gebhart/patrepeval huggingface dataset:
The Shape of Sight: A Homological Framework for Unifying Visual Perception (2018)

Visual perception, the brain's construction of a stable world from sensory data, faces several long-standing, fundamental challenges. While often studied separately, these problems have resisted a single, unifying computational framework. In this perspective, we propose a homological framework for visual perception. We argue that the brain's latent representations are governed by their topological parity. This parity interpretation functionally separates homological structures into two distinct classes: 1) Even-dimensional homology ($H_{even}$) acts as static, integrative scaffolds. These structures bind context and content into ``wholes'' or ``what'', serving as the stable, resonant cavities for perceptual objects; 2) Odd-dimensional homology ($H_{odd}$) acts as dynamic, recurrent flows. These structures represent paths, transformations, and self-sustaining ``traces'' or ``where'' that navigate the perceptual landscape. This scaffold-and-flow model is supported by the ventral-dorsal pathway separation and provides a unified solution to three core problems in visual perception. Homological parity hypothesis recasts visual perception not as a linear computation, but as a dynamic interaction between stable, integrative structures and the recurrent, self-sustaining flows that run on them. This perspective offers a new mathematical foundation for linking neural dynamics to perception and cognition.
Lasing and intermode correlation of whispering gallery mode in dye-doped polystyrene microspheres (1996)

The advantage of organic materials like polystyrene is their plasticity so that they can be made into any shape. Polystyrene has a rather large refractive index of 1.58 and can be easily doped with the required laser dye and also can be made into spheres of the required size. Fabrication of microspheres was basically carried out by J. Vanderhoff and his assistants at Lehigh University. The host material in all of these samples is polystyrene. Microspheres doped with Bis-MSB, PPO and alpha-NPO dyes were studied with suitable lasers like UV, N<SUB>2</SUB> and XeCl excimer. We have observed enhanced emission and lasing action at certain wavelengths which correspond to the whispering gallery modes of polystyrene spheres. Characterization of the lasing process in microspheres with respect to their sizes will be presented. The 2D crystalline structure on a periodic array thin films of polystyrene microspheres has been studied by both diffraction and microscopic techniques and will be presented as well.
Tailoring the refractive index of nanoimprint resist by blending with TiO_2 nanoparticles (2014)

We demonstrate that blending of TiO2 nanoparticles into nanoimprint polymer resist yields a composite material with an increased optical refractive index suitable for nanoimprint lithography. Complex refractive indices of n400nm = 1.94-i0.009, n500nm = 1.86-i0.003, and n600nm = 1.83-i0.002 are predicted for composite materials with 30% TiO2 nanoparticles of 35-nm diameter in Amonil UV nanoimprint resist. Layers with concentrations of 1 to 30 volume% of TiO2 nanoparticles blended into the composite resist material are prepared by spin-coating. Good agreement between measured and predicted optical properties is obtained. Using the composite imprint resist periodic linear gratings with periods of 370 nm are fabricated on glass substrates using UV nanoimprint lithography. Subsequently, an organic light emitting diode (OLED) is fabricated on top of the grating. Due to the high-index grating structure, waveguide modes are extracted from the OLED, which are observed in the OLED emission spectrum.
ANSwer: Combining NFV and SDN features for network resilience strategies (2016)

Software-Defined Networking (SDN) relies on open programmability of network devices, which is achieved by defining new communication interfaces, network operating systems, and changing the traditional decision-making logic of regular TCP/IP networks. Network Functions Virtualization (NFV), in turn, permits virtualizing network functions that are traditionally performed by physical middleboxes (e.g., firewalling and intrusion detection/prevention). Although SDN and NFV improve the flexibility of the management of computer networks, SDN remains vulnerable to major network security problems, such as Distributed Denial of Service (DDoS) attacks. These attacks typically result in the disruption of network services and resources. In this paper, we introduce ANSwer, an architecture that combines NFV and SDN features to create sophisticated network resilience strategies. ANSwer relies on a feedback control-loop which explores SDN features to monitor and analyze the behavior of the network infrastructure, indicating whether parts of an existing resilience strategy can be reconfigured to achieve more satisfactory results, or if an entire resilience strategy needs to be added or replaced. Our experiments demonstrate that ANSwer can rapidly identify and handle distinct anomalies in different scenarios, indicating that the reconfiguration and deployment of resilience strategies can be performed in real-time.
P1 plasmid replication: multiple functions of RepA protein at the origin. (1985)

Replication functions of a bacteriophage P1 miniplasmid are carried on a 1.2-kilobase pair (kb) segment that can be subdivided into a 245-base pair (bp) replication origin and a 959-bp region that encodes a protein required for replication (RepA). The origin region contains five 19-bp direct repeats. By using primer extension and gene-fusion assays, we mapped the promoter of the repA gene within the repeated sequences and showed that the promoter is repressed by RepA. Regulation of RepA synthesis is apparently achieved by the binding of RepA to the repeat sequences. This regulation might be a key step in the replication-control circuit, as we found that overproduction of RepA (from a foreign promoter) inhibits replication. Thus, in addition to being an autoregulated activator of replication, the protein also can have a negative regulatory role.
Fibrillar organization of fibronectin is expressed coordinately with cell surface gangliosides in a variant murine fibroblast. (1986)

NCTC 2071A cells, a line of transformed murine fibroblasts, grow in serum-free medium, are deficient in gangliosides, synthesize fibronectin, but do not retain and organize it on the cell surface. When the cells are exposed to exogenous gangliosides, fibrillar strands of fibronectin become attached to the cell surface. A morphologically distinct variant of NCTC 2071A cells was observed to both retain cell surface fibronectin and organize it into a fibrillar network when the cells were stained with anti-fibronectin antibodies and a fluorescent second antibody. A revertant cell type appeared to resemble the parental NCTC 2071A cells in terms of morphology and fibronectin organization. All three cell types were subjected to mild NaIO4 oxidation and reduction with KB3H4 of very high specific radioactivity in order to label the sialic acid residues of surface gangliosides. The variant had much more surface gangliosides than the parental, particularly more complex gangliosides corresponding to GM1 and GD1a. The surface gangliosides of the revertant were intermediate between the parental and the variant. By using sialidase, which hydrolyzes GD1a to GM1, and 125I-labeled cholera toxin, which binds specifically to GM1, the identity and levels of these gangliosides were confirmed in the three cell types. When variant cells were exposed to sialidase for 2 d, there appeared to be little change in fibronectin organization. Concomitant treatment of the cells with the B subunit of cholera toxin, which bound to all the surface GM1 including that generated by the sialidase, however, eliminated the fibrillar network of fibronectin. In addition, exposure of the variant cells to a 70,000-mol-wt fragment of fibronectin, which lacks the cell attachment domain but contains a matrix assembly domain, inhibited the formation of fibers. Finally, all three cell types were assayed for their ability to attach to and spread on fibronectin-coated surfaces; no significant differences were found. Our results further establish that the ability of a cell to organize fibronectin into an extracellular matrix is dependent on certain gangliosides, but they also indicate that cell adhesion to fibronectin is independent of these gangliosides. We suggest that matrix organization and cell attachment and spreading are based on separate mechanisms and that these functions are associated with different cell surface "receptors."
Manganese Levels in a Jaundiced Long‐Term Total Parenteral Nutrition Patient: Potentiation of Haloperidol Toxicity?: Case Report and Literature Review (1990)

Manganese is vital in human nutrition. When oral intake is precluded, the recommended parenteral supplementation is 0.15 to 0.8 mg/day. Manganese is excreted primarily in the bile; during cholestasis, serum manganese levels may rise, and manganese toxicity ensue. Neuropsychiatric symptoms are prominent. Phenothiazine-derivative drugs may potentiate manganese toxicity. Serum or whole blood manganese levels should guide manganese therapy in jaundiced patients.
Clock tree optimization in synchronous CMOS digital circuits for substrate noise reduction using folding of supply current transients (2002)

In a synchronous clock distribution network with zero latencies, digital circuits switch simultaneously on the clock edge, therefore they generate substrate noise due to the sharp peaks on the supply current. We present a novel methodology optimizing the clock tree for less substrate generation by using statistical single cycle supply current profiles computed for every clock region taking the timing constraints into account. Our methodology is novel as it uses an error-driven compressed data set during the optimization over a number of clock regions specified for a significant reduction in substrate noise. It also produces a quality analysis of the computed latencies as a function of the clock skew. The experimental results show >x2 reduction of substrate noise generation from the circuits having four clock regions of which the latencies are optimized.
Active pixel sensors on high-resistivity silicon and their readout (2002)

The concept of X-ray active matrix pixel sensor (XAMPS) is introduced. XAMPSs are direct illumination, position sensitive X-ray detectors with the possibility of containing 1000 000 pixels. They count the number of diffracted X-rays in each pixel by measuring the total charge released by converted X-rays in the body of the sensor. Readout is accomplished with a relatively small number of channels equal to the square root of the number of pixels. The estimated readout time can be about 1 ms. Noise of the readout electronics can be so low that practically no additional fluctuations in the number of incident X-rays per pixel are added and, therefore, the XAMPS performance is very close to that of an ideal detector for X-ray crystallography.
Photoperiod differentially regulates the expression of Per1 and ICER in the pars tuberalis and the suprachiasmatic nucleus of the Siberian hamster (2000)

Abstract Previous studies demonstrated that the clock gene Per1 and the transcription factor ICER are expressed rhythmically in the suprachiasmatic nucleus (SCN) and in the pars tuberalis (PT). In the Syrian hamster the duration of photoperiod affects the amplitude of gene expression in the PT, and melatonin administered before lights‐on suppressed the peak of Per1/ICER expression; these effects were not seen in the SCN. It was speculated that the inefficacy of melatonin was due to the low density of melatonin receptors in the SCN of this species. The aim of the present study was to determine whether this phenomenon also occurs in the Siberian hamster, which expresses a higher density of melatonin receptors in the SCN. Male Siberian hamsters were housed in long days (16 h light : 8 h dark) or short days (8 h light : 16 h dark) and expression of Per1 and ICER mRNA was studied by in situ hybridization. The expression of Per1 and ICER mRNA in the PT peaked 3 h following lights‐on (ZT3) under both photoperiods. The amplitudes of these peaks were greatly attenuated under short photoperiod. In the SCN, the duration of Per1 gene expression was proportional to the length of the light phase, but only a modest amplitude effect was observed. Injections of melatonin (25 μg) 1 h before lights‐on significantly reduced the expression of both genes in the PT at ZT3, but had no effect in the SCN. These data demonstrate that photoperiod‐dependent amplitude modulation of Per1 and ICER gene expression in the PT is conserved across species, and reinforce the argument that this phenomenon is driven by melatonin.
Joint Transmitter Power Control and Mobile Cache Management in Wireless Computing (2008)

We investigate efficient schemes for data communication from a server (base station and access point) to a mobile terminal over a wireless channel of randomly fluctuating quality. The terminal user generates requests for data items. If the buffer (cache) of the terminal contains the requested data, no access delay/latency is incurred. If not, the data is downloaded from the server, and until becoming available locally at the terminal, the user incurs a delay cost. Moreover, a transmission/power cost is incurred to transmit the data over the wireless link at a dynamically selected power level. To lower both the access delay and transmission costs, the system may prefetch data predictively and cache them on the terminal (especially during high-link-quality periods), anticipating future user requests. The goal is to jointly minimize the overall latency and power costs by dynamically choosing what data to (pre)fetch, what power level to use, and when to use it. We develop a modeling framework (based on dynamic programming and controlled Markov chains) that captures essential performance trade-offs. It allows for the computation of optimal decisions regarding what data to (pre)fetch and what power levels to use. To cope with emerging complexities, we then design efficient online heuristics whose simulation analysis demonstrates substantial performance gains over standard approaches.
Spatial HRTF Interpolation using Spectral Phase Constraints (2020)

In this paper, a novel method for spatial Head Related Transfer Function (HRTF) interpolation is proposed. The property of linearity of HRTF spectral phase with frequency is first illustrated. An optimization problem is then formulated to compute the interpolated HRTF phase by imposing linearity constraints on the spectral phase of adjacent spatial angles. A weighted error minimization is carried out in an alternating optimization framework to obtain the solution to this problem. Phase-only reconstruction is used to obtain the HRIR for subsequent rendering of binaural audio. Interpolated HRTFs obtained by using the CIPIC and SYMARE database are evaluated using statistical analysis. Subjective evaluations are also performed to evaluate the quality of the binaural audio rendered using the proposed method.
Tri-dimensional elastic-plastic fem of rolling force during strip finishing rolling process (2005)

A tri-dimensional elastic-plastic rolling model is developed using the software ANSYS/LS-DYNA.FEM. Calculations of rolling force for different temperature,strip thickness and depression are made by this model. Comparing rolling force values of the FEM calculation with theoretical calculation showed that the relative error between them was less than 11?%。
High-resolution digital retroillumination imaging of the posterior lens capsule after cataract surgery (1997)

This system produced excellent images for objective documentation and quantitative measurement of PCO.
Determination of minimal sequence for binding of an aptamer. A comparison of truncation and hybridization inhibition methods (2014)

A thermodynamic analysis of the effects of truncation or competitive hybridisation of an aptamer on target binding is presented.
Genome-based drug discovery: prioritizing disease-susceptibility/disease-associated genes as novel drug targets for schizophrenia. (2003)

The search for new classes of antipsychotics based on novel targets identified from linkage/linkage association in diseased cohorts and microarray approaches using tissue from affected individuals is a high priority in central nervous system research. Genes linked to schizophrenia, a disease affecting 1% of the population, have been identified on nearly every chromosome of the human genome leading to a diverse choice of targets for validation. Interestingly, while the majority of currently used antipsychotic medications act by blocking dopamine receptors, there have been few genetic studies implicating the dopamine receptor family in disease etiology. Recently, four genes have been identified that encode dysbindin, neuroregulin, D-amino acid oxidase and G72, respectively, that support previous studies suggesting that schizophrenia may result from a hypofunction of glutamatergic neurotransmission. Linkage and microarray studies have similarly supported studies implicating the alpha 7 neuronal nicotinic receptor in the etiology of schizophrenia. Microarray studies using brain tissue from schizophrenic patients have shown changes in gene expression that number in the thousands, involving a number of proteins related to synaptic structure and function (PSYN gene group) and cellular metabolism. The majority of these proteins are not traditional drug discovery targets, nor are their functional roles in schizophrenia obvious, providing a challenge to validate them from the drug target identification/drug discovery perspective. The current state-of-the-art in genome-based approaches to schizophrenia, target discovery highlights a need for a multidisciplinary, integrative, null hypothesis-based approach to sort through these novel genes as drug targets.
The Emergence of Augmented Reality (AR) as a Storytelling Medium in Journalism (2013)

Digital technology holds the potential to transform journalism and the media in several beneficial ways, including new forms of storytelling that might better engage citizens and provide more context, nuance, and texture to reported events and issues. However, the extent to which these benefits have been realized is mixed and subject to debate. In this monograph, we examine how digital technology might transform the content of journalism through augmented reality (AR). The significance of digital storytelling through AR is manifest in its potential to engage a citizenry increasingly disengaged from traditional news and to provide more contextualized information.
Binding sites of a novel neuropeptide pituitary‐adenylate‐cyclase‐activating polypeptide in the rat brain and lung (1990)

Pituitary-adenylate-cyclase-activating polypeptide (PACAP) is a novel 38-amino-acid neuropeptide isolated from ovine hypothalamic tissues based on its activity of stimulating adenylate cyclase of rat pituitary cells. Binding sites for PACAP were studied in rat tissue membranes using a 27-amino-acid N-terminal derivative of PACAP [PACAP(1-27)] labelled with 125I. Particularly high specific binding sites of 125I-PACAP(1-27) were noted in the hypothalamus, brain stem, cerebellum and lung. Specific binding sites are also present in the pituitary gland, but at a lower concentration, and mainly in the anterior lobe. Very low concentration of 125I-PACAP(1-27)-binding sites were found in the colon, aorta and kidney membranes and no binding sites were detected in the pancreas and testis. Maximal binding of 125I-PACAP(1-27) was observed at pH 7.4. Interaction of 125I-PACAP(1-27) with its binding site was rapid, specific and saturable as well as time, pH and temperature dependent. PACAP(1-27) is more potent than PACAP in displacing the binding of 125I-PACAP(1-27) with brain membranes [concentration that inhibits 50% of the binding (IC50) = 7.45 +/- 1.52 nM and 11.45 +/- 3.65 nM, respectively; mean +/- SEM, n = 4] and lung membranes (IC50 = 4.41 +/- 0.87 nM and 10.68 +/- 3.09 nM, respectively). Vasoactive intestinal peptide displaced the binding of 125I-PACAP(1-27) in lung membrane (IC50 = 16.88 +/- 5.14 nM) but not in brain membranes. The equilibrium binding of 125I-PACAP(1-27) at 4 degrees C was characterized by a single class of binding site for the brain membrane with a dissociation constant (Kd) of 2.46 +/- 0.53 nM and a maximal binding capacity (Bmax) of 8.44 +/- 3.13 pmol/mg protein, but there were two classes of binding site for lung membranes with Kd of 1.02 +/- 0.51 nM and 5.19 +/- 0.99 nM, and Bmax of 2.84 +/- 0.72 pmol/mg protein and 9.13 +/- 1.89 pmol/mg protein, respectively. These findings suggest that subtypes of PACAP-binding sites exist and PACAP may have a physiological role in the hypothalamus/pituitary axis as well as in other regions of the brain and lung.
On the orchestration of dorsal closure in drosophila melanogaster: from tissue-scale control to cellular-scale remodelling (2016)

La gran diversidad de vida en la tierra se desarrollo a raiz de unos inicios relativamente uniformes y mediante movimientos autoorganizados que ocurrieron entre grupos de celulas. Mientras que la variedad de formas que surgen de la morfogenesis es ilimitada, el numero de cambios geometricos y topologicos que la constituyen es limitado. El control de la forma biologica surge de la interaccion entre la biologia molecular y la biomecanica. En este trabajo hemos adoptado una aproximacion biofisica para estudiar la regulacion de una transformacion topologica que tiene lugar durante el desarrollo de la mosca de la fruta Drosophila melanogaster. 
Justo antes de que el embrion de Drosophila se convierta en larva, su cuerpo se cubre con un unico estrato de tejido epidermico. Para conseguirlo, dos capas de epidermis se estiran lateralmente rodeando el embrion y se fusionan dorsalmente, sellando un locus que previamente estaba lleno de un tejido muerto y pulsatil llamado amnioserosa (AS). Este proceso se conoce como dorsal y resulta de gran interes como modelo para estudiar otros tipos de fusion tisular, como la cicatrizacion de heridas o el cierre del tubo neuronal.
En este trabajo hemos considerado primero el control global del proceso, derivando una descripcion biofisica del sistema a partir de los principios primordiales de la fisica: a saber, un equilibrio de la fuerza en las dos esquinas (canthi) de la abertura, y la relacion de Young-Laplace alrededor de su contorno. Este modelo representa un avance en relacion a trabajos previos como consecuencia de su simplicidad, y la introduccion de un termino para la perdida de volumen de la AS en una descripcion de dos dimensiones. En la segunda parte de la tesis, nos hemos centrado en el papel que tiene el comportamiento pulsatil de la AS, ampliando el conocimiento existente sobre un nuevo ensayo experimental que perturba mecanicamente el embrion de la mosca Drosophila. Combinando esta aproximacion con un nuevo metodo para extraer informacion cuantitativa de imagenes confocales de las celulas, hemos investigado la respuesta de la AS bajo el estiramento mecanico. Finalmente, proponemos una doble funcion para los flujos corticales de miosina a la AS: dando soporte estructural a las uniones que se estiran y promoviendo la eliminacion del exceso de uniones mediante la endocitosis.