).
A hybrid algorithm for speaker adaptation using MAP transformation and adaptation (1997)

We present a hybrid algorithm for adapting a set of speaker-independent hidden Markov models (HMMs) to a new speaker based on a combination of maximum a posteriori (MAP) parameter transformation and adaptation. The algorithm is developed by first transforming clusters of HMM parameters through a class of transformation functions. Then, the transformed HMM parameters are further smoothed via Bayesian adaptation. The proposed transformation/adaptation process can be iterated for any given amount of adaptation data, and it converges rapidly in terms of likelihood improvement. The algorithm also gives a better speech recognition performance than that obtained using transformation or adaptation alone for almost any practical amount of adaptation data.
Hierarchical random additive model for the spanwise and wall-normal velocities in wall-bounded flows at high Reynolds numbers (2018)

Both the spanwise and the vertical velocity components in high-Reynolds-number wall-bounded flows may be modeled via a random additive process. Evidence shows that a hierarchical, treelike structure exists for the spanwise velocity component.
Simple Gabor feature space for invariant object recognition (2004)

Invariant object recognition is one of the most challenging problems in computer vision. Authors propose a simple Gabor feature space, which has been successfully applied to facial feature extraction in invariant face detection in demanding environments (Kamarainen et al., 2002c; Hamouz et al., 2003). In the proposed feature space, illumination, rotation, scale, and translation invariant recognition of objects can be established within a reasonable amount of computation. In this study, the fundamental properties of Gabor features, construction of the simple feature space, and invariant search operations in the feature space are discussed in more detail. Key words: Gabor filtering, invariant object recognition 1
Deriving accurate microbiota profiles from human samples with low bacterial content through post-sequencing processing of Illumina MiSeq data (2015)

The application of the presented workflow to a set of challenging clinical samples demonstrates its utility in removing the spurious signal from the dataset, allowing clinical insight to be derived from what would otherwise be highly misleading output. While other approaches could potentially achieve similar improvements, the methodology employed here represents an accessible means to exclude the signal from contamination and other artefacts.
08041 Abstracts Collection – Recurrent Neural Networks - Models, Capacities, and Applications (2008)

From January 20 to 25 2008, the Dagstuhl Seminar 08041 ``Recurrent Neural Networks- Models, Capacities, and Applications'' was held in the International Conference and Research Center (IBFI), Schloss Dagstuhl. During the seminar, several participants presented their current research, and ongoing work and open problems were discussed. Abstracts of the presentations given during the seminar as well as abstracts of seminar results and ideas are put together in this paper. The first section describes the seminar topics and goals in general. Links to extended abstracts or full papers are provided, if available.
Pattern reconstruction of scanning electron microscope images using long-range content complexity analysis of the edge ridge signal (2006)

Based on the observation that human visual system connects broken edge segments according to long-range pattern contents, the authors here describe a general methodology for pattern reconstruction from scanning electron microscope (SEM) based on intuitive conjectures of human intelligence. In particular, we formulate the problem of pattern reconstruction as a problem of minimizing an objective function, which includes the information of pattern complexity and template matching. This approach of objective function minimization is also consistent with the famous “Occam’s razor” principle. They then describe a potential objective function formulation, introduce implementations with acceptable computation complexity, and demonstrate reconstruction results on edge ridge signals extracted from real SEM images. This methodology can greatly improve the robustness of SEM image processing and has the potential to be applied to many other fields, such as computer vision and robust human voice detection as well as inspection of nanoscale structures in the SEM.
Estudio piloto para la adaptación al casteliano del cuestionario de estrategias de afrontamiento a la lesión medular (SCL CSQ) (2010)

Estudio piloto para la adaptacion al casteliano del cuestionario de estrategias de afrontamiento a la lesion medular (SCL CSQ)
ChemInform Abstract: H+/K+‐ATPase Inhibitors (1993)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Delayed leaf senescence induces extreme drought tolerance in a flowering plant (2007)

Drought, the most prominent threat to agricultural production worldwide, accelerates leaf senescence, leading to a decrease in canopy size, loss in photosynthesis and reduced yields. On the basis of the assumption that senescence is a type of cell death program that could be inappropriately activated during drought, we hypothesized that it may be possible to enhance drought tolerance by delaying drought-induced leaf senescence. We generated transgenic plants expressing an isopentenyltransferase gene driven by a stress- and maturation-induced promoter. Remarkably, the suppression of drought-induced leaf senescence resulted in outstanding drought tolerance as shown by, among other responses, vigorous growth after a long drought period that killed the control plants. The transgenic plants maintained high water contents and retained photosynthetic activity (albeit at a reduced level) during the drought. Moreover, the transgenic plants displayed minimal yield loss when watered with only 30% of the amount of water used under control conditions. The production of drought-tolerant crops able to grow under restricted water regimes without diminution of yield would minimize drought-related losses and ensure food production in water-limited lands.
Strategies to eradicate HIV from infected patients: elimination of latent provirus reservoirs (2019)

35 years since identification of HIV as the causative agent of AIDS, and 35 million deaths associated with this disease, significant effort is now directed towards the development of potential cures. Current anti-retroviral (ART) therapies for HIV/AIDS can suppress virus replication to undetectable levels, and infected individuals can live symptom free so long as treatment is maintained. However, removal of therapy allows rapid re-emergence of virus from a highly stable reservoir of latently infected cells that exist as a barrier to elimination of the infection with current ART. Prospects of a cure for HIV infection are significantly encouraged by two serendipitous cases where individuals have entered remission following stem cell transplantation from compatible HIV-resistant donors. However, development of a routine cure that could become available to millions of infected individuals will require a means of specifically purging cells harboring latent HIV, preventing replication of latent provirus, or destruction of provirus genomes by gene editing. Elimination of latently infected cells will require a means of exposing this population, which may involve identification of a natural specific biomarker or therapeutic intervention to force their exposure by reactivation of virus expression. Accordingly, the proposed "Shock and Kill" strategy involves treatment with latency-reversing agents (LRA) to induce HIV provirus expression thus exposing these cells to killing by cellular immunity or apoptosis. Current efforts to enable this strategy are directed at developing improved combinations of LRA to produce broad and robust induction of HIV provirus and enhancing the elimination of cells where replication has been reactivated by targeted immune modulation. Alternative strategies may involve preventing re-emergence virus from latently infected cells by "Lock and Block" intervention, where transcription of provirus is inhibited to prevent virus spread or disruption of the HIV provirus genome by genome editing.
The influence of solder mask and hygroscopic flux residues on water layer formation on PCBA surface and corrosion reliability of electronics (2017)

The presence of solder flux residue on the Printed Circuit Board Assembly (PCBA) surface compromises the corrosion reliability of electronics under humid conditions and can lead to degradation of the device’s lifetime. In this work, the effect of solder mask morphology and hygroscopic residues were studied towards assessment of their influence on the water film formation on the PCBA surface. The in-situ observations of water layer build-up was studied on the solder mask substrates as a function of surface finish and residue type (adipic and glutaric acids). The effect of solder flux residues was described in terms of their varying hygroscopicity defined by chemical structure and test temperature. The climatic testing of two acids was performed under relative humidity (RH) conditions varying from 30% to ~99% at 25˚C and 40˚C using gravimetric water vapour sorption/desorption and electrochemical impedance methods. The corrosivity of WOAs was evaluated via leakage current measurements using surface insulation resistance (SIR) comb patterns. The corrosion studies were correlated with the hygroscopicity studies. The results show that the water layer formation depends on the PCBA surface topography and the type of post-production residue present on the surface. Moreover, the hygroscopic nature of typical flux residue depends on its chemical structure and temperature. An increase of temperature shifts the critical RH level for water vapour absorption towards lower RH range accelerating the formation of well-conductive electrolyte and the occurrence of ionic-induced electrochemical migration (ECM).
Numerical investigation of abdominal aortic aneurysm hemodynamics using the reduced unified continuum formulation for vascular fluid-structure interaction (2022)

We recently demonstrated the reduction of the unified continuum and variational multiscale formulation to a computationally efficient fluid-structure interaction (FSI) formulation via three sound modeling assumptions pertaining to the vascular wall. Similar to the coupled momentum method introduced by Figueroa et al., the resulting semi-discrete formulation yields a monolithically coupled FSI system posed in an Eulerian frame of reference with only a minor modification of the fluid boundary integral. To achieve uniform second-order temporal accuracy and user-controlled high-frequency algorithmic damping, we adopt the generalized-$\alpha$ method for uniform temporal discretization of the entire coupled system. In conjunction with a fully consistent, segregated predictor multi-corrector algorithm preserving the block structure of the incompressible Navier-Stokes equations in the implicit solver's associated linear system, a three-level nested block preconditioner is adopted for improved representation of the Schur complement. In this work, we apply our reduced unified continuum formulation to an appropriately prestressed patient-specific abdominal aortic aneurysm and investigate the effects of varying spatial distributions of wall properties on hemodynamic and vascular wall quantities of interest.
Concepts and basic designs of various nuclear fuels (6) (2021)

日本原子力学会核燃料部会の連載企画｢多様な原子燃料の概念と基礎設計｣の最終回として，新しい原子炉のための核燃料開発を概説する。核燃料に要求される性質を簡単にまとめ，核燃料の種類と分類を概説した後，新しい原子炉のための核燃料開発に際しての照射炉と照射試験の重要性を説く。そのうえで，わが国の核燃料開発に期待することとして著者の考えを示す。