gebhart/patrepeval huggingface dataset:
Neurofibrillary Pathology in Transgenic Mice Overexpressing V717F β-Amyloid Precursor Protein (2001)

Overexpression of mutated human amyloid precursor protein (hAPP717V-->F) under control of the platelet-derived growth factor promoter (PDAPP minigene) in transgenic (tg) mice results in plaque formation and astroglial activation similar to Alzheimer disease (AD). However, the extent of the neurofibrillary pathology in this model is less understood. In order to determine if these mice develop AD-like neurofibrillary pathology, vibratome sections from PDAPP tg mice (4- to 20-months-old) were immunolabeled with antibodies against phosphorylated tau (AT8) and phosphorylated neurofilaments (SMI 312, TA51), and analyzed by laser scanning confocal and electron microscopy. Phosphorylated neurofilament-immunoreactive dystrophic neurites in plaques were first seen in mice at 10 to 12 months of age, while phosphorylated tau-immunoreactive dystrophic neurites were observed after 14 months of age. Immunoelectron microscopic analysis revealed that phosphorylated neurofilament immunoreactivity was diffusely distributed along filamentous aggregates (12-15 nm in diameter) in the plaque dystrophic neurites, and occasionally in neuronal cell bodies. In contrast, phosphorylated tau immunoreactivity was observed as clusters distributed along filamentous structures accumulating in the dystrophic neurites and around neurotubules in the axons. However, no paired helical filaments were observed. Taken together, these studies indicate that the PDAPP tg model recapitulates early cytoskeletal pathology similar to that observed in AD.
The plaque‐inhibiting effect of chlorhexidine‐containing dentifrices (1971)

abstract – In a double blind longitudinal study the plaque‐inhibiting effect of two chlorhexidine‐containing dentifrices was tested on 53 students for 2 months. The mean Plaque Index values of the groups employing active toothpastes were significantly lower than in a placebo group (p &lt; 0.5). The differences tended to increase with time. Standardized color photographs were taken of all participants at the start and at the termination of the experiment. Brownish stains on silicate fillings and tooth surfaces were observed frequently. No damage to the oral mucosa or discoloration of the dorsum of the tongue could be detected. Storing of the dentifrices at room temperature up to 6 months caused no changes in the antibacterial activity against salivary bacteria in vitro. It is concluded that the use of a dentifrice as a vehicle for chlorhexidine might be of value in the general preventive application of the agent.
Influence of Zona Pellucida Area Expansion Stiffness on the Passive Response of Oocytes to Osmotic Loading (2011)

The zona pellucida (ZP) is a thick glycoprotein shell surrounding the mammalian egg cell (oocyte) that regulates spermatozoa access during fertilization and protects the zygote during early embryonic development [1]. Hardening of the zona pellucida over the cell fertilization cycle is a well-recognized phenomenon and has been investigated using contact methods to measure shear and bending elasticity from indentation and micropipette aspiration [2, 3]. However, the area elasticity of the ZP, which provides resistance to cell swelling under variable osmotic environments, has not yet been reported. A recently devised theoretical model [4] suggests that the ZP area expansion modulus may be determined through non-contact hypo-osmotic loading of the oocyte. If successful, this method may be suited for implementation by practicing fertility health professionals during routine manipulation.
A clonality analysis based on T-cell receptor beta and delta loci for high-grade gastrointestinal lymphoma in dogs (2022)

Clonality assays based on antigen receptors are used as adjunct examinations in the diagnosis of lymphoproliferative diseases. We investigated the usefulness of the T-cell receptor beta (<i>TRB</i>) and T-cell receptor delta (<i>TRD</i>) loci in clonality assays for high-grade gastrointestinal (GI) lymphoma in dogs. For <i>TRB</i>, we used primers reported previously; for <i>TRD</i>, we designed primers for each of the <i>V</i> and <i>J</i> genes based on genomic sequences. Genomic DNA was extracted from 39 formalin-fixed, paraffin-embedded sections of high-grade GI lymphoma diagnosed histologically. The sensitivity of <i>TRB</i> and <i>TRD</i> primers for GI lymphoma was 41.0% and 38.5%, respectively, which was lower than the 82.1% sensitivity of T-cell receptor gamma (<i>TRG</i>) primers However, some cases that could not be detected using <i>TRG</i> primers had clonality with either <i>TRB</i> or <i>TRD</i> primers. We found the <i>TRG</i> locus to be more suitable as a first choice for the assay of canine lymphoma clonality than the <i>TRB</i> and <i>TRD</i> loci. However, the detection rate of T-cell clonality may be enhanced using <i>TRB</i> and <i>TRD</i> primers for lymphoma cases not detected using <i>TRG</i> primers.
Extraction of concanavalin A affinity material from rat testicular and epididymal spermatozoa (1977)

Immature and mature rat spermatozoa obtained by cannulation of the rete testis and the cauda epididymidis, respectively, have been labeled by the lactoperoxidase iodination technique. After solubilization with SDS or Triton X-100, the labeled glycoproteins have been fractionated by affinity chromatography using a Concanavalin A-agarose column. Comparison of the fractions eluted by methyl-a-D-glucopyranoside after labeling of immature and mature spermatozoa revealed an increase in Concanavalin A binding sites on the spermatozoa during their passage through the epididymis.
Thoughts on characteristics of teaching management of BCIT (2001)

British Colombia Institute of Technology (BCIT) establishes the purpose of running school according to the development of the national and international economic condition and the social requirement. It also establishes and developes the teaching management system to separate teaching running management and teaching quality management in institution setup. It regards the teaching capacity and teaching level of the faculties and compilation of the textbooks as the important teaching resources to make scientific management so as to ensure the realization of the purpose of running school.
Design of low-power fast VCSEL drivers for high-density links in 90-nm SOI CMOS (2006)

The continuous decrease of the supply voltage to 1 V and below in CMOS makes the design of laser drivers a challenging task. Hence, a detailed comparison of three basic driver architectures, namely, common source (CS), CS with source degeneration, and source follower (SF) is presented using transistor models including short channel effects. Based on this comparison, two power-optimized driver topologies are implemented in a 90-nm silicon-on-insulator CMOS technology. The SF driver features a bandwidth of 18 GHz on a 50-/spl Omega/ load. The required chip area is only 140 /spl mu/m/spl times/140 /spl mu/m, which is very beneficial for high-density short-distance optical interconnects. This allows a data rate of 12.5 Gb/s at a bit error ratio of less than 10/sup -12/ to be achieved even with a 10-Gb/s oxide confined vertical-cavity surface-emitting laser (VCSEL). The power consumption is 27 mW. The drivers were optimized for maximal eye opening by applying a fast and accurate VCSEL model.
Hardware Design and Algorithm Optimization of Video Encoder Based on DSP and FPGA Techniques (2005)

With the development of video encoding techniques, video compression algorithms become more complicated. A real-time high resolution video encoder cannot be implemented with a single CPU or DSP. A MPEG-4 video encoder is designed and implemented based on coordinated DSP and FPGA techniques. The FPGA module takes the tasks of video acquisition, YUV separation and data I/O functions, while the DSP is dedicated for video compression. The data flow scheme of the MPEG-4 video compression is optimized by utilizing the DSP′s on-chip memory. A Macro Block (MB) type judging algorithm is proposed based on MB′s space complexity. It reduces effectively the computational complexity of the video compression. The experimental results indicate that the MPEG-4 video encoder implementation can encode 39.2 f/s in CIF resolution.
Surrogate endpoints: wishful thinking or reality? (2008)

Surrogate endpoints: wishful thinking or reality?Generally, before a new drug can be accepted for the use in clinical practice, its efficacy and safety needs to be rigorously assessed in a series of clinical trials.This process of testing a new therapy can (and, in fact, does) take many years.One of the reasons is the use of long-term clinical endpoints like clinical progression or survival.However, recent advances in the understanding of the biological mechanisms of disease development have resulted in the emergence of a large number of potentially effective new agents.There is also increasing public pressure for promising new drugs to receive marketing approval as rapidly as possible, in particular for life threatening diseases such as cancer.For these reasons, there is an urgent need to find ways of shortening the duration of cancer clinical trials.A possible solution to this problem is to replace the endpoint of interest, the 'true' endpoint, by another one, a 'surrogate' endpoint, which might be measured earlier or more frequently.However, before a surrogate can replace a true endpoint, it should be validated.This means that it should be checked whether the use of the surrogate leads to correct conclusions about the effect of the treatment on the true endpoint.The validation of a candidate surrogate endpoint is not straightforward.Merely establishing a correlation between both endpoints is not sufficient. 1 Formal methods, allowing for validation of surrogate endpoints, have become the subject of intensive research over the past decades. 2Until recently, the statistical approaches developed for this purpose were based on the definition of a surrogate proposed by Prentice, 3 according to which a surrogate endpoint is 'a response variable for which a test of the null hypothesis of no relationship to the treatment groups under comparison is also a valid test of the corresponding null hypothesis based on the true endpoint.'4][5] These methods suffer from numerous drawbacks: some of them are too stringent to be of practical value, while others are based on non-testable assumptions. 6][9][10] They are based on an alternate definition, according to which 'a surrogate endpoint is expected to predict clinical benefit (or harm or lack of benefit or harm)'. 11These methods use large databases from multiple randomized clinical trials and aim at measuring directly the association between the treatment effects on the surrogate and the true endpoint.At the 33rd International Biometric Conference, which took place on 16-21 July, 2006, in Montreal, a special Topic Contributed Session 'Surrogate Endpoints: Wishful Thinking or Reality?' was devoted to the issue of surrogate endpoint validation.Each speaker was provided with two datasets, containing data from multiple randomized clinical trials in colorectal cancer.The speakers were asked to evaluate, using different
Irreversible genetic switch to transactivate mom gene during lytic cycle of bacteriophage Mu (2008)

Expression of genes is regulated by ‘on’ and ‘off’ mechanisms executed at various levels. At the transcriptional level, the positive regulators (activators) turn ‘on’ gene expression while negative regulators (repressors) turn ‘off’ the expression. The genetic switches essentially achieve either induction or repression driven by the cellular requirement mediated by timely signaling events. The reversibility of the well characterized control circuits ensure optimized expression of genes. I will describe a genetic switch which appears to be irreversible.
Plasma guanosine3′,5′‐cyclic monophosphate and severity of peri/intraventricular haemorrhage in the preterm newborn (2002)

Increased cGMP levels are associated with the development of PIVH. It is suggested that vasodilatory nitric oxide-induced impairment of cerebral autoregulation plays a role here.
Optical intensity modulation to 40 GHz using a waveguide electro-optic switch (1987)

We report the intensity modulation of an optical carrier at frequencies as high as 40 GHz using a Ti:LiNbO3 optical waveguide switch. The device is shown to exhibit a small-signal electrical 3 dB bandwidth of &amp;gt;22 GHz and −8 dB response at 40 GHz. A high-speed self-electro-optic-sampling arrangement based on a mode-locked injection laser is used to observe the modulation in the time domain.
Cyberology: Cyber-Physical-Social-Thinking Spaces based Discipline and Inter-discipline Hierarchy for Metaverse (General Cyberspace) (2022)

&lt;p&gt;It is well known that the metaverse, also named general cyberspace, is virtual-real fusion spaces, consisting of a virtual space namely cyberspace and virtual-real spaces namely cyber-enabled physical, social, and thinking (cyber-enabled) spaces. This paper discusses the open issues of the metaverse in terms of science and technology and proposes a new discipline and inter-discipline hierarchy for the metaverse first. Then, it ex?plores various relevant standards of discipline classification and a discipline and inter-discipline hierarchy based on physical, social and thinking spaces, and investigates the cyberspace and cyber?enabled spaces. On the basis of the above research, this paper proposes the detailed metaverse discipline and inter-discipline hierarchy based on cyber-physical-social-thinking spaces and enriches the content of cyberology from the aspects of cyberspace and cyber-enabled spaces. Finally, this paper predicts the future development of cyberology in terms of society, enterprise and humankind. &lt;/p&gt;
Crossover from ionic hopping to nearly constant loss in the fast ionic conductorLi0.18La0.61TiO3 (2002)

Electrical conductivity measurements of the fast ionic conductor ${\mathrm{Li}}_{0.18}{\mathrm{La}}_{0.61}{\mathrm{TiO}}_{3}$ have been conducted at temperatures ranging from 8 to 300 K and frequencies between 20 Hz and 5 MHz. A detailed analysis of the ac conductivity shows the existence of a crossover between two different regimes. At high temperatures and/or low frequencies correlated ion hopping is responsible for a power-law frequency dependent and thermally activated ac conductivity. On the other hand, at sufficiently low temperatures and/or high frequencies, the ions do not have enough thermal energy or time to hop between neighboring sites, and remain caged. The ac conductivity is then characterized by a linear frequency dependence (i.e., the equivalent of a nearly constant loss) and by a weak exponential temperature dependence of the form $\mathrm{exp}{(T/T}_{0}).$ A crossover between the two regimes is found, which is thermally activated with an activation energy $E=0.17 \mathrm{eV},$ significantly lower than that observed for the dc conductivity, ${E}_{\ensuremath{\sigma}}=0.4 \mathrm{eV}.$ From this result, it is shown that the so-called ``augmented Jonscher expression'' fails to describe the ac conductivity in the whole frequency and temperature ranges. All these findings suggest that the nearly constant loss originates from electrical loss occurring during the time regime while the ion is still confined in the potential-energy minimum. Further, it is proposed that the loss mechanism involves some type of process where the potential-energy minimum relaxes in time on a time scale much shorter than the ionic hopping time scale. At longer times, as soon as the ion has significant probability of being thermally activated out of the potential well, the nearly constant loss terminates and correlated ion hopping becomes the only contribution to the ac conductivity.
Analyzing websites for user-visible security design flaws (2008)

An increasing number of people rely on secure websites to carry out their daily business. A survey conducted by Pew Internet states 42% of all internet users bank online. Considering the types of secure transactions being conducted, businesses are rigorously testing their sites for security flaws. In spite of this testing, some design flaws still remain that prevent secure usage. In this paper, we examine the prevalence of user-visible security design flaws by looking at sites from 214 U.S. financial institutions. We specifically chose financial websites because of their high security requirements. We found a number of flaws that may lead users to make bad security decisions, even if they are knowledgeable about security and exhibit proper browser use consistent with the site's security policies. To our surprise, these design flaws were widespread. We found that 76% of the sites in our survey suffered from at least one design flaw. This indicates that these flaws are not widely understood, even by experts who are responsible for web security. Finally, we present our methodology for testing websites and discuss how it can help systematically discover user-visible security design flaws.
Precisely Lateral Alignment of Gold Nanorods Array via Hydrophilic-Hydrophobic Pattern (2018)

A simple strategy which combines the controlled solvent evaporation and hydrophilic-hydrophobic pattern to allow assembling gold nanorods (GNRs) on a flat substrate with arbitrary shapes is presented in this work. Soft polydimethylsiloxane (PDMS) template as a pattern transfer stamp were utilized and transferred the structures onto the substrate successfully. By tuning the structures and sizes of templates, oriented large area lateral aligned GNRs arrays were fabricated as expected. Scan electron microscopy (SEM) images revealed that GNRs had been precisely placed as expected and the assembly is uniform.
dsRNA-Seq: Identification of viral infection by purifying and sequencing dsRNA (2019)

Abstract RNA viruses are a major source of emerging and re-emerging infectious diseases around the world. We developed a method to identify RNA viruses that is based on the fact that all RNA viruses produce dsRNA while replicating. Purifying and sequencing dsRNA from total RNA isolated from infected tissue allowed us to recover replicating viral sequences. We refer to this approach as dsRNA-Seq. By assembling dsRNA sequences into contigs we identified full length RNA viruses of varying genome types infecting mammalian culture samples, identified a known viral disease agent in laboratory infected mice, and successfully detected naturally occurring RNA viral infections in reptiles. Here we show that dsRNA-Seq is a preferable method for identifying viruses in organisms that don’t have sequenced genomes and/or commercially available rRNA depletion reagents. Similar to other metagenomic strategies, dsRNA-Seq has the potential to identify unknown viral disease agents that share little to no similarity to known viruses. However, the significant advantage of this method is the ability to identify replicated viral sequences, which is useful for distinguishing infectious viral agents from potential noninfectious viral particles or contaminants.
Epitaxial Crystallization and AFM Investigation of a Frustrated Polymer Structure:  Isotactic Poly(propylene), β Phase (1998)

The metastable phase of isotactic polypropylene (βiPP) is crystallized epitaxially on two specific nucleating agents: γ-quinacridone and dicyclohexylterephthalamide (DCHT). The resulting thin films are investigated by electron microscopy and atomic force microscopy. Epitaxial crystallization yields a biaxially oriented sample of βiPP, an orientation which cannot be achieved by mechanical means due to the β → α phase transformation on stretching. Electron diffraction indicates that the βiPP (110) plane is the contact face involved in both epitaxies. AFM investigation with methyl group resolution reveals a lateral periodicity of 19 Å in that (110) contact face, which corresponds to the distance between three chains and is a trademark indicator of the frustrated packing of βiPP. AFM further indicates some variability of the surface pattern, suggesting that two different frustrated structures may coexist in the surface layer; this, in turn, suggests some type of surface reconstruction. Structural requirements that efficient βiPP nucleating agents must meet are analyzed.
Microtubule Destabilization Is Shared by Genetic and Idiopathic Parkinson’s Disease Patient Fibroblasts (2012)

Data from both toxin-based and gene-based models suggest that dysfunction of the microtubule system contributes to the pathogenesis of Parkinson's disease, even if, at present, no evidence of alterations of microtubules in vivo or in patients is available. Here we analyze cytoskeleton organization in primary fibroblasts deriving from patients with idiopathic or genetic Parkinson's disease, focusing on mutations in parkin and leucine-rich repeat kinase 2. Our analyses reveal that genetic and likely idiopathic pathology affects cytoskeletal organization and stability, without any activation of autophagy or apoptosis. All parkinsonian fibroblasts have a reduced microtubule mass, represented by a higher fraction of unpolymerized tubulin in respect to control cells, and display significant changes in microtubule stability-related signaling pathways. Furthermore, we show that the reduction of microtubule mass is so closely related to the alteration of cell morphology and behavior that both pharmacological treatment with microtubule-targeted drugs, and genetic approaches, by transfecting the wild type parkin or leucine-rich repeat kinase 2, restore the proper microtubule stability and are able to rescue cell architecture. Taken together, our results suggest that microtubule destabilization is a point of convergence of genetic and idiopathic forms of parkinsonism and highlight, for the first time, that microtubule dysfunction occurs in patients and not only in experimental models of Parkinson's disease. Therefore, these data contribute to the knowledge on molecular and cellular events underlying Parkinson's disease and, revealing that correction of microtubule defects restores control phenotype, may offer a new therapeutic target for the management of the disease.
A method for a priori estimation of best feasible DVH for organs‐at‐risk: Validation for head and neck VMAT planning (2017)

For the validation of VMAT plans, the OAR DVHs optimized one-at-a-time were similar in shape to and bound on the low side by the FDVHs, within the confines of planner's ability to precisely cover the target(s) with the prescription dose(s). The method is best suited for the OARs close to the target. This approach is fundamentally different from "knowledge-based planning" because it is (a) independent of the treatment plan and prior experience, and (b) it approximates, from nearly first principles, the lowest possible boundary of the OAR DVH, but not necessarily its actual shape in the presence of competing OAR sparing and target dose homogeneity objectives.