Miracle-dz/UniFAR-FTUs huggingface dataset:
Protein aggregation with poly(vinyl) alcohol surfactant reduces double emulsion-encapsulated mammalian cell-free expression

Development of artificial cell models requires encapsulation of biomolecules within membrane-bound compartments. There have been limited studies of using mammalian cell-free expression (CFE) system as the ‘cytosol’ of artificial cells. We exploit glass capillary droplet microfluidics for the encapsulation of mammalian CFE within double emulsion templated vesicles. The complexity of the physicochemical properties of HeLa cell-free lysate poses a challenge compared with encapsulating simple buffer solutions. In particular, we discovered the formation of aggregates in double emulsion templated vesicles encapsulating mammalian HeLa CFE, but not with bacterial CFE. The aggregates did not arise from insolubility of the proteins made from CFE nor due to the interaction of mammalian CFE with the organic solvents in the middle phase of the double emulsions. We found that aggregation is dependent on the concentration of poly(vinyl) alcohol (PVA) surfactant, a critical double emulsion-stabilizing surfactant, and the lysate concentration in mammalian CFE. Despite vesicle instability and reduced protein expression, we demonstrate protein expression by encapsulating mammalian CFE system. Using mass spectrometry and Western blot, we identified and verified that actin is one of the proteins inside the mammalian CFE that aggregated with PVA surfactant. Our work establishes a baseline description of mammalian CFE system encapsulated in double emulsion templated vesicles as a platform for building artificial cells.
Transformation-invariant image descriptors for change monitoring based on multi-modality imagery

An area-based multi-scale method for transformation-invariant descriptor extraction called multi-location feature saliency pattern (MFSP) is proposed in this paper in the context of image matching for change detection and monitoring. Multi-location image descriptors are extracted in salient circular fragments of variable size (scale), which indicate image locations with high intensity contrast, regional homogeneity and shape saliency. The MFSP is a set of relational descriptor vectors corresponding to a set of salient image fragments located in a neighborhood of a given feature point. The method proceeds without any image segmentation since the feature points are extracted by a fast recursive algorithm in a multi-scale manner analyzing circular high-contrast sub-regions of various sizes in every pixel location. The experimental results confirm the robustness of descriptor extraction by the proposed method and effectiveness of the multi-location feature saliency patterns for change detection and feature-based image matching.
Experimental evaluation of haptic control for human activated command devices

Haptics refers to a widespread area of research that focuses on the interaction between humans and machine interfaces as applied to the sense of touch. A haptic interface is designed to increase the realism of tactile and kinesthetic sensations in applications such as virtual reality, teleoperation, and other scenarios where situational awareness is considered important, if not vital. This paper investigates the use of electric actuators and non-linear algorithms to provide force feedback to an input command device for providing haptics to the human operator. In particular, this work involves the study and implementation of a special case of feedback linearization known as inverse dynamics control and several outer loop impedance control topologies. It also investigates the issues concerned with force sensing and the application of model based controller functions in order to vary the desired inertia and the desired mass matrix. Results of the controllers’ abilities to display any desired impedance and provide the required kinesthetic constraint of virtual environments are shown on two experimental test rigs designed for this purpose.
Excitatory and inhibitory STDP jointly tune feedforward neural circuits to selectively propagate correlated spiking activity

Spike-timing-dependent plasticity (STDP) has been well established between excitatory neurons and several computational functions have been proposed in various neural systems. Despite some recent efforts, however, there is a significant lack of functional understanding of inhibitory STDP (iSTDP) and its interplay with excitatory STDP (eSTDP). Here, we demonstrate by analytical and numerical methods that iSTDP contributes crucially to the balance of excitatory and inhibitory weights for the selection of a specific signaling pathway among other pathways in a feedforward circuit. This pathway selection is based on the high sensitivity of STDP to correlations in spike times, which complements a recent proposal for the role of iSTDP in firing-rate based selection. Our model predicts that asymmetric anti-Hebbian iSTDP exceeds asymmetric Hebbian iSTDP for supporting pathway-specific balance, which we show is useful for propagating transient neuronal responses. Furthermore, we demonstrate how STDPs at excitatory–excitatory, excitatory–inhibitory, and inhibitory–excitatory synapses cooperate to improve the pathway selection. We propose that iSTDP is crucial for shaping the network structure that achieves efficient processing of synchronous spikes.
Expression of c‐myc, c‐raf‐1, and c‐Ki‐ras in azaserine‐induced pancreatic carcinomas and growing pancreas in rats

We examined the pattern of expression of several proto‐oncogenes during nonneoplastic growth and in acinar cell neoplasms in the rat pancreas. The levels of c‐myc, c‐raf‐1, and c‐Ki‐ras mRNAs were increased in regenerating pancreata following surgical partial pancreatectomy and following administration of camostat. We also investigated proto‐oncogene expression associated with the progression of pancreatic cancers in azaserine‐treated rats. Injection of a single dose (30 mg/kg) of azaserine (O‐diazoacetyl‐L‐serine) to 14‐d‐old rats leads to a variety of neoplastic lesions in the rat pancreas. Total RNA was isolated from lesions in various stages of tumor progression, including adenomas, carcinomas in situ, and invasive carcinomas. We observed increased expression of c‐myc, c‐raf‐1, and c‐Ki‐ras in azaserine‐induced adenomas and carcinomas. Actin expression was also increased in these tissues, whereas amylase expression was variable. However, when compared to the normal growing pancreas, the level of proto‐oncogene expression in the adenomas and carcinomas was disproportionate to the degree of cellular division in those tissues. Thus, the alterations induced by azaserine apparently caused a deregulated increase in expression of cellular oncogenes associated with growth regulation.
Fine‐scale genetic structure and dispersal in cooperatively breeding apostlebirds

In cooperatively breeding species, restricted dispersal of offspring leads to clustering of closely related individuals, increasing the potential both for indirect genetic benefits and inbreeding costs. In apostlebirds (Struthidea cinerea), philopatry by both sexes results in the formation of large (up to 17 birds), predominantly sedentary breeding groups that remain stable throughout the year. We examined patterns of relatedness and fine‐scale genetic structure within a population of apostlebirds using six polymorphic microsatellite loci. We found evidence of fine‐scale genetic structure within the study population that is consistent with behavioural observations of short‐distance dispersal, natal philopatry by both sexes and restricted movement of breeding groups between seasons. Global FST values among breeding groups were significantly positive, and the average level of pairwise relatedness was significantly higher for individuals within groups than between groups. For individuals from different breeding groups, geographical distance was negatively correlated with pairwise relatedness and positively correlated with pairwise FST. However, when each sex was examined separately, this pattern was significant only among males, suggesting that females may disperse over longer distances. We discuss the potential for kin selection to influence the evolution and maintenance of cooperative breeding in apostlebirds. Our results demonstrate that spatial genetic structural analysis offers a useful alternative to field observations in examining dispersal patterns of cooperative breeders.
Integrated safety of levodopa‐carbidopa intestinal gel from prospective clinical trials

Continuous administration of levodopa‐carbidopa intestinal gel (carbidopa‐levodopa enteral suspension) through a percutaneous endoscopic gastrojejunostomy is a treatment option for advanced Parkinson disease (PD) patients with motor fluctuations resistant to standard oral medications. Safety data from 4 prospective studies were integrated to assess the safety of this therapy.
Comparison of Chromogenic In Situ Hybridization and Fluorescence In Situ Hybridization for the Evaluation of MDM2 Amplification in Adipocytic Tumors

Atypical lipomatous tumor/well‐differentiated liposarcoma (ALT‐WDLPS) and dedifferentiated liposarcoma (DDLPS) are characterized cytogenetically by a 12q13–15 amplification involving the mouse double minute 2 (MDM2) oncogene. Fluorescence in situ hybridization (FISH) is used frequently to detect this amplification and aid with the diagnosis of these entities, which is difficult by morphology alone. Recently, bright‐field in situ hybridization techniques such as chromogenic in situ hybridization (CISH) have been introduced for the determination of MDM2 amplification status.
Sharing control of dispersed situated displays between nand residential users

As the number of public displays in the environment increases, new opportunities open up to improve situated interaction and to enable new kinds of applications. In order to make distributed display resources available to nomadic users, a key issue to address is how control can be dynamically shared between display users. It is important to study how control over a shared display can be acquired, released or shared by nomadic and residential users given their competing demands for display resources.In this paper, we present a system and a user study investigating these issues in the context of two applications both competing for display resources provided by a deployment of interactive office doorplates. The first application (Hermes II) provides situated note leaving and messaging services whereas the second one (GAUDI) supports user navigating a university department. Office occupants (i.,e. residential users) can control whether the navigation application may (temporarily) use their doorplate display (thus giving priority to the navigation needs of nomadic users to the department). We report on findings from a user study, and discuss interface design implications for specifying display control.
Effects of Quantity and Position of Guides on Pedestrian Evacuation

Guides play very important roles in leading pedestrians to evacuate when emergency occurs. An extended guided crowd model is adopted in this paper to investigate the influence of the quantity and position of guides on pedestrian evacuation dynamics. Simulation results indicate that the number of guides has relationship with evacuation efficiency, it is not the more guides the better evacuation effects. Furthermore, different positions of guides can result in different evacuation consequences, and the choice of the reasonable guides' positions has the relationship with the layout of the room and the density of pedestrians inside the room.
Fatores Associados ao Desempenho dos Concluintes de Cursos de Engenharia no ENADE 2011

Este artigo busca identificar, com dados do Exame Nacional de Desempenho dos Estudantes realizado em 2011 (Enade 2011) e por meio de modelagens hierarquico-lineares, fatores associados ao desempenho dos novos engenheiros formados no Brasil naquele ano. Espera-se, com isso, fornecer aos gestores das instituicoes e aos formuladores de politicas para o ensino superior indicios sobre o que se mostra mais relevante na formacao nas engenharias, principalmente no que concerne a fatores susceptiveis a interveniencia de decisoes gerenciais e/ou de formulacao de politicas. Nao obstante as limitacoes da base de dados e da endogeneidade esperada, os resultados reforcam a percepcao geral de que cursos seletivos de instituicoes publicas destacam-se na formacao de engenheiros, mas tambem apontam a importância, em muitos cursos, da disponibilidade do professor para atendimento fora do horario de aula e, ao menos nos cursos de engenharia de producao, da utilizacao de planos de ensino completos. Na media, auferem desempenho melhor os novos engenheiros que cursaram o ensino superior na idade correta e que passaram por escolas publicas durante o ensino medio. Ja mulheres e minorias etnicas ainda tem notas menores que homens que se declaram brancos. This paper applies multilevel models to Brazilian’s tertiary education assessment data in order to test whether some of the factors pointed out by the literature as relevant to achievement are associated with the performance of last year engineering students in 2011. Brazil is the only country where compulsory national exams are applied to last year tertiary education students. This sets a unique opportunity to model student achievement on tertiary education as a function of discretionary and non-discretionary factors. Results confirm that selective courses produce better-prepared graduates, but also show that out-of-class availability of teachers is positively associated to performance in most types of engineering courses, and well-designed teaching-and-learning plans seem to be particularly relevant for industrial students. In average, students coming from publicly run secondary schools and attaining engineering courses in the appropriate age perform better, but women and non-whites still achieve lower grades than white men.
CS 264 : Beyond Worst-Case Analysis Lecture # 5 : Parameterized Approximation and Running Time Guarantees ∗

Recall the two-step approach of parameterized analysis. The first step is to choose a natural parameterization of the inputs, which intuitively measures the “easiness” of an input. The second step is a performance analysis of an algorithm — running time, cost incurred, etc. — as a function of this parameter. We have already seen several examples. In Lecture #2, we gave three parameterized running time analyses of the Kirkpatrick-Seidel algorithm: a bound parameterized solely by the input size n (O(n log n)), a bound parameterized by both the input size and the output size h (O(n log h)), and a more complex “entropy parameter” necessary for proving the instance-optimality of the algorithm. Last lecture, we analyzed the page fault rate of the LRU paging algorithm, parameterized by the “degree of locality” of the input. This is our final lecture that focuses squarely on the parameterized analysis of algorithms, though the theme will resurface frequently in forthcoming lectures. Parameterized analysis can make inroads on all three of our goals (the Prediction/Explanation Goal, the Comparison Goal, and the Design Goal). First, parameterized analysis is strictly stronger and more informative than worst-case analysis parameterized solely by the input size. Last lecture we saw how such finer-grained analyses can achieve the Comparison Goal, allowing us to differentiate algorithms (like LRU vs. FIFO) that coarser analyses deem equivalent. Second, a parameterized performance guarantee suggests when — meaning on which inputs, or in which domains — a given algorithm should be used. (Namely, on the inputs where the performance of the algorithm is good! ) Such advice is progress toward the Prediction Goal and is often useful in practice, in scenarios where someone has no time and/or interest in developing their own novel algorithm for a problem, and merely wishes to be an
Chronic suppurative otitis media: Socio-economic implications in a tertiary hospital in Northern Nigeria

Background: In developing countries, ear infections and deafness are usually neglected conditions due to insufficient funds, work force, facilities, and knowledge. This paper highlights the socio-economic burden of chronic suppurative otitis media on a northern Nigerian population with suggestions on ways to reduce this burden. Method: Seventy-four patients presenting to the Otorhinolaryngology unit, Department of surgery, Jos University Teaching Hospital, Plateau state, Nigeria with chronic suppurative otitis media from June 2007 to May 2008 were evaluated for age, gender, occupation, otomicroscopy and audiologic findings, microscopy, culture and sensitivity results, cost of consultation, investigations and treatment, type of complications and the social impact on individuals. Results: Patients were aged 2 to 37 years (Mean age=9.23 years, SD=7.92). Forty-one (55.4%) patients were aged between 1 and 5 years. There were 8 (10.8%) students, 12 (16.2%) unskilled workers, 11 (14.9%) unemployed individuals and 2 (2.7%) professionals. Deafness was the commonest sequel. Minimum monthly wage was 7,500 ($47.5US). Initial cost of treatment per patient per year was 8,100 Naira ($51.3US) increasing to 73,100 Naira ($462.7US) if surgery and hearing aid was required. Eleven (15%) patients required surgery, only 2 (2.7%) patients could afford it. Four patients lost their jobs. Fourteen (18.9%) patients were lost to follow up. Conclusion: The estimated cost of treatment for chronic suppurative otitis media is higher than the monthly minimum wage for individuals in our environment where the cost of health care is the sole responsibility of the patient.
Size and aggregation of corticosteroids used for epidural injections.

OBJECTIVE The purpose of this study was to document particulate size in commonly used corticosteroid preparations. Inadvertent injection of particulate corticosteroids into a vertebral or foraminal artery can cause brain and spinal cord embolic infarcts and the size of the particles could be directly related to the chance that a clinically significant infarct would occur. One might assume that corticosteroids with particles significantly smaller than red blood cells might be safer. DESIGN The following four types of corticosteroid preparations were used in various solutions and evaluated under light microscopy: dexamethasone sodium phosphate injection, triamcinolone acetonide injectable suspension, betamethasone sodium phosphate and betamethasone acetate injectable suspension, and methylprednisolone acetate injectable suspension. RESULTS Dexamethasone sodium phosphate particle size was approximately 10 times smaller than red blood cells and the particles did not appear to aggregate; even mixed with 1% lidocaine HCl solution and with contrast dye, the size of the particles were unchanged. Triamcinolone acetonide and betamethasone sodium phosphate showed variable sizes; some particles were larger than red blood cells, and aggregation of particles was evident. Methylprednisolone acetate showed uniformity in size and the majority were smaller than red blood cells which were not aggregated, but the particles were densely packed. CONCLUSIONS Compared with the particulate steroid solutions, dexamethasone sodium phosphate had particles that were significantly smaller than red blood cells, had the least tendency to aggregation, and had the lowest density. These characteristics should significantly reduce the risk of embolic infarcts or prevent them from occurring after intra-arterial injection. Until shown otherwise in clinical studies, interventionalists might consider using dexamethasone or another corticosteroid preparation with similar high solubility and negligible particle size when performing epidural injections.
An algorithm for dynamically reconfigurable FPGA placement

In this paper, we introduce a new placement problem motivated by the Dynamically Reconfigurable FPGA (DRFPGA) architectures. Unlike traditional placement, the problem for DRFPGAs must consider the precedence constraints among logic components. For the placement, we develop an effective metric that can consider wirelength, register requirement, and power consumption simultaneously. With the considerations of the new metric and the precedence constraints, we then present a three-stage scheme of partitioning, initial placement generation, and placement refinement to solve the new placement problem. Experimental results show that our placement scheme with the new metric achieves respective improvements of 17.2%, 27.0%, and 35.9% in wirelength, the number of registers, and power consumption requirements, compared with the list scheduling method.
Channel and Energy Modeling for Self-Contained Wireless Sensor Networks in Oil Reservoirs

Wireless communication is the prerequisite for the highly desired in-situ and real-time monitoring capability in underground environments, including oil reservoirs, groundwater aquifers, volcano’s, among others. However, existing wireless communication techniques do not work in such environments due to the harsh transmission medium with very high material absorption and the inaccessible nature of underground environment that requires extremely small device size. Although Magnetic Induction (MI) communication has been shown to be a promising technique in underground environments, the existing MI system utilizes very large coil antennas, which are not suitable for deployment in underground. In this paper, we propose a metamaterial enhanced magnetic induction communication mechanism that can achieve over meter scale communication range by using millimeter scale coil antennas in the harsh underground environment. An analytical channel model for the new mechanism is developed to explore the fundamentals of metamaterial enhanced MI communication in various underground environments. The effects of important system and environmental factors are quantitatively captured, including the operating frequency, bandwidth, and parameters of metamaterial antennas, as well as permittivity, permeability, and conductivity of underground medium. The theoretical model is validated through the finite element simulation software, COMSOL Multiphysics.
DNA Microarray Analysis of Redox-Responsive Genes in the Genome of the Cyanobacterium Synechocystis sp. Strain PCC 6803

ABSTRACT Whole-genome DNA microarrays were used to evaluate the effect of the redox state of the photosynthetic electron transport chain on gene expression in Synechocystis sp. strain PCC 6803. Two specific inhibitors of electron transport, 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU) and 2,5-dibromo-3-methyl-6-isopropyl-p-benzoquinone (DBMIB), were added to the cultures, and changes in accumulation of transcripts were examined. About 140 genes were highlighted as reproducibly affected by the change in the redox state of the photosynthetic electron transport chain. It was shown that some stress-responsive genes but not photosynthetic genes were under the control of the redox state of the plastoquinone pool in Synechocystis sp. strain PCC 6803.