Miracle-dz/UniFAR-FTUs huggingface dataset:
Label-free Isolation and Enrichment of Cells Through Contactless Dielectrophoresis

Dielectrophoresis (DEP) is the phenomenon by which polarized particles in a non-uniform electric field undergo translational motion, and can be used to direct the motion of microparticles in a surface marker-independent manner. Traditionally, DEP devices include planar metallic electrodes patterned in the sample channel. This approach can be expensive and requires a specialized cleanroom environment. Recently, a contact-free approach called contactless dielectrophoresis (cDEP) has been developed. This method utilizes the classic principle of DEP while avoiding direct contact between electrodes and sample by patterning fluidic electrodes and a sample channel from a single polydimethylsiloxane (PDMS) substrate, and has application as a rapid microfluidic strategy designed to sort and enrich microparticles. Unique to this method is that the electric field is generated via fluidic electrode channels containing a highly conductive fluid, which are separated from the sample channel by a thin insulating barrier. Because metal electrodes do not directly contact the sample, electrolysis, electrode delamination, and sample contamination are avoided. Additionally, this enables an inexpensive and simple fabrication process. cDEP is thus well-suited for manipulating sensitive biological particles. The dielectrophoretic force acting upon the particles depends not only upon spatial gradients of the electric field generated by customizable design of the device geometry, but the intrinsic biophysical properties of the cell. As such, cDEP is a label-free technique that avoids depending upon surface-expressed molecular biomarkers that may be variably expressed within a population, while still allowing characterization, enrichment, and sorting of bioparticles. Here, we demonstrate the basics of fabrication and experimentation using cDEP. We explain the simple preparation of a cDEP chip using soft lithography techniques. We discuss the experimental procedure for characterizing crossover frequency of a particle or cell, the frequency at which the dielectrophoretic force is zero. Finally, we demonstrate the use of this technique for sorting a mixture of ovarian cancer cells and fluorescing microspheres (beads).
Fast-time filtering with multichannel SAR

Large regions of a Synthetic Aperture Radar (SAR) image can potentially be destroyed by an airborne broadband jammer. Jammer components include both the direct-path and multipath reflections from the ground, known as hotclutter or terrain scattered interference. Using multiple antennas on a SAR provides spatial degrees of freedom and allows for beamforming to reject the direct-path signal. However, to effectively suppress non-stationary hot-clutter components, fast-time taps from within a pulse have shown to be effective for airborne radar, [1]-[2]. The goal of interference suppression for SAR is to successfully suppress these interferences while not significantly effecting the image quality by blurring, reducing the resolution or raising the side-lobe level. This paper looks at two fast-time STAP algorithms, the Minimum Variance Distortionless Response (MVDR) and the Generalised Sidelobe Canceller (GSC) to study the effect of non-stationary interference suppression for SAR images.
Bridging physical and virtual worlds with electronic tags

The role of computers in the modern office has divided ouractivities between virtual interactions in the realm of thecomputer and physical interactions with real objects within thetraditional office infrastructure. This paper extends previous workthat has attempted to bridge this gap, to connect physical objectswith virtual representations or computational functionality, viavarious types of tags. We discuss a variety of scenarios we haveimplemented using a novel combination of inexpensive, unobtrusiveand easy to use RFID tags, tag readers, portable computers andwireless networking. This novel combination demonstrates theutility of invisibly, seamlessly and portably linking physicalobjects to networked electronic services and actions that arenaturally associated with their form.
Supervised Neural Network Training with a Hybrid Global Optimization Technique

A novel hybrid global optimization method applied for feedforward neural networks (NN) supervised learning is investigated. The network weights are determined by minimizing the traditional mean-square error function. The optimization technique, called GLPtauS is a combination of novel global optimization heuristic search based on low-discrepancy sequences of points, called LPtau Optimization (LPtauO), a Genetic Algorithm, and a Simplex local search. The proposed method is initially tested on 10 multimodal mathematical functions of 30 and 100 dimensions. Subsequently, it is applied for training moderate size NN for function fitting and solving benchmark classification problems, such as the parity problem (XOR and 4-Parity), Iris dataset, and a medical diagnosis problem (Diabetes). The investigated technique is also tested on predicting continuous output of a mechanical system dataset (Servo). Finally, the results are analysed, discussed, and compared with others.
Analysis of quantum effects in nonuniformly doped MOS structures

This paper presents results from the self-consistent solution of Schrodinger and Poisson equations obtained in one-dimensional (1-D) nonuniformly doped MOS structures suitable for the fabrication of very short transistors. Different issues are considered and investigated, including quantum-induced threshold voltage shifts, low-field electron effective mobility and gate-to-channel capacitance. The reported results give indications for the optimization of n-MOS channel doping profiles suitable for the fabrication of ultrashort MOSFETs.
Shape and arrangement of columns in cat's striate cortex

Cells in the cat's striate cortex show marked specificity in their responses to restricted retinal stimulation (Hubel & Wiesel, 1959, 1962). The most effective stimulus shapes are long narrow rectangles of light ('slits'), dark bars against a light background ('dark bars'), and straight-line borders separating areas of different brightness ('edges'). A given cell responds vigorously when an appropriate stimulus is shone on the receptive field or moved across it, provided the stimulus is presented in a specific orientation. This orientation is termed the 'receptive-field axis orientation'. It is critical, and constant for any particular cell, but may differ for different cells. The visual cortex is subdivided into discrete regions or columns extending from surface to white matter, in which all cells have the same receptivefield axis orientation (Hubel & Wiesel, 1962). The present experiments were undertaken with the object of learning more about the anatomical configuration of the columns. We wished to have a clearer idea of their shape, especially if the walls of a column were, as previous work suggested, parallel to the radial fibre bundles of the cortex and perpendicular to the cortical layers, and whether the columns were uniform or irregular in their cross-sectional shape and size. Furthermore, we were curious to know if there was any relationship between the receptive-field axis orientations of neighbouring columns, or whether, on the contrary, the different columns were intermixed in a random way throughout the cortex. These questions were approached: (1) by making several deep, closely spaced, parallel micro-electrode penetrations, placing electrolytic lesions at every shift in receptive-field orientation, and(2) by making many short penetrations in a small cortical area, noting the axis orientation of cells lying in the upper one or two layers of cortex.
Urokinase-Deficient Mice Fail To Generate a Type 2 Immune Response following Schistosomal Antigen Challenge

ABSTRACT Activated lymphocytes express urokinase-type plasminogen activator (uPA). Previous work suggests that uPA modulates T-lymphocyte responses. Mice deficient in uPA (uPA−/−) fail to generate type 1 (T1) immune responses during infection with Cryptococcus neoformans. Failure to generate either a T1 or a T2 immune response is not predictive of defects in the alternative response. Conversely, down-regulation of one type of immune response may result in inappropriate overactivation of the other. It is not known whether the immune defect in uPA−/− mice affects only T1 responses or whether T2 responses are also impaired. Impairment of both T1 and T2 responses would suggest a global T-cell defect in the absence of uPA. To determine the role of uPA in T2 immune responses, wild-type (WT) and uPA−/− mice were primed and challenged with schistosomal egg antigen (SEA). This elicits strong polarization to T2 immune responses in immunocompetent mice. The challenged WT mice developed delayed-type hypersensitivity (DTH) to SEA; high levels of serum immunoglobulin E (IgE); a strong T2 cytokine phenotype with markedly elevated levels of interleukin-4 (IL-4), IL-5, and IL-13; and eosinophil-rich pulmonary granulomas. uPA−/− mice failed to develop DTH to SEA; did not polarize Ig production to IgE; did not produce high levels of IL-4, IL-5, or IL-13; and had markedly reduced numbers of granuloma-associated eosinophils. uPA−/− mice fail to generate polarized T2 immune responses to a T2-inducing pathogen. These findings, in conjunction with our previous work, demonstrate that mice deficient in uPA have profoundly impaired immunity involving both T1 and T2 polarization and are largely immunologically unresponsive.
Using Syntax-Based Machine Translation to Parse English into Abstract Meaning Representation

We present a parser for Abstract Meaning Representation (AMR). We treat English-to-AMR conversion within the framework of string-to-tree, syntax-based machine translation (SBMT). To make this work, we transform the AMR structure into a form suitable for the mechanics of SBMT and useful for modeling. We introduce an AMR-specific language model and add data and features drawn from semantic resources. Our resulting AMR parser improves upon state-of-the-art results by 7 Smatch points.
Molar and Molecular Models of Performance for Rewarding Brain Stimulation

This dissertation reports analyses of performance for rewarding brain stimu- lation in a three-part sequential task. A session of self-stimulation was composed of three trial types, during which the strength and opportunity cost of electrical stim- ulation were kept constant. Within a trial, a lever allowed animals to harvest brain stimulation rewards as soon as the lever had been held for a set, cumulative amount of time. When the time spent holding reached this criterion, the lever retracted and a burst of rewarding electrical stimulation was delivered. A flashing house light and 10s inter-trial interval signalled the start of a new trial. Rats were presented with strong/inexpensive/certain stimulation on one trial, a randomly selected strength, cost and risk on the next trial, and weak/inexpensive/certain stimulation on the third trial of a sequence. The sequence then repeated. Rewards during the second trial of this sequence were delivered with cued probabilities ranging from 0.5 to 1.0. The current thesis evaluates the ability of a previously published (molar) model of performance during a trial to accurately detect the effect of risk on payoff but not reward intensity. Although animals were less willing to work for stimulation trains that may not be delivered than those delivered with certainty, risk did not change the relative reward produced by stimulation. We also present evidence on a fine time scale that self-stimulating rats develop a model of their world. The first pause made as a trial began was a function of the payoff the animal had yet to receive, indicat- ing that rats had a model of the triad sequence. Analysis of the conditions under which pauses were uncharacteristic also provides evidence of what this model might be. Analysis of the fine scale of performance provides evidence that animals had a model of the stability of trial conditions. Finally, we present a (molecular) model of performance for brain stimulation rewards in real-time. Our results demonstrate that rats develop a model of the testing paradigm and can adjust to changes in reward contingencies with as few as one exemplar.
Active Role of Glutamate Uptake in the Synaptic Transmission from Retinal Nonspiking Neurons

We examined the role of glutamate uptake in the synaptic transmission of graded responses from newt retinal bipolar cells (BCs) to ganglion layer cells (GLCs). In dissociated Müller cells (retinal glia), glutamate evoked an uptake current that was effectively inhibited byl-trans-pyrrolidine-2,4-dicarboxylic acid (PDC). PDC had no effect on the non-NMDA receptors of dissociated spiking neurons. In the retinal slice preparation, dual whole-cell recordings were performed from a pair of BC and GLC. A depolarizing pulse applied to a BC activated the Ca2+ current (ICa) in the BC and evoked an EPSC in the GLC. Application of PDC prolonged both non-NMDA and NMDA receptor-mediated components of the evoked EPSC but changed neither the amplitude nor time course of ICa. When the slice preparation was superfused with a solution containing glutamate but not PDC, the evoked EPSC decreased in amplitude without changing the time course, suggesting that the prolongation of the evoked EPSC is not attributable to a simple increase in ambient glutamate concentration after inhibition of glutamate uptake. Because PDC did not affect the amplitude, time course, or frequency of spontaneous EPSCs, it is unlikely that PDC modified presynaptic and/or postsynaptic mechanisms. These results indicate that inhibition of glutamate uptake slows the clearance of glutamate accumulated in the synaptic cleft by multiple quantal release and prolongs the evoked EPSC. The role of glutamate uptake at synapses in the inner retina is not only to maintain the extracellular glutamate concentration at a low level but also to terminate the light-evoked EPSCs rapidly.
Moderating effects of coping on associations between stress reactivity and internalizing and externalizing problems

The present study was motivated by a need to employ multilevel studies to better understand why the experience of stressful life events is predictive of increased rates of psychopathology. Specifically, this study aimed to test the moderating role of coping on associations between stress reactivity (autonomic arousal) and broad-spectrum internalizing and externalizing problems in a normative sample. Participants were 140 adolescents and emerging adults (ages 14-30 years; 60% female) who completed questionnaires on coping, stressful life events, personality, and behavioral/emotional problems. Skin conductance and heart rate data were also measured while participants completed two laboratory stress tasks: a public speaking task and a task involving serial subtraction. Path analytic results suggested negative main effects for primary and secondary control coping, and positive main effects for disengagement coping, on internalizing and externalizing problems. Evidence was also found for interactive effects of skin conductance reactivity to the public speaking task and secondary control coping on externalizing problems for adolescents only, such that there was a negative association between SCL reactivity and externalizing problems for individuals reporting low use of secondary control coping, but SCL reactivity and externalizing problems were unrelated for individuals reporting high use of secondary control coping. Associations were also found between personality variables and both coping and internalizing and externalizing problems, but not with autonomic arousal. Although a priori hypotheses regarding interaction effects were mainly unsupported, results from the present study suggest that future research examining the interplay among stress reactivity, coping, and personality will be important in furthering our understanding of the development of psychopathology and helping to tailor effective efforts at prevention and intervention.
Perceived partner commitment and implicit self-esteem predicts connectedness accessibility in response to relationship threat

The current research examined the impact of perceived partner commitment, implicit self-esteem, and relationship threat on connectedness. The present study predicted that individuals with high (versus low) implicit self-esteem are more likely to access connectedness goals (on an unconscious level) after experiencing a relationship threat, when they perceive their significant others are highly committed to the relationship. This relation between implicit self-esteem and connectedness goal accessibility will not be evident in the control condition. The findings reveal perceived partner commitment moderated the relation between implicit self-esteem and relationship threat on accessing connectedness goals. However, people with high implicit self-esteem were more likely to access connectedness goals after experiencing a relationship threat, when partner commitment was low, not high. A discussion of why the results are opposite to the predictions is presented.
Morph-fitting: Fine-Tuning Word Vector Spaces with Simple Language-Specific Rules

Morphologically rich languages accentuate two properties of distributional vector space models: 1) the difficulty of inducing accurate representations for low-frequency word forms; and 2) insensitivity to distinct lexical relations that have similar distributional signatures. These effects are detrimental for language understanding systems, which may infer that ‘inexpensive’ is a rephrasing for ‘expensive’ or may not associate ‘acquire’ with ‘acquires’. In this work, we propose a novel morph-fitting procedure which moves past the use of curated semantic lexicons for improving distributional vector spaces. Instead, our method injects morphological constraints generated using simple language-specific rules, pulling inflectional forms of the same word close together and pushing derivational antonyms far apart. In intrinsic evaluation over four languages, we show that our approach: 1) improves low-frequency word estimates; and 2) boosts the semantic quality of the entire word vector collection. Finally, we show that morph-fitted vectors yield large gains in the downstream task of dialogue state tracking, highlighting the importance of morphology for tackling long-tail phenomena in language understanding tasks.
SEMANTIC SIMILARITY KNOWLEDGE AND ITS APPLICATIONS

Semantic relatedness refers to the degree to which two concepts or words are related. Humans are able to easily judge if a pair of words are related in some way. For example, most people would agree that apple and orange are more related than are apple and toothbrush. Semantic similar- ity is a subset of semantic relatedness. In this article we describe several methods for computing the similarity of two words, following two directions: dictionary-based methods that use WordNet, Roget's thesaurus, or other re- sources; and corpus-based methods that use frequencies of co-occurrence in corpora (cosine method, latent semantic indexing, mutual information, etc). Then, we present results for several applications of word similarity knowl- edge: solving TOEFL-style synonym questions, detecting words that do not t into their context in order to detect speech recognition errors, and syn- onym choice in context, for writing aid tools. We also present a method for computing the similarity of two short texts, based on the similarities of their words. Applications of text similarity knowledge include: designing exercises for second language-learning, acquisition of domain-specic corpora, informa- tion retrieval, and text categorization. Before concluding, we briey describe cross-language extensions of the methods for similarity of words and texts.
Requirement of cell nucleus for Sindbis virus replication in cultured Aedes albopictus cells

The ability of Sindbis virus to grow in enucleated BHK-21 (vertebrate) and Aedes albopictus (invertebrate) cells was tested to determine the dependence of this virus upon nuclear function in these two phylogenetically unrelated hosts. Although both cell types could be demonstrated to produce viable cytoplasts (enucleated cells) which produced virus-specific antigen subsequent to infection. BHK cytoplasts produced a significant number of progeny virions, whereas mosquito cytoplasts did not. The production of vesicular stomatitis virus in mosquito cells was not significantly reduced by enucleation. That such a host function was not essential for vesicular stomatitis virus growth in insect cells is supported by the observation that the production of this virus by mosquito cells is not actinomycin D sensitive. This result agrees with a previously published report in which it was shown that Sindbis virus maturation in invertebrate cells is inhibited by actinomycin D, indicating a possible requirement for host cell nuclear function (Scheefers-Borchel et al., Virology, 110:292-301, 1981).
Quantifying uncertainty in partially specified biological models: how can optimal control theory help us?

Mathematical models in biology are highly simplified representations of a complex underlying reality and there is always a high degree of uncertainty with regards to model function specification. This uncertainty becomes critical for models in which the use of different functions fitting the same dataset can yield substantially different predictions—a property known as structural sensitivity. Thus, even if the model is purely deterministic, then the uncertainty in the model functions carries through into uncertainty in model predictions, and new frameworks are required to tackle this fundamental problem. Here, we consider a framework that uses partially specified models in which some functions are not represented by a specific form. The main idea is to project infinite dimensional function space into a low-dimensional space taking into account biological constraints. The key question of how to carry out this projection has so far remained a serious mathematical challenge and hindered the use of partially specified models. Here, we propose and demonstrate a potentially powerful technique to perform such a projection by using optimal control theory to construct functions with the specified global properties. This approach opens up the prospect of a flexible and easy to use method to fulfil uncertainty analysis of biological models.
Corticocortical connections of area F3 (SMA‐proper) and area F6 (pre‐SMA) in the macaque monkey

The monkey mesial area 6 comprises two distinct cytoarchitectonic areas: F3 [supplementary motor area properly defined (SMA‐proper)], located caudally, and F6 (pre‐SMA), located rostrally. The aim of the present study was to describe the corticocortical connections of these two areas. To this purpose restricted injections of neuronal tracers (wheat germ‐agglutinin conjugated to horseradish peroxidase, fluorescent tracers) were made in different somatotopic fields of F3, F6, and F1 (area 4) and their transport plotted.
Proper authentication of ancient DNA is essential, yes; but so are undogmatic approaches.

1 Environmental Microbiology Laboratory, Department of Biology, University of Puerto Rico, San Juan, Puerto Rico 00932; 2 Center for Applications in Biotechnology, California Polytechnic State University, San Luis Obispo, CA, USA 93407; 3 Department of Biology, California Polytechnic State University, San Luis Obispo, CA, USA 93407; 4 Institute for Life Science Entrepreneurship, Union, NJ, USA 07083; 5 Department of Translational Research on New Technologies in Medicine and Surgery, Division of Paleopathology, University of Pisa, Pisa 56126, Italy; 6 Center for Anthropological, Paleopathological and Historical Studies of the Sardinian and Mediterranean Populations, Department of Biomedical Sciences, University of Sassari, Sassari 07100, Italy