gebhart/patrepeval huggingface dataset:
A multicast routing protocol for ad-hoc networks (1999)

The Core Assisted Mesh Protocol (CAMP) is introduced for multicast routing in ad hoc networks. CAMP generalizes the notion of core-based trees introduced for internet multicasting into multicast meshes that have much richer connectivity than trees. A shared multicast mesh is defined for each multicast group; the main goal of using such meshes is to maintain the connectivity of multicast groups even while network routers move frequently. CAMP consists of the maintenance of multicast meshes and loop-free packet forwarding over such meshes. Within the multicast mesh of a group, packets from any source in the group are forwarded along the reverse shortest path to the source, just as in traditional multicast protocols based on source-based trees. CAMP guarantees that, within a finite time, every receiver of a multicast group has a reverse shortest path to each source of the multicast group. Multicast packets for a group are forwarded along the shortest paths from sources to receivers defined within the group's mesh. CAMP uses cores only to limit the traffic needed for a router to join a multicast group; the failure of cores does not stop packet forwarding or the process of maintaining the multicast meshes.
<title>Influence of beam loading on the operation of the relativistic klystron amplifier</title> (1990)

Experiments in modulating an electron beam of power greater than 30 GW revealed a mechanism that limits the output RF power of the NRL relativistic klystron amplifier. This mechanism is beam loading of high voltage gaps. It is found that the presence of charge at the gaps is analogous to connecting a capacitor in parallel with the HV gap. This capacitor has a component that depends only on the electron density and on the geometry. Its presence causes detuning of the cavity, resulting in a slow build-up time for the electron beam modulation, saturation of the RF current amplitude and occasionally erratic fluctuations in the RF current. The nonlinear components of this capacitor cause the spectrum of the current modulation to be shifted toward the high frequencies.
Effects of Diabetes on Salivary Gland Protein Expression of Tetrahydrobiopterin and Nitric Oxide Synthesis and Function (2016)

These results indicate that a decrease in submandibular NO-BH4 protein expression may provide insight pertaining to mechanisms for the development of hyposalivation in DM-induced xerostomia. Furthermore, understanding the role of the NO-BH4 pathway may give insight into possible treatment options for the patient with DM experiencing xerostomia.
Carboxyl Analogue of Mutacin 1140, a Scaffold for Lead Antibacterial Discovery (2017)

Mutacin 1140 belongs to the epidermin group of lantibiotics. Epidermin class lantibiotics are ribosomally synthesized and posttranslationally modified antibiotics with potent activity against Gram-positive bacteria. In particular, this class is effective at targeting drug-resistant <i>Streptococcus pneumoniae</i>, methicillin-resistant <i>Staphylococcus aureus</i> (MRSA), <i>Mycobacterium tuberculosis</i>, and <i>Clostridium difficile</i> A C-terminal <i>S</i>-[(Z)-2-aminovinyl]-d-cysteine (AviCys) residue is derived from a decarboxylation of a terminal cysteine that is involved in lanthionine ring formation. Studies on mutacin 1140 have revealed new insight into the structural importance of the C-terminal AviCys residue. A C-terminal carboxyl analogue of mutacin 1140 was engineered. Capping the C-terminal carboxyl group with a primary amine restores bioactivity and affords a novel opportunity to synthesize new analogues. A C-terminal fluorescein-labeled mutacin 1140 analogue traps lipid II into a large lipid II lantibiotic complex, similar to that observed <i>in vivo</i> for the lantibiotic nisin. A C-terminal carboxyl analogue of mutacin 1140 competitively inhibits the activity of native mutacin 1140 and nisin. The presence of a C-terminal carboxyl group prevents the formation of the large lipid II lantibiotic complexes but does not prevent the binding of the lantibiotic to lipid II.<b>IMPORTANCE</b> This study addressed the importance of the C-terminal <i>S</i>-[(Z)-2-aminovinyl]-d-cysteine (AviCys) residue for antibacterial activity. We have learned that the posttranslational modification for making the AviCys residue is presumably important for the lateral assembly mechanism of activity that traps lipid II into a large complex. The C-terminal carboxyl analogue of this class of lantibiotics is agreeable to the addition of a wide variety of substrates. The addition of fluorescein enabled <i>in vivo</i> visualization of the epidermin class of lantibiotics in action. These results are significant because, as we demonstrate, the presence of the AviCys residue is not essential for bioactivity, but, more importantly, the removal of the carboxyl group is essential. The ability to make a C-terminal carboxyl analogue that is modifiable will facilitate the synthesis of novel analogues of the epidermin class of lantibiotics that can be developed for new applications.
Sodium‐Ion‐Selective Two‐Photon Fluorescent Probe for In Vivo Imaging (2009)

Zwei Photonen sind besser als eines: Eine Zweiphotonensonde (ANa1, siehe Bild) in Zellen reagiert auf Na+ mit einer starken Zweiphotonenfluoreszenzverstärkung und einer Dissoziationskonstante Kdi von (26±2) mM. Sie lässt sich einfach in Zellen einführen und weist über lange Zeit selektiv intrazelluläres freies Na+ in lebenden Zellen und Geweben in einer Tiefe von 100–200 μm nach. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Synthesis of (3-carboxy-5-oxo-5H-(1)benzopyrano(2,3-b)pyridin-2-yl)acetic acid derivatives, potential antiarthritic agents. (1986)

(3-Carboxy-5-oxo-5H[1]benzopyrano[2, 3-b]pyridin-2-yl)acetic acid derivatives (3 and 4) were found to possess potent antiarthritic activity in the rat adjuvant arthritis model. The mode of action of these compounds differs from that of acidic antiinflammatory drugs. Various modifications in these compounds (e.g., elongation, removal, or substitution of the methylene group of the acetic acid moiety; and substitution of the benzene ring) were made in order to study the structure-activity relationships. However, it was found that the structural requirements for the compounds to show activity are rather severe.
Assessing post-anterior cruciate ligament reconstruction ambulation using wireless wearable integrated sensors (2013)

Abstract A hardware/software co-design for assessing post-Anterior Cruciate Ligament (ACL) reconstruction ambulation is presented. The knee kinematics and neuromuscular data during walking (2-6 km h(-1)) have been acquired using wireless wearable motion and electromyography (EMG) sensors, respectively. These signals were integrated by superimposition and mixed signals processing techniques in order to provide visual analyses of bio-signals and identification of the recovery progress of subjects. Monitoring overlapped signals simultaneously helps in detecting variability and correlation of knee joint dynamics and muscles activities for an individual subject as well as for a group. The recovery stages of subjects have been identified based on combined features (knee flexion/extension and EMG signals) using an adaptive neuro-fuzzy inference system (ANFIS). The proposed system has been validated for 28 test subjects (healthy and ACL-reconstructed). Results of ANFIS showed that the ambulation data can be used to distinguish subjects at different levels of recuperation after ACL reconstruction.
Utility of esophageal mucosal impedance as a diagnostic test for esophageal disease (2017)

MI can differentiate esophageal disorders instantly during endoscopy, and can monitor treatment responses in GERD and eosinophilic esophagitis.
Measuring Linkability of Protected Biometric Templates Using Maximal Leakage (2023)

As the applications of biometric recognition systems are increasing rapidly, there is a growing need to secure the sensitive data used within these systems. Considering privacy challenges in such systems, different biometric template protection (BTP) schemes were proposed in the literature, and the ISO/IEC 24745 standard defined a number of requirements for protecting biometric templates. While there are several studies on evaluating different requirements of the ISO/IEC 24745 standard, there have been few studies on how to measure the linkability of biometric templates. In this paper, we propose a new method for measuring linkability of protected biometric templates. The proposed method is based on maximal leakage, which is a well-studied measure in information-theoretic literature. We show that the resulting linkability measure has a number of important theoretical properties and an operational interpretation in terms of statistical hypothesis testing. We compare the proposed measure to two other linkability measures: one previously introduced in the literature, and a similar measure based on differential privacy. In our experiments, we use the proposed measure to evaluate the linkability of biometric templates from different biometric characteristics (face, voice, and finger vein), which are protected with different BTP schemes. The source codes of our proposed measure and all experiments are publicly available.
PP68. APTAMER TARGETING OF KU 70/80 IN GLIOMA (2017)

INTRODUCTION: Aptamers are in vitro generated DNA and RNA sequences. Aptamer sequences have multiple permutations and combinations of nucleotides and are then ‘selected’, using Sequential Enumeration of Ligands by Exponential Enrichment (SELEX) towards the desired, known or unknown target. Modified aptamers based on published sequences against glioma cell lines and newly generated sequences were used in the project to identify and confirm the targets. METHODS: Commercially available glioma cell lines and short term cultures from anonymised patient tissue were used. Fluorescent and biotin conjugated aptamers were incubated with glioma cell cultures and imaged using confocal or light microscopy. Aptamers were then reacted with glial cell lysate and subjected to precipitation using streptavidin agarose beads and SDS polyacrylamide electrophoresis. Proteins were analysed by mass spectroscopy. Ku 70 (X-ray Repair Cross Complementing protein 6), and Ku80 (X-ray Repair Cross Complementing protein 5) were identified as the most abundant protein when compared to control aptamer precipitation. Western blot analysis and siRNA knockdown was used to further confirm the target. RESULTS: Ku70 and Ku80 were precipitated along with known proteins associated proteins such as nucleolin as well as a few unknown proteins. Western blot analysis confirmed abundant precipitation of Ku70 and Ku80 when compared to control aptamer. DAB staining of cell cultures revealed over-expression of Ku70 and Ku80 throughout the cell. Knock down with siRNA showed reduced binding of the aptamer to the nucleus when compared to untreated cell cultures. CONCLUSIONS: Certain aptamers appear to be targeting DNA repair proteins Ku70 and Ku80 and could be used for developing targeted therapy towards glioma. Western and knockdown analysis, confirm the specificity of binding and leads the way for in-vivo testing of aptamers.
Improved Decoding of Staircase Codes: The Soft-Aided Bit-Marking (SABM) Algorithm (2019)

Staircase codes (SCCs) are typically decoded using iterative bounded-distance decoding (BDD) and hard decisions. In this paper, a novel decoding algorithm is proposed, which partially uses soft information from the channel. The proposed algorithm is based on marking certain number of highly reliable and highly unreliable bits. These marked bits are used to improve the miscorrection-detection capability of the SCC decoder and the error-correcting capability of BDD. For SCCs with 2-error-correcting Bose-Chaudhuri-Hocquenghem component codes, our algorithm improves upon standard SCC decoding by up to 0.30 dB at a bit-error rate (BER) of 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-7</sup> . The proposed algorithm is shown to achieve almost half of the gain achievable by a genie decoder with this structure. The increased complexity caused by bit marking and additional calls to the component BDD decoder is discussed as well. Our algorithm is also extended (with minor modifications) to product codes. The simulation results show that in this case, the algorithm offers gains of up to 0.5 dB at a BER of 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-7</sup> .
Efficient Synthesis of Antisense Phosphorothioate Oligonucleotides:  Evaluation of Dichloroacetic Acid at Higher Concentration to Reduce Cycle Time (2003)

Efficiency of phosphorothioate oligonucleotide syntheses could be improved by increasing the concentration of dichloroacetic acid in toluene to 10% from 3% (v/v) during the detritylation step. It was also found that dichloroacetic acid is better than dichloropropionic acid when compared at similar concentrations.
Techniques for improving the performance of CELP type speech coders (1991)

Techniques for improving the performance of CELP (code excited linear prediction) type speech coders while maintaining reasonable computational complexity are explored. A harmonic noise weighting function which enhances the perceptual quality of the processed speech is introduced. The combination of harmonic noise weighting and subsample resolution pitch significantly improves the coder performance for voiced speech. A 6.9 kb/s VSELP speech coder which incorporates subsample resolution pitch and harmonic noise weighting is described. Complexity reduction techniques are discussed which allow the coder to be implemented using a single fixed point digital signal processor.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Tunable compensation of the dispersion slope mismatch in dispersion-managed systems using a sampled nonlinearly chirped FBG (2000)

We demonstrate dispersion slope compensation for three 10-Gbit/s wavelength-division-multiplexing (WDM) channels using a sampled nonlinearly chirped fiber Bragg grating (FBG) in a dispersion-managed transmission system. The replicated wavelength bands of the sampled FBG have a different wavelength separation than the WDM channels, causing each channel to experience a different dispersion compensation that can be tuned upon stretching of the FBG. We achieve significant power penalty reduction for all three channels using our dispersion-slope-compensation method with a tunable amount of dispersion over 900 and 1200 km fiber links.
Tissue-engineered intervertebral discs: MRI results and histology in the rodent spine (2014)

The TE-IVDs remained viable over 8 months in vivo and maintained a structure similar to that of native discs. Tissue-engineered intervertebral discs should be explored further as an option for the potential treatment of degenerative disc disease.
Body temperature triggered shape‐memory polymers with high elastic energy storage capacity (2016)

ABSTRACT Shape‐memory polymers (SMPs) that respond near body temperature are attracting broad interest, especially in the biomedical fields. In this study, the triggering temperature of poly(caprolactone) SMP networks is precisely adjusted by inclusion of non‐crystallizable molecular linkers and by variation of prepolymer molecular weight. Longer, non‐crystalline linkers and lower molecular weight prepolymers interfere with crystallization, lowering the transition temperature. Networks are prepared with crystallization temperatures that are beneath the human body temperature and yet are above room temperature. Upon cooling such amorphous networks to room temperature, crystallization is sluggish. There, elastomers can be easily strained by several hundred‐percent to induce crystallization, thereby fixing strained states. If subsequently heated, programmed SMPs can release significant amounts of stored strain energy (∼3 MJ/m 3 ). SMPs that combine elastic energy storage and exhibit triggering temperatures near the human body temperature could benefit emerging applications in the biomedical space. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2016 , 54 , 1397–1404
A Sensitive Enzyme-Linked Assay of ADAMTS13 Antibodies for Diagnosis of TTP. (2005)

Abstract Thrombotic thrombocytopenic purpura (TTP), a serious disorder characterized by the development of VWF-platelet rich thrombi in the arterioles and capillaries, requires reliable diagnostic assays for optimal management of the patients. Simple, reliable assays of ADAMTS13 inhibitors or antibodies are not yet widely available. To develop an ELISA for antibodies of ADAMTS13, we analyze the levels of patient IgG bound to immobilized recombinant ADAMTS13 in a microtiter plate format. The mean (±SD) IgG binding value is 5.1 ± 1.5 arbitrary units (AU)/mL among a group of 36 normal subjects and is 5.3 ± 2.7 AU/mL among 31 random patients (P &gt; 0.1). Two (5%) of the normal group and 2 (6%) of the random group are outliers. When applied to patients with thrombotic microangiopathy, this assay yields IgG binding values ranging from 2.0 – 58.3 (median = 5.4) AU/mL in a group of 40 subjects with other thrombotic microangiopathy and 10.1 - &gt; 60.0 (median 49.0) AU/mL in a group of 56 patients with acute TTP. Excluding 2 (5%) outlying samples, the mean (±SD) for the “other TM” group is 5.9 ±2.5 AU/mL, which is not different from the values of the normal and random subjects. In contrast, the IgG binding values are &gt; 10.0 AU/mL in each of the acute TTP patients. Furthermore, heating the plasma samples at 56oC, presumably by dissociating ADAMTS13 from immune complexes, increases IgG binding of 4 weakly positive TTP samples from 10.1 – 12.7 to 28.3 – 154.3 AU/mL. Addition of native ADAMTS13 lacking the tag sequences decreases the binding of TTP IgG to 40% ± 20% of control, but does not affect the binding of 6 outlying non-TTP IgG (120% ± 20% vs. control, P &lt; 0.001), suggesting that the IgG of non-TTP samples do not recognize ADAMTS13. In summary, the ELISA for ADAMTS13 antibodies is highly sensitive for detection of ADAMTS13 antibodies. A subset of the general population contains IgG molecules that react with the recombinant ADAMTS13 fusion protein but not with native ADAMTS13. Blocking with native ADAMTS13 enhances the specificity of the assay for TTP. Figure Left: Binding of IgG to immobilized rADAMTS13-FLAG/His in four groups of study subjects. Right: Suppression of IgG binding by untagged ADAMTS13 in TTP but not in non-TTP samples. Figure. Left: Binding of IgG to immobilized rADAMTS13-FLAG/His in four groups of study subjects. . / Right: Suppression of IgG binding by untagged ADAMTS13 in TTP but not in non-TTP samples.
3VQM: A vision-based quality measure for DIBR-based 3D videos (2011)

In this paper, we present a new method for objectively evaluating the quality of stereoscopic 3D videos generated by depth-image-based rendering (DIBR). First we show how to derive an ideal depth estimate at each pixel value that would constitute a distortion-free rendered video. The ideal depth estimate will then be used to derive three distortion measures to objectify the visual discomfort in the stereoscopic videos. The three measures are temporal outliers (TO), temporal inconsistencies (TI), and spatial outliers (SO). The combination of the three measures will constitute a vision-based quality measure for 3D DIBR-based videos, 3VQM. Finally, 3VQM will be presented and verified against a fully conducted subjective evaluation. The results show that our proposed measure is significantly accurate, coherent and consistent with the subjective scores.
Gel electrophoresis of human sperm: a simple method for evaluating sperm protein quality (2018)

One-dimensional PAGE constitutes a simple, rapid, reliable, inexpensive method for analyzing proteins associated with sperm motility in individual human ejaculates.
Engineering of the Rose Flavonoid Biosynthetic Pathway Successfully Generated Blue-Hued Flowers Accumulating Delphinidin (2007)

Flower color is mainly determined by anthocyanins. Rosa hybrida lacks violet to blue flower varieties due to the absence of delphinidin-based anthocyanins, usually the major constituents of violet and blue flowers, because roses do not possess flavonoid 3',5'-hydoxylase (F3'5'H), a key enzyme for delphinidin biosynthesis. Other factors such as the presence of co-pigments and the vacuolar pH also affect flower color. We analyzed the flavonoid composition of hundreds of rose cultivars and measured the pH of their petal juice in order to select hosts of genetic transformation that would be suitable for the exclusive accumulation of delphinidin and the resulting color change toward blue. Expression of the viola F3'5'H gene in some of the selected cultivars resulted in the accumulation of a high percentage of delphinidin (up to 95%) and a novel bluish flower color. For more exclusive and dominant accumulation of delphinidin irrespective of the hosts, we down-regulated the endogenous dihydroflavonol 4-reductase (DFR) gene and overexpressed the Irisxhollandica DFR gene in addition to the viola F3'5'H gene in a rose cultivar. The resultant roses exclusively accumulated delphinidin in the petals, and the flowers had blue hues not achieved by hybridization breeding. Moreover, the ability for exclusive accumulation of delphinidin was inherited by the next generations.
An automatic threshold-converged CMOS optical receiver for high-definition digital audio interfaces (2007)

This paper proposes an automatic threshold converged CMOS optical receiver employing a threshold convergence technique to reduce pulse width distortion and design complexity in high-definition digital audio interfaces. A threshold concentrator is introduced at the receiver, in order to improve digital audio quality by aligning various logic thresholds of the input signals into a constant one. Simulation results demonstrate that the designed optical receiver in a 0.18-µm CMOS technology can successfully reduce pulse width distortion within -2% and circuit complexity.
<title><emph type="1">In vivo</emph> detection of cervical dysplasia with near-infrared Raman spectroscopy</title> (2002)

Raman spectroscopy has been shown to have the potential for providing differential diagnosis in the cervix with high sensitivity and specificity in previous in vitro and in vivo studies. A clinical study was designed at Vanderbilt University Medical Center to further evaluate the potential of near IR Raman spectroscopy for in vivo detection of squamous intra-epithelial neoplasia, a pre-cursor to cervical cancer, in a clinical setting. In this pilot in vivo clinical study, using a portable system, Raman spectra are collected using clinically feasible integration times during colposcopic evaluation. Multiple Raman spectra were acquired form colposcopically normal and abnormal sites prior to excision of tissue from patients with known abnormalities of the cervix. Measured Raman spectra were processed for nosie and background fluorescence using novel signal processing techniques. The resulting spectra were correlated with the corresponding histological diagnosis to determine empirical differences in spectra between different diagnostic categories. Using histology as the gold standard, multivariate statistical techniques were also used to develop discrimination algorithms with the hopes of developing this technique into a real time, non-invasive diagnostic tool.