gebhart/patrepeval huggingface dataset:
Comparison of physical characteristics and collection and elution performance of clinical swabs (2013)

Diagnostic sensitivity of a clinical test is a function of the number of organisms collected and eluted from the swab head that is attributed to the type of fibers and their physical characteristics. To relate these properties, water and protein absorption of nylon flocked, rayon flocked, and HydraFlock® and macrofoam swabs manufactured by Puritan Medical Products, and nylon flocked swab made by Copan Diagnostics were determined. The water and protein absorption capacities of whole swabs ranged from 17 to 21.5% and 13.6 to 19.6%, respectively. The HydraFlock® swab exhibited the highest water and protein absorption capacities in the group. Among the swab tip materials tested, macrofoam exhibited the highest water absorption capacity. Zeta potential of flocked swab fibers as a function of pH showed differences in charged groups depending on fiber types. The collection and release of bacteria with swabs using suspensions of clinically important pathogenic bacteria demonstrated the highest (69%) overall recovery by HydraFlock® swab and macrofoam swab ranked second (62%). The recovery of Gram-negative bacteria was significantly higher compared to Gram-positive bacteria across the swab types. The results of the present study indicate potential superiority of HydraFlock® swab over other swabs in a clinical setting and by collecting and releasing significantly larger numbers of bacteria.

	 

	Key words: Flocked swabs, water absorption, zeta potential, and pathogenic bacteria.
Exploring Peptide Space for Enzyme Modulators (2010)

A method is presented for screening high-density arrays to discover peptides that bind and modulate enzyme activity. A polyvinyl alcohol solution was applied to array surfaces to limit the diffusion of product molecules released from enzymatic reactions, allowing the simultaneous measurement of enzyme activity and binding at each peptide spot. For proof of concept, it was possible to identify peptides that bound to horseradish peroxidase, alkaline phosphatase, and beta-galactosidase and substantially altered enzyme activity by comparing the binding level of peptide to enzyme and bound enzyme activity. This basic technique may be generally applicable to find peptides or other small molecules that modify enzyme activity.
Single-Ended and Differential Ka-Band BiCMOS Phased Array Front-Ends (2008)

Single-ended and differential phased array front-ends are developed for Ka-band applications using a 0.12 mum SiGe BiCMOS process. The phase shifters are based on CMOS switched delay networks and have 22.5deg phase resolution and <4deg rms phase error at 35 GHz, and can handle +10 dBm of RF power (P <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1dB</sub> ) with a 3rd order intermodulation intercept point (IIP3) of +21 dBm. For the single-ended design, a SiGe low noise amplifier is placed before the CMOS phase shifter, and the LNA/phase shifter results in 11 plusmn 1.5 dB gain and <3.4 dB of noise figure (NF), for a total power consumption of only 11 mW. For the differential front-end, a variable gain LNA is also developed and shows 9-20 dB gain and <1deg rms phase imbalance between the eight different gain states. The differential variable gain LNA/phase shifter consumes 33 mW, and results in 10 + 1.3 dB gain and 3.8 dB of NF. The gain variation is reduced to 9.1 plusmn 0.45 dB with the variable gain function applied. The single-ended and differential front-ends occupy a small chip area, with a size of 350 times 800 mum <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> and 350 times 950 mum2, respectively, excluding pads. These chips are competitive with GaAs and InP designs, and are building blocks for low-cost millimeter-wave phased array front-ends based on silicon technology.
Formal modeling and analysis of an audio/video protocol: an industrial case study using UPPAAL (2002)

A formal and automatic verification of a real-life protocol is presented. The protocol, about 2800 lines of assembler code, has been used in products from the audio/video company Bang & Olufsen throughout more than a decade, and its purpose is to control the transmission of messages between audio/video components over a single bus. Such communications may collide, and one essential purpose of the protocol is to detect such collisions. The functioning is highly dependent on real-time considerations. Though the protocol was known to be faulty in that messages were lost occasionally, the protocol was too complicated in order for Bang & Olufsen to locate the bug using normal testing. However using the real-time verification tool UPPAAL, an error trace was automatically generated, which caused the detection of "the error" in the implementation. The error was corrected and the correction was automatically proven correct, again using UPPAAL. A future, and more automated, version of the protocol, where this error is fatal, will incorporate the correction. Hence, this work is an elegant demonstration of how model checking has had an impact on practical software development. The effort of modeling this protocol has in addition generated a number of suggestions for enriching the UPPAAL language. Hence, it's also an excellent example of the reverse impact.
Development and Characterization of a Novel, Graded Model of Clip Compressive Spinal Cord Injury in the Mouse: Part 2. Quantitative Neuroanatomical Assessment and Analysis of the Relationships between Axonal Tracts, Residual Tissue, and Locomotor Recovery (2002)

A detailed examination of the histopathological features of the clip compression injury in mice was performed to understand the relationships between neurological function and existing pathology of the spinal cord. Adult, female CD1 mice underwent three grades of extradural clip compression injury (3-g, 8-g, and 24-g FEJOTA mouse clips), transection, and sham injury at T3-4. Quantitative behavioural assessments were performed for 4 weeks following SCI. After 4 weeks, Fluoro-Gold was introduced caudal to the SCI site, at T9, and was retrogradely transported for 5 days to the origin of spared axons through the injury site. Counts of retrogradely labeled neurons in the brain-stem, midbrain, and sensory-motor cortex indicated that the number of intact descending axons that traversed the lesion decreased with increasing injury severity (F > 28; df = 4; p < 0.0001; one-way ANOVA). Independent linear correlation analyses were performed between indices of neurological recovery (BBB and IP test), counts of retrogradely labeled neurons and morphometric assessments of normal residual tissue at the injury epicenter. The BBB test correlated strongly with the amount of residual tissue at the injury epicenter (R = 0.945, df = 28, p < 0.0001). Counts of neurons retrogradely labeled with Fluoro-Gold were also strongly correlated with the BBB scores. The extrapyramidal (raphespinal, reticulospinal, vestibulospinal, and rubrospinal) tracts had Pearson correlation coefficients (R) of 0.814, 0.812, 0.813, and 0.747, respectively (df = 28, p < 0.0001). The pyramidal (corticospinal) tract had a correlation of R = 0.747, df = 28, p < 0.0001 with the BBB scores. The IP scores also correlated strongly with the persistence of extrapyramidal (raphespinal, reticulospinal, vestibulospinal and rubrospinal) tracts with correlation coefficients of 0.801, 0.782, 0.790, and 0.836, respectively (df = 28, p < 0.0001). These data indicate that the counts of retrogradely labeled neurons at the origin of distinct descending motor pathways are predictors of the variance of the functional recovery measured by the BBB and IP tests following spinal cord injury. In addition, we provide a detailed neuroanatomical study of clip compression injury in mice that can be used to study the molecular mechanisms of SCI in knockout and transgenic mice.
Role of STAT3 in inflammatory bowel disease (2008)

Signal transducers and activators of transcription 3 (STAT3) play an important role in various autoimmune disorders including inflammatory bowel disease (IBD). Recent studies have revealed that STAT3 activation plays distinctly different roles between innate immune responses and acquired immune responses in colitis. STAT3-mediated activation of acquired immune responses plays a pathogenic role in colitis by enhancing the survival of pathogenic T cells. In contrast, STAT3-mediated activation of innate responses contributes to the suppression of colitis. This review will summarize the current understanding of the roles of STAT3 in IBD and the potential of targeting STAT3 for the treatment of IBD, emphasizing recent observations.
The role of dipeptidyl peptidase IV in human T lymphocyte activation. Inhibitors and antibodies against dipeptidyl peptidase IV suppress lymphocyte proliferation and immunoglobulin synthesis in vitro (1987)

Dipeptidyl peptidase IV (DP IV), an ectoenzyme in the cell membrane of T lymphocytes, is an important constituent in the process of lymphocyte activation. This conclusion is drawn from the following observations: (a) Proliferation of peripheral blood lymphocytes induced by mitogenic lectins (phytohemagglutinin, concanavalin A, pokeweed mitogen) is suppressed in the presence of DP IV inhibitors. This effect is specific and applies to an irreversible suicide inhibitor as well as to a competitive one in a dose-dependent fashion. (b) Inhibition of DNA synthesis was also induced by a polyclonal anti-DP IV immunoglobulin. (c) As a consequence of impaired T cell function the production of immunoglobulins by pokeweed mitogen-stimulated lymphocytes is also markedly reduced in the presence of DP IV inhibitors.
A 64Gb/s PAM-4 transceiver utilizing an adaptive threshold ADC in 16nm FinFET (2018)

ADC-based transceivers having up to 8 bits of resolution have been reported for PAM-4 links above 50Gb/s [1,2], although fewer bits are sufficient and offer lower power for short reach (SR) channels. To further reduce the power consumption of ADC-based wireline transceivers, non-uniform quantization has been explored [3,4] using performance metrics for the complete link, such as bit-error rate (BER), to optimize the quantizer thresholds. Both [3,4] are PAM-2 (NRZ) receivers, demonstrating non-uniform quantization specifically for a decision feedback equalizer (DFE) at 10Gb/s and a feedforward equalizer (FFE) at 4Gb/s respectively. An LMS algorithm in [4] adjusts the threshold levels requiring fine-tuning (8b resolution). This paper presents a 64Gb/s PAM-4 transceiver utilizing an ADC-based receiver (RX), with an analog front-end (AFE) based on a 6b, 1b folding, flash ADC with adaptive threshold levels. A fast greedy-search algorithm is used to choose the optimal quantizer thresholds for minimum BER over a given channel. This provides a near-optimal way of power-scaling the ADC when the channel loss doesn't require the ADC's full resolution. The optimization can work in the background for any equalizer structure, does not place additional requirements on the ADC design, and never diverges, unlike LMS-based approaches [4].
Next-Generation Sequencing of Stage IV Squamous Cell Lung Cancers Reveals an Association of PI3K Aberrations and Evidence of Clonal Heterogeneity in Patients with Brain Metastases (2015)

We performed next-generation sequencing of metastatic SQCLCs and primary lung-brain metastasis pairs, identifying PI3K-aberrant tumors as an aggressive subset associated with brain metastases. We identified genetic heterogeneity between lung primaries-brain metastases as well as clonal populations that may highlight alterations important in the metastatic process.
A 3D-printed device for a smartphone-based chemiluminescence biosensor for lactate in oral fluid and sweat (2014)

Increasingly, smartphones are used as portable personal computers, revolutionizing communication styles and entire lifestyles. Using 3D-printing technology we have made a disposable minicartridge that can be easily prototyped to turn any kind of smartphone or tablet into a portable luminometer to detect chemiluminescence derived from enzyme-coupled reactions. As proof-of-principle, lactate oxidase was coupled with horseradish peroxidase for lactate determination in oral fluid and sweat. Lactate can be quantified in less than five minutes with detection limits of 0.5 mmol L(-1) (corresponding to 4.5 mg dL(-1)) and 0.1 mmol L(-1) (corresponding to 0.9 mg dL(-1)) in oral fluid and sweat, respectively. A smartphone-based device shows adequate analytical performance to offer a cost-effective alternative for non-invasive lactate measurement. It could be used to evaluate lactate variation in relation to the anaerobic threshold in endurance sport and for monitoring lactic acidosis in critical-care patients.
[The strength of the elements of the human spinal column and the problems of the etiology, pathogenesis and principles of the treatment of degenerative spinal lesions]. (1994)

The study was made of strength characteristics of the vertebra and intervertebral disks of moving parts of human spine in postembryonic ontogenesis. The authors have obtained statistically significant data on degenerative dystrophic changes and lesions of human spine. Pathogenetic issues, conservative and surgical treatment policies in degenerative lesions are considered. The authors hold, that osteochondrosis is not the right term to denote degenerative lesions of the spine.
Modulation of central nervous system–specific microRNA-124a alters the inflammatory response in the formalin test in mice (2012)

microRNAs (miRNAs) are small noncoding RNAs that have been linked to a number of disease-related signal transduction pathways. Several studies indicate that they are also involved in nociception. It is not clear, however, which miRNAs are important and which genes are modulated by miRNA-associated mechanisms. This study focuses on the regulation and function of the central nervous system (CNS)-specific miRNA-124a in the spinal cord of mice in a formalin model of inflammatory nociception. miRNA-124a is constitutively expressed in the spinal cord of mice, particularly in neurons of the dorsal horn. Peripheral noxious stimulation with formalin led to significant down-regulation of its expression. Knock-down of miRNA-124a by intravenous administration of a specific miRNA-124a inhibitor further increased the nociceptive behavior associated with an upregulation of the pain-relevant miRNA-124a target MeCP2 and proinflammatory marker genes. In contrast, administration of a miRNA-124a mimic counteracted these effects and decreased nociception by down-regulation of the target gene. In conclusion, our results indicate that miRNA-124a is involved in inflammatory nociception by regulation of relevant target proteins and might therefore constitute a novel target for anti-inflammatory therapy.
Structure−Antiviral Activity Relationship in the Series of Pyrimidine and Purine N-[2-(2-Phosphonomethoxy)ethyl] Nucleotide Analogues. 1. Derivatives Substituted at the Carbon Atoms of the Base (1999)

A series of dialkyl esters of purine and pyrimidine N-[2-(phosphonomethoxy)ethyl] derivatives substituted at position 2, 6, or 8 of the purine base or position 2, 4, or 5 of the pyrimidine base were prepared by alkylation of the appropriate heterocyclic base with 2-chloroethoxymethylphosphonate diester in the presence of sodium hydride, cesium carbonate, or 1,8-diazabicyclo[5,4, 0]undec-7-ene (DBU) in dimethylformamide. Additional derivatives were obtained by the transformations of the bases in the suitably modified intermediates bearing reactive functions at the base moiety. The diesters were converted to the corresponding monoesters by sodium azide treatment, while the free acids were obtained from the diester by successive treatment with bromotrimethylsilane and hydrolysis. None of the PME derivatives in the pyrimidine series, their 6-aza or 3-deaza analogues, exhibited any activity against DNA viruses or retroviruses tested, except for the 5-bromocytosine derivative. Substitution of the adenine ring in PMEA at position 2 by Cl, F, or OH group decreased the activity against all DNA viruses tested. PMEDAP was highly active against HSV-1, HSV-2, and VZV in the concentration range (EC50) of 0.07-2 microg/mL. Also the 2-amino-6-chloropurine derivative was strongly active (EC50 = 0.1-0. 4 microg/mL) against herpes simplex viruses and (EC50 = 0.006-0.3 microg/mL) against CMV and VZV. PMEG was the most active compound of the whole series against DNA viruses (EC50 approximately 0.01-0.02 microg/mL), though it exhibited significant toxicity against the host cells. The base-modified compounds did not show any appreciable activity against DNA viruses except for 7-deazaPMEA (IC50 approximately 7.5 microg/mL) against HIV-1 and MSV. The neutral (diisopropyl, diisooctyl) diesters of PMEA were active against CMV and VZV, while the corresponding monoesters were inactive. The diisopropyl ester of the 2-chloroadenine analogue of PMEA showed substantially (10-100x) higher activity against CMV and VZV than the parent phosphonate. Also, the diisopropyl and diisooctyl ester of PMEDAP inhibited CMV and VZV, but esterification of the phosphonate residue did not improve the activity against either MSV or HIV.
Cytokine production induced by Mycobacterium tuberculosis lipoarabinomannan. Relationship to chemical structure (1992)

Lipoarabinomannan (LAM), a major cell wall component of Mycobacterium tuberculosis, exhibits a wide spectrum of immunoregulatory effects. To identify cytokines produced by human PBMC in response to LAM, we used PCR amplification to detect cytokine mRNA. LAM-induced transcription of mRNA for cytokines characteristically produced by macrophages, including TNF, granulocyte-macrophage-CSF, IL-1 alpha, IL-1 beta, IL-6, IL-8, and IL-10. In contrast, LAM did not induce transcription of mRNA for cytokines produced predominantly by lymphocytes, such as lymphotoxin, IFN-gamma, IL-2, IL-3, or IL-4. Measurement of concentrations of TNF, granulocyte-macrophage-CSF, IL-6, IL-10, IFN-gamma, IL-2, and IL-4 in cell culture supernatants indicated that cytokine release correlated with mRNA patterns. Lipomannan (LM) and phosphatidylinositol mannosides (PIM) are simpler versions of LAM. LM lacks arabinan, whereas PIM lacks both arabinan and most mannan residues. LAM, LM, and PIM induced transcription of cytokine mRNA, elicited cytokine production, and suppressed Ag-induced T cell proliferation, indicating that most of the biologic activity of LAM was associated with the phosphatidylinositol end of the molecule. In support of this conclusion, deacylation of LAM abrogated its capacity to induce cytokine production and suppress Ag-induced proliferation. The production of macrophage-derived cytokines induced by LAM may mediate clinical manifestations of tuberculosis such as fever, weight loss, and tissue necrosis, as well as immunoregulatory effects such as inhibition of Ag-induced proliferation and hyperglobulinemia.
Sensory innervation of the calvarial bones of the mouse (2009)

Migraine sufferers frequently testify that their headache feels as if the calvarial bones are deformed, crushed, or broken (Jakubowski et al. [2006] Pain 125:286-295). This has lead us to postulate that the calvarial bones are supplied by sensory fibers. We studied sensory innervation of the calvaria in coronal and horizontal sections of whole-head preparations of postnatal and adult mice, via immunostaining of peripherin (a marker of thinly myelinated and unmyelinated fibers) or calcitonin gene-related peptide (CGRP; a marker more typical of unmyelinated nerve fibers). In pups, we observed nerve bundles coursing between the galea aponeurotica and the periosteum, between the periosteum and the bone, and between the bone and the meninges; as well as fibers that run inside the diploë in different orientations. Some dural fibers issued collateral branches to the pia at the frontal part of the brain. In the adult calvaria, the highest concentration of peripherin- and CGRP-labeled fibers was found in sutures, where they appeared to emerge from the dura. Labeled fibers were also observed in emissary canals, bone marrow, and periosteum. In contrast to the case in pups, no labeled fibers were found in the diploë of the adult calvaria. Meningeal nerves that infiltrate the periosteum through the calvarial sutures may be positioned to mediate migraine headache triggered by pathophysiology of extracranial tissues, such as muscle tenderness and mild trauma to the skull. In view of the concentration of sensory fibers in the sutures, it may be useful to avoid drilling the sutures in patients undergoing craniotomies for a variety of neurosurgical procedures.
Synthesis of Some New 5-Dialkylaminomethylhydantoins and Related Compounds (2012)

In this paper, we describe the synthesis of new 5-dialkylaminomethyl-substituted hydantoin derivatives (3 and 9) from !-aminoalanines (1 or 6) and some chemical properties of the synthesized compounds.A synthetic trial for the preparation of a new twin-drug type molecule (12) is also described.In connection with studies on new antibacterial compounds, many synthetic studies on molecular modifications have been carried out to find new promising candidates.Many reports on molecular recognition properties of artificial molecules have appeared, and many chemists are naturally interested in studying such biologically active substances.We have been interested in substances that interfere with molecular recognition process 1-4 in order to find new leads for antibacterial agents.We have already examined molecular modification of a bioisosteric replacement of the oxazolidinone ring in linezolid by a hydantoin nucleus. 5-7Regarding biological activities of synthesized hydantoin derivatives, we have observed that most of the 5-dialkylaminomethy-3-arylhydantoin derivatives (A) show a wide range of significant antibacterial activities against either gram-positive or gram-negative strains. 7For this attractive bioactivity of 5-dialkylaminomethyl-substituted hydantoins, further molecular modifications of this class of compounds seemed to be interesting.In this article, we describe a novel synthetic route for new 5-dialkylaminomethylhydantoin-related heterocycles and some chemical properties of the synthesized hydantoin derivatives.
Chromophore-Assisted Light Inactivation of HaloTag Fusion Proteins Labeled with Eosin in Living Cells (2011)

Chromophore-assisted light inactivation (CALI) is a potentially powerful tool for the acute disruption of a target protein inside living cells with high spatiotemporal resolution. This technology, however, has not been widely utilized, mainly because of the lack of an efficient chromophore as the photosensitizing agent for singlet oxygen ((1)O(2)) generation and the difficulty of covalently labeling the target protein with the chromophore. Here we choose eosin as the photosensitizing chromophore showing 11-fold more production of ((1)O(2)) than fluorescein and about 5-fold efficiency in CALI of β-galactosidase by using an eosin-labeled anti-β-galactosidase antibody compared with the fluorescein-labeled one. To covalently label target protein with eosin, we synthesize a membrane-permeable eosin ligand for HaloTag technology, demonstrating easy labeling and efficient inactivation of HaloTag-fused PKC-γ and aurora B in living cells. These antibody- and HaloTag-based CALI techniques using eosin promise effective biomolecule inactivation that is applicable to many cell biological assays in living cells.
Decreased function of peripheral blood dendritic cells in patients with hepatocellular carcinoma with hepatitis B and C virus infection (2000)

These findings suggest that the depressed function of DC is associated with pathogenesis of HCC with HBV or HCV infection.