gebhart/patrepeval huggingface dataset:
In vitro isolation of small-molecule-binding aptamers with intrinsic dye-displacement functionality (2018)

Aptamer-based sensors offer a powerful tool for molecular detection, but the practical implementation of these biosensors is hindered by costly and laborious sequence engineering and chemical modification procedures. We report a simple strategy for directly isolating signal-reporting aptamers in vitro through systematic evolution of ligands by exponential enrichment (SELEX) that transduce binding events into a detectable change of absorbance via target-induced displacement of a small-molecule dye. We first demonstrate that diethylthiatricarbocyanine (Cy7) can stack into DNA three-way junctions (TWJs) in a sequence-independent fashion, greatly altering the dye's absorbance spectrum. We then design a TWJ-containing structured library and isolate an aptamer against 3,4-methylenedioxypyrovalerone (MDPV), a synthetic cathinone that is an emerging drug of abuse. This aptamer intrinsically binds Cy7 within its TWJ domain, but MDPV efficiently displaces the dye, resulting in a change in absorbance within seconds. This assay is label-free, and detects nanomolar concentrations of MDPV. It also recognizes other synthetic cathinones, offering the potential to detect newly-emerging designer drugs, but does not detect structurally-similar non-cathinone compounds or common cutting agents. Moreover, we demonstrate that the Cy7-displacement colorimetric assay is more sensitive than a conventional strand-displacement fluorescence assay. We believe our strategy offers an effective generalized approach for the development of sensitive dye-displacement colorimetric assays for other small-molecule targets.
A simple and fast method to determine the parameters for fuzzy c–means cluster analysis (2010)

Estimation of the optimal parameter values is achieved by evaluation of the results of the clustering procedure applied to randomized datasets. In this case, the optimal value of the fuzzifier follows common rules that depend only on the main properties of the dataset. Taking the dimension of the set and the number of objects as input values instead of evaluating the entire dataset allows us to propose a functional relationship determining the fuzzifier directly. This result speaks strongly against using a predefined fuzzifier as typically done in many previous studies. Validation indices are generally used for the estimation of the optimal number of clusters. A comparison shows that the minimum distance between the centroids provides results that are at least equivalent or better than those obtained by other computationally more expensive indices.
IMGT/GeneInfo: T cell receptor gamma TRG and delta TRD genes in database give access to all TR potential V(D)J recombinations (2006)

IMGT/GeneInfo allows all TR information sequences to be in the same spot, and are now available within two computer-mouse clicks. This is useful for biologists and bioinformaticians for the study of T lymphocyte V(D)J gene rearrangements and their applications in immune response analysis.
Polymere bis(oxazolo)pyrene. Synthesen und charakterisierung von poly(2,8‐oxazolo[2′,3′:7,8]pyreno[4,5‐<i>d</i>]‐oxazoldiyl‐1,4‐phenylen)en und einigen dazugehörigen modellverbindungen (1976)

Abstract Durch Reaktion von 4,5,9,10‐Pyrendichinon mit verschiedenen aromatischen Dialdehyden wurden neuartige Polyoxazole synthetisiert. Ihre Struktur wurde durch Vergleich ihrer IR‐Spektren mit denjenigen von entsprechend aufgebauten niedermolekularen Modellsubstanzen bestätigt. Die Thermostabilität der Polymeren wurde untersucht.
Application of Natural Blends of Phytochemicals Derived from the Root Exudates of Arabidopsis to the Soil Reveal That Phenolic-related Compounds Predominantly Modulate the Soil Microbiome (2013)

The roots of plants have the ability to influence its surrounding microbiology, the so-called rhizosphere microbiome, through the creation of specific chemical niches in the soil mediated by the release of phytochemicals. Here we report how these phytochemicals could modulate the microbial composition of a soil in the absence of the plant. For this purpose, root exudates of Arabidopsis were collected and fractionated to obtain natural blends of phytochemicals at various relative concentrations that were characterized by GC-MS and applied repeatedly to a soil. Soil bacterial changes were monitored by amplifying and pyrosequencing the 16 S ribosomal small subunit region. Our analyses reveal that one phytochemical can culture different operational taxonomic units (OTUs), mixtures of phytochemicals synergistically culture groups of OTUs, and the same phytochemical can act as a stimulator or deterrent to different groups of OTUs. Furthermore, phenolic-related compounds showed positive correlation with a higher number of unique OTUs compared with other groups of compounds (i.e. sugars, sugar alcohols, and amino acids). For instance, salicylic acid showed positive correlations with species of Corynebacterineae, Pseudonocardineae and Streptomycineae, and GABA correlated with species of Sphingomonas, Methylobacterium, Frankineae, Variovorax, Micromonosporineae, and Skermanella. These results imply that phenolic compounds act as specific substrates or signaling molecules for a large group of microbial species in the soil.
The TP53 codon 72 polymorphism and predisposition to adrenocortical cancer in Polish patients (2006)

The TP53 polymorphism occurs at codon 72 of exon 4 with two alleles encoding either arginine or proline. The association between this common polymorphism and risk of different cancers has been extensive studied, however various reports are controversial. We have analyzed the 72Pro polymorphic variant in patients with adrenocortical tumors to evaluate whether 72G--> C substitution at codon 72 of TP53 gene may be associated with increased risk for malignancy in adrenal cortex in comparison to the control group. DNA extracted from peripheral leucocytes of 46 Polish patients with adrenocortical tumors (17 malignant and 29 benign) and 50 controls was examined by PCR-HD method followed by direct sequencing. TP53 polymorphism in codon 72 was found in 47% of ACC cases, in 28% of patients with adenomas and in 24% of controls. The genotype Arg/Arg, Arg/Pro and Pro/Pro distribution was respectively 53%/35%/12% for cancers, 72%/28%/0% for benign tumors and 76%/24%/0% for controls. High frequency of 72Pro allele in patients with carcinoma (29%) in comparison to the benign tumors (14%) and controls (12%) was statistically analyzed. We found that 72Pro variant of TP53 gene was associated with a significantly increased risk of ACC (OR = 3.05; 95% CI = 1.17-7.91, p=0.03). Our results suggest that the TP53 codon 72 polymorphism could be associated with susceptibility for adrenocortical cancer in the examined Polish patients.
Naturalistically observed swearing, emotional support, and depressive symptoms in women coping with illness. (2011)

These exploratory results are consistent with the notion that swearing can sometimes repel emotional support at the expense of psychological adjustment. This is one of the first studies to examine the role of swearing, a ubiquitous but understudied psychological phenomenon, in a medical context.
Discrete Buffer and Wire Sizing for Link-Based Non-Tree Clock Networks (2009)

Clock network is a vulnerable victim of variations as well as a main power consumer in many integrated circuits. Recently, link-based non-tree clock network attracts people's attention due to its appealing tradeoff between variation tolerance and power overhead. In this work, we investigate how to optimize such clock networks through buffer and wire sizing. A two-stage hybrid optimization approach is proposed. It considers the realistic constraint of discrete buffer/wire sizes and is based on accurate delay models. In order to provide reliable and efficient guidance for the optimization, we suggest to apply support vector machine (SVM)-based machine learning as a surrogate for expensive circuit-level simulation. Experimental results on benchmark circuits show that our sizing method can reduce clock skew by 45% on average with very small increase on power dissipation.
An Accurate Iris Segmentation Framework Under Relaxed Imaging Constraints Using Total Variation Model (2015)

This paper proposes a novel and more accurate iris segmentation framework to automatically segment iris region from the face images acquired with relaxed imaging under visible or near-infrared illumination, which provides strong feasibility for applications in surveillance, forensics and the search for missing children, etc. The proposed framework is built on a novel total-variation based formulation which uses l1 norm regularization to robustly suppress noisy texture pixels for the accurate iris localization. A series of novel and robust post processing operations are introduced to more accurately localize the limbic boundaries. Our experimental results on three publicly available databases, i.e., FRGC, UBIRIS.v2 and CASIA.v4-distance, achieve significant performance improvement in terms of iris segmentation accuracy over the state-of-the-art approaches in the literature. Besides, we have shown that using iris masks generated from the proposed approach helps to improve iris recognition performance as well. Unlike prior work, all the implementations in this paper are made publicly available to further advance research and applications in biometrics at-d-distance.
Vaccine and Immunotherapeutic Approaches for the Prevention of Cryptococcosis: Lessons Learned from Animal Models (2012)

Cryptococcus neoformans and C. gattii, the predominant etiological agents of cryptococcosis, can cause life-threatening infections of the central nervous system in immunocompromised and immunocompetent individuals. Cryptococcal meningoencephalitis is the most common disseminated fungal infection in AIDS patients, and C. neoformans remains the third most common invasive fungal infection among organ transplant recipients. Current anti-fungal drug therapies are oftentimes rendered ineffective due to drug toxicity, the emergence of drug resistant organisms, and/or the inability of the host's immune defenses to assist in eradication of the yeast. Therefore, there remains an urgent need for the development of immune-based therapies and/or vaccines to combat cryptococcosis. Studies in animal models have demonstrated the efficacy of various vaccination strategies and immune therapies to induce protection against cryptococcosis. This review will summarize the lessons learned from animal models supporting the feasibility of developing immunotherapeutics and vaccines to prevent cryptococcosis.
Thermally conductive plastics for innovative thermal management solutions (2016)

The use of thermally conductive plastics (TCPs) to achieve novel solutions to challenging thermal management problems is discussed in this paper. Theoretical, computational and experimental approaches are all used to explore the use of TCPs for thermal management. This paper examines the possibility of using TCP heat sinks under free- and forced-convection environments to achieve equivalent or even better thermal management solutions than traditional aluminum heat sinks. An alternate approach of enhancing existing plastic housings / enclosures and including them in the thermal management solution is also proposed. Various ways to formulate TCPs and the trade-offs to consider for each of them are also discussed.
ELIMINATION OF SPERMATOZOA IN THE URINE OF ISOLATED MALE RATS (1971)

Evidence has been reported to indicate that non-ejaculated spermatozoa in adult animals of different mammalian species may be eliminated by phagocytosis (Morgenstern, 1924), voiding in the urine (Oslund, 1928; Wilhelm & Seligmann, 1937; Bolliger & Carrodus, 1938), and dissolution into the vas deferens (Simeone & Young, 1931), though the phenomenon does not appear to have been studied quantitatively. The purpose of the present study was to investigate the presence and numbers of spermatozoa in the urine of isolated male rats. Six adult male rats of the Wistar strain, weighing 277 to 385 g, and of proven fertility, were separated from the female rats with which they had been mated. After 2 weeks, they were kept in individual metabolic cages, where the urine passed through a glass funnel into a 125-ml
Autophagy in Gaucher disease due to saposin C deficiency (2010)

Gaucher disease, due to a deficit of glucosylceramidase or, rarely, of its activator saposin C, is characterized by accumulation of glucosylceramide in the lysosomes of monocyte/macrophage lineage. In our study we demonstrate that saposin C deficiency due to mutations involving a cysteine residue results in increased autophagy. Autophagy was monitored by LC3 analysis and confirmed by electron microscopy; we observed a correlation among saposin C mutation, Gaucher phenotype and increased autophagy.
Depth Template Based 2D-to-3D Video Conversion and Coding System (2012)

A Depth Template based 2D-to-3D Video Conversion and Coding system (DTVCC) is proposed by this paper. In DTVCC, triangle meshes are exploited to describe depth template for scenes in 2D video, an interactive system is designed to generate reliable depth template, depth map can be automatically reconstructed based on the depth template and 2D video frame pixels information, and the generated 3D video is compressed just by coding the 2D video plus depth template. Experiment results show that not only high quality 3D video is generated, but also the bit rate of coding the converted 3D video is saved by 12%~38% with our proposed system of DTVCC.
MODELING, ANALYSIS, AND DESIGN OF SUBCARRIER MULTIPLEXING ON MULTIMODE FIBER (2003)

This dissertation focuses on the use of subcarrier multiplexing (SCM) in multimode fibers, utilizing carrier frequencies above what is generally utilized for multimode fiber transmission, to achieve high bit rates. In the high frequency region (i.e., frequencies larger than the intermodal bandwidth), the magnitude response of multimode fiber does not decrease monotonically as a function of the frequency but is shown to become relatively flat (but with several deep nulls) with an amplitude below that at DC. The statistical properties of this frequency response at high frequencies are analyzed. The probability density function of the magnitude response at high frequencies is found to be a Rayleigh density function. The average amplitude in this high frequency region does not depend on the frequency but depends on the number of modes supported by the fiber. To transmit a high bit rate signal over the multimode fiber, subcarrier multiplexing is adopted. The performance of the SCM multimode fiber system is presented. The performance of the SCM system is significantly degraded if there are some subcarriers located at the deep nulls of the fiber. Equalization and spread spectrum techniques are investigated but are shown to be not effective in combating the effects of these nulls. To cancel the effects of these deep nulls, training process and diversity coding are considered. The basic theory of diversity coding is given. It is found that the performances of the system with training process and the system with diversity coding are almost identical. However, diversity coding is more appropriate since it requires less system complexity. Finally, the practical limits and capacity of the SCM multimode fiber system are investigated. It is shown that a signal with a bit rate of 1.45 Gbps can be transmitted over a distance up to 5 km.
Ultraprecise Absolute Time Synchronization for Distributed Acquisition Systems (2007)

In this paper, we describe an algorithm built on top of a precision time protocol (PTP) implementation that allows for synchronization, syntonization and absolute time referencing to coordinated universal time (UTC), including the estimation of timestamp uncertainty. We call this the software grandmaster (SWGM) algorithm, since it provides similar services to a PTP grandmaster clock. We show that SWGM allows timestamps to be coordinated between multiple participants in a distributed measurement system with typical performance of plusmn 86 ns [root mean square (rms)] over commodity switched Ethernet connections using hardware PTP and hardware-derived timestamps. We further show that when software-derived timestamps are used the uncertainty in the timestamps is primarily driven by the latency of the system calls to read the PTP hardware, and may be on the order of 15-25 s (rms) depending on process priority, hardware bus speed, and host processor clock rate. We also show that SWGM is robust against dropped network packets up to approximately 60% loss of packets.
Quantum information technology (2003)

A new quantum information technology (QIT) could emerge in the future, based on current research in the fields of quantum information processing and communication1, 2, 3 (QIPC). In contrast to conventional IT, where quantum mechanics plays a support role in improving the building blocks, fundamental quantum phenomena play a central role in QIPC — information is stored, processed, and communicated according to the laws of quantum physics. This additional freedom could enable future QIT to perform tasks we will never achieve with ordinary IT. Today many people are familiar with at least the consequences of Moore’s Law — the fastest computer in the shops doubles in speed about every 18 months to two years. This exponential progress, first noted4 by Gordon Moore — cofounder and former CEO of Intel — in 1965, has continued ever since. But it cannot go on forever. Hurdles exist, for example: silicon will hit problems, with oxide thinness or track width5; new materials or even new paradigms, such as self-assembled nano-devices or molecular electronics, will be needed; lots of dollars will be required as Moore’s second law tells us that fabrication costs are also growing exponentially. However, even if the hurdles can be overcome, we will eventually run into nature.
Narrow-band spectral filter made of W-index and step-index fibers (1992)

An all-fiber spectral filter constructed with a W-index fiber, supporting a dominant mode with nonzero cutoff frequency, and a step-index single-clad fiber is proposed and analyzed. The proposed filter offers a spectral width on the order of one nanometer, considerably narrower than that provided by a filter made of two single-clad fibers having the same transmission wavelength. The narrow spectral width is achieved by exploiting a relatively large slope difference between the dispersion characteristics of the W-index and step-index fibers constituting the filter. As an example case, the transmission characteristic of the proposed filter with peak transmission at 1300 nm is calculated and compared with that of a corresponding filter made of two single-clad fibers.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
'Minting' electronic cash (1997)

Electronic equivalents of traditional cash payment systems are being launched worldwide. Electronic cash can combine the benefits of traditional cash with those of payment by debit and credit card, while circumventing both their shortcomings. As with traditional cash, electronic cash should have high acceptability and be suitable for low value payment from person to person. With the possible exception of online payment platforms such as the Internet, it is preferred that payments be verifiable offline, without the bank's involvement, for reasons of cost effectiveness and speed. To facilitate electronic cash payments over the phone and the Internet, physical proximity of payer and payee should not be necessary. Moreover, electronic cash should offer privacy of payments. In particular, payments by an honest payer should be untraceable, and information about transaction content should remain privy to payer and payee. Yet a payer ought to always be able to trace the payee; traceability suits electronic cash and is as open to extortion, money laundering, and bribery as a check or wire transfer. Lastly, as with payments by debit and credit card, electronic cash should be convenient to store and transport, while protecting users against loss, theft, and accidental destruction.
Self-Cleaning Flexible Infrared Nanosensor Based on Carbon Nanoparticles (2011)

Highly flexible, robust, and sensitive infrared nanosensors were fabricated based on carbon nanoparticles that were synthesized through a simple and low-cost flame method. The infrared nanosensor devices showed sharp infrared photoresponse with a response time of ∼68 ms and a maximum photocurrent change of ∼52.9%. The devices showed a superhydrophobic property with a contact angle larger than 150° and a sliding angle of ∼4°. The mechanism for the enhanced infrared photoresponse from carbon nanoparticles is discussed.
Synthesis of(<i>E</i>)7‐[[2‐[4‐(<i>m</i>‐trifluoromethylphenoxy)‐3α and 3β‐hydroxy‐1‐butenyl]‐5‐oxo‐1 ‐pyrrolidinyl]]heptanoic acids (1983)

Abstract The synthesis of an 8‐aza‐PGE 1 analog, ( E )‐7‐[[2‐[4‐( m ‐trifluoromethylphenoxy)‐3α and 3β‐hydroxy‐1‐butenyl]‐5‐oxo‐pyrrolidinyl]]heptanoic acids is reported.
Parametric studies in industrial distillation: Part II. Heuristic optimization (1978)

Abstract State optimization should not be ignored in the evaluation of distillation alternatives. However, heuristic rank order algorithms can greatly simplify the analysis. Optimal operating pressures correlate well with feed bubble points, and intertower economic interactions are often small.
TNAP, TrAP, ecto‐purinergic signaling, and bone remodeling (2008)

Bone remodeling is a process of continuous resorption and formation/mineralization carried out by osteoclasts and osteoblasts, which, along with osteocytes, comprise the bone multicellular unit (BMU). A key component of the BMU is the bone remodeling compartment (BRC), isolated from the marrow by a canopy of osteoblast-like lining cells. Although much progress has been made regarding the cytokine-dependent and hormonal regulation of bone remodeling, less attention has been placed on the role of extracellular pH (pH(e)). Osteoclastic bone resorption occurs at acidic pH(e). Furthermore, osteoclasts can be regarded as epithelial-like cells, due to their polarized structure and ability to form a seal against bone, isolating the lacunar space. The major ecto-phosphatases of osteoclasts and osteoblasts, acid and alkaline phosphatases, both have ATPase activity with pH optima several units different from neutrality. Furthermore, osteoclasts and osteoblasts express plasma membrane purinergic P2 receptors that, upon activation by ATP, accelerate bone osteoclast resorption and impair osteoblast mineralization. We hypothesize that these ecto-phosphatases help regulate [ATP](e) and localized pH(e) at the sites of bone resorption and mineralization by pH-dependent ATP hydrolysis coupled with P2Y-dependent regulation of osteoclast and osteoblast function. Furthermore, osteoclast cellular HCO3(-), formed as a product of lacunar V-ATPase H(+) secretion, is secreted into the BRC, which could elevate BRC pH(e), in turn affecting osteoblast function. We will review the existing data addressing regulation of BRC pH(e), present a hypothesis regarding its regulation, and discuss the hypothesis in the context of the function of proteins that regulate pH(e).