gebhart/patrepeval huggingface dataset:
Gap junction coupling‐mediated membrane potential oscillations drive activity in cutaneous but not muscle vasoconstrictor sympathetic preganglionic neurones in situ (2009)

A population of sympathetic preganglionic neurones (SPN) recorded in vitro show gap junction‐mediated oscillations in membrane potential that underlie their spike discharge (Logan et al , 1996, J Physiol), but the role of such coupling in vivo is uncertain. We made whole‐cell recordings from functionally identified SPN in the rat (aged p5‐16) working heart‐brainstem preparation (WHBP, (Paton, 1996, J Neurosci Meths)) to examine the neural mechanisms generating their firing activity. 108 SPNs identified in the T3‐4 segment were functionally categorised by responses to activation of peripheral chemoreflex (NaCN, ia) and diving response (cold to snout). Muscle vasoconstrictor (MVC, 38%) SPN were activated by both tests and converseley cutaneous vasoconstrictor (CVC, 27%) SPN were inhibited by both. MVCs had a higher baseline firing frequency in comparison with CVC (2.6±0.3 vs. 1.4±0.3 Hz; p =0.007) and shorter after‐hyperpolarization (156±10 vs. 296±39 ms, p =0.0001). MVC SPN showed a respiratory‐modulated pattern of firing generated by a torrent of kynurenate‐sensitive, excitatory synaptic inputs. By contrast, the activity of CVC SPN was driven by large, slow, biphasic membrane potential oscillations (n=14 of 15 examined) that resembled filtered action potentials which were relatively insensitive to membrane potential, not blocked by spinal kynurenate and were indistinguishable from those previously reported in vitro . Antidromic activation of CVC SPN evoked short latency depolarization confirming the presence of coupling. These findings indicate that gap junctional coupling plays an important functional role in the patterning and synchronization of the output from CVC but not MVC SPN. Funded by BHF.
Cycloquest: Identification of Cyclopeptides via Database Search of Their Mass Spectra against Genome Databases (2011)

Hundreds of ribosomally synthesized cyclopeptides have been isolated from all domains of life, the vast majority having been reported in the last 15 years. Studies of cyclic peptides have highlighted their exceptional potential both as stable drug scaffolds and as biomedicines in their own right. Despite this, computational techniques for cyclopeptide identification are still in their infancy, with many such peptides remaining uncharacterized. Tandem mass spectrometry has occupied a niche role in cyclopeptide identification, taking over from traditional techniques such as nuclear magnetic resonance spectroscopy (NMR). MS/MS studies require only picogram quantities of peptide (compared to milligrams for NMR studies) and are applicable to complex samples, abolishing the requirement for time-consuming chromatographic purification. While database search tools such as Sequest and Mascot have become standard tools for the MS/MS identification of linear peptides, they are not applicable to cyclopeptides, due to the parent mass shift resulting from cyclization and different fragmentation patterns of cyclic peptides. In this paper, we describe the development of a novel database search methodology to aid in the identification of cyclopeptides by mass spectrometry and evaluate its utility in identifying two peptide rings from Helianthus annuus, a bacterial cannibalism factor from Bacillus subtilis, and a θ-defensin from Rhesus macaque.
Abstract IA02: Defects in DNA repair genes revealed by clinical sequencing of advanced cancer patients (2017)

Abstract In 2011, we introduced the Mi-Oncoseq program, an IRB-approved protocol to carry out integrative sequencing of advanced cancer patients. It was one of the first comprehensive DNA and RNA sequencing programs offered for cancer patients. The purpose of this program was to determine the utility of genomic sequencing of tumors and germline coupled with a multi-disciplinary Precision Medicine Tumor Board (PMTB) in the management of advanced cancer patients. Collectively across all patient cohorts we have enrolled over 1500 patients since inception of Mi-Oncoseq where molecular results for both somatic and germline aberrations are returned to physicians. Both common and rare mutations were identified in numerous cellular pathways that are involved in carcinogenesis including those in the DNA repair pathway. We identified homozygous deletions, deleterious mutations and/or LOH in genes including BRCA1/2, ATM, Fanconi's anemia genes, and CHEK2 that are potentially actionable. For example, a multi-institutional, collaborative SU2C-PCF study of men with metastatic castrate-resistant prostate cancer (mCRPC) found that treatment with the PARP inhibitor olaparib in patients whose prostate cancers were no longer responding to standard treatments and who had defects in DNA-repair genes led to a high response rate (Mateo et al. NEJM, 2015). Additionally, a follow-up study found 11.8% of mCRPC patients had a germline mutation in a DNA-repair gene, including moderate risk genes (ATM, CHEK2, PALB2, RAD51D) for which clinical testing criteria do not exist (Pritchard et al, NEJM, 2016). Most of these patients would not qualify for germline genetic testing under current clinical care models. Our studies demonstrate that DNA repair mutations are common in mCRPC patients who may benefit from therapies such as PARP inhibitors and when identified in the germline, could have a significant impact on their family members where early cancer screening could be implemented as appropriate. Citation Format: Arul Chinnaiyan. Defects in DNA repair genes revealed by clinical sequencing of advanced cancer patients [abstract]. In: Proceedings of the AACR Special Conference on DNA Repair: Tumor Development and Therapeutic Response; 2016 Nov 2-5; Montreal, QC, Canada. Philadelphia (PA): AACR; Mol Cancer Res 2017;15(4_Suppl):Abstract nr IA02.
Photoconductive Properties of Regioregular Poly(3-hexylthiophene) (2007)

We investigate the photoconductivity of regioregular poly(3-hexylthiophene) using 400 and 800 nm light. We observe a linear dependence of the photocurrent on optical power at both wavelengths.
Structurally chiral photonic crystals with magneto-optic activity: indirect photonic bandgaps, negative refraction, and superprism effects (2005)

We have theoretically investigated the general properties of photonic crystals without time-reversal and space-inversion symmetries by examining the case of one-dimensional periodic, lossless dielectric helical media (HM) with magneto-optic (MO) activity. We show that photonic bandgap formation in the absence of these two symmetry elements leads to a remarkable set of properties: indirect photonic bandgaps (edges not aligned in k space), backward wave propagating eigenmodes (which allow for negative refraction), unusual nonpropagating modes in the gap (their complex-valued wave vectors have frequency-dependent, nonzero real parts, which do not change sign for opposite decay directions), anomalous propagation, and group-velocity-based unidirectional superprism effects. Particular properties of MO HM are discussed in detail.
<title>Electroluminescence and cathodoluminescence from inorganic CdSe nanocrystals embedded in thin films</title> (1998)

Electroluminescence (EL) from heterostructure devices made of organic poly (phenylene vinylene), PPV, and inorganic semiconductor CdSe nanocrystals have been investigated, along with cathodoluminescence (CL) from thin films of ZnS doped with CdSe-ZnS core-shell nanocrystals. In the EL devices, the organic PPV structure, built next to the anode using the technique of molecular layer-by-layer sequential adsorption, serves as the hole transport layer. The inorganic layer, adjacent to the electrode and made of spin cast CdSe nanocrystals passivated with either organic groups or with a thin layer of ZnS, is the emitting layer. The ZnS host film in the CL devices, built using chemical vapor deposition, serves as the support medium for the dispersed nanocrystals, but also provides additional passivation to the surface of those nanocrystals. We find that the EL and CL signals almost exclusively originate from the inorganic nanocrystal in both cases, i.e., EL comes from the nanocrystal layer in the heterostructure device while CL is generated from the dispersed particles in the composite film. The external EL quantum efficiency, (eta) <SUB>EL</SUB>, is not enhanced by the presence of ZnS overcoating, opposed to the observed increase in the photoluminescence (PL) quantum yield. However, we find that the CL emission and its stability are substantially improved by the presence of ZnS around the emitting nanocrystal cores. These observations reflect a difference in the effects of overcoating ont he various luminescence processes. On the one hand, a ZnS overlayer is associated with an additional energetic barrier that reduces the efficiency of charge injection into the nanocrystals for EL. On the other hand, PL and CL processes only benefit from the surface passivation with ZnS.
Interference-Modulated Conductance in a Three-Terminal Nanotube System (1999)

We study ballistic conductance in a three-terminal carbon nanotube system and show that conductance between two of the terminals can be controlled via the third terminal. The conductance is modulated by tuning the energy spectrum of the third terminal. Such a system may provide the core of a nanotransistor. We show more generally that the quasi one-dimensional nature of nanotubes can persist in branched topologies and that insights gained in analyzing one-dimensional systems can therefore be applied in analyzing networks of nanotubes.
Figure S5 from <i>SLC43A3</i> Is a Biomarker of Sensitivity to the Telomeric DNA Damage Mediator 6-Thio-2′-Deoxyguanosine (2023)

&lt;p&gt;Supplementary Data 5&lt;/p&gt;
Tailoring repulsive optical forces in nanophotonic waveguides (2011)

We describe a mechanism and propose design strategies to selectively tailor repulsive-gradient-optical forces between parallel, nanophotonic waveguides via morphology augmented by slow-light band-edge modes. We show that at small separation lengths, the repulsive force can be made nearly 2 orders of magnitude larger than that of standard dielectric waveguides with a square cross section. The increased coupling interactions should enable a wider dynamic range of optomechanical functionality for potential applications in sensing, switching, and nanoelectromechanical systems.
An explicit vector algorithm for high-girth MaxCut (2022)

We give an approximation algorithm for MaxCut and provide guarantees on the average fraction of edges cut on d-regular graphs of girth ≥ 2k. For every d ≥ 3 and k ≥ 4, our approximation guarantees are better than those of all other classical and quantum algorithms known to the authors. Our algorithm constructs an explicit vector solution to the standard semidefinite relaxation of MaxCut and applies hyperplane rounding. It may be viewed as a simplification of the previously best known technique, which approximates Gaussian wave processes on the infinite d-regular tree.
Detecting cancers through tumor-activatable minicircles that lead to a detectable blood biomarker (2015)

Earlier detection of cancers can dramatically improve the efficacy of available treatment strategies. However, despite decades of effort on blood-based biomarker cancer detection, many promising endogenous biomarkers have failed clinically because of intractable problems such as highly variable background expression from nonmalignant tissues and tumor heterogeneity. In this work we present a tumor-detection strategy based on systemic administration of tumor-activatable minicircles that use the pan-tumor-specific Survivin promoter to drive expression of a secretable reporter that is detectable in the blood nearly exclusively in tumor-bearing subjects. After systemic administration we demonstrate a robust ability to differentiate mice bearing human melanoma metastases from tumor-free subjects for up to 2 wk simply by measuring blood reporter levels. Cumulative change in reporter levels also identified tumor-bearing subjects, and a receiver operator-characteristic curve analysis highlighted this test's performance with an area of 0.918 ± 0.084. Lung tumor burden additionally correlated (r(2) = 0.714; P < 0.05) with cumulative reporter levels, indicating that determination of disease extent was possible. Continued development of our system could improve tumor detectability dramatically because of the temporally controlled, high reporter expression in tumors and nearly zero background from healthy tissues. Our strategy's highly modular nature also allows it to be iteratively optimized over time to improve the test's sensitivity and specificity. We envision this system could be used first in patients at high risk for tumor recurrence, followed by screening high-risk populations before tumor diagnosis, and, if proven safe and effective, eventually may have potential as a powerful cancer-screening tool for the general population.
Effects of mitogens on ornithine decarboxylase activity and messenger RNA levels in normal and protein kinase C-deficient NIH-3T3 fibroblasts. (1986)

Ornithine decarboxylase activity was assessed in serum-deprived quiescent NIH-3T3 murine fibroblasts after exposure to a variety of growth-promoting factors. Ornithine decarboxylase activity increased after treatment with phorbol 12-myristate 13-acetate (PMA), fetal calf serum, bovine pituitary fibroblast growth factor (FGF), platelet-derived growth factor (PDGF), and the synthetic diacyglycerol sn-1,2-dioctanolyglycerol but not after treatment with epidermal growth factor, insulin, 4 alpha-phorbol 12,13-didecanoate, sn-1,2-dibutyrylglycerol, or the calcium ionophore A23187. Activity peaked at 3-4 h and returned to basal levels after 8 h. To determine the importance of protein kinase C in this increase, cells were pretreated with PMA for 16 h to make the cells effectively deficient in protein kinase C; this deficiency was documented by direct measurement of enzyme activity and immunoreactivity. The ornithine decarboxylase response to each mitogen was then compared in cells pretreated with PMA or control conditions. PMA pretreatment abolished the increase in ornithine decarboxylase activity due to additional PMA and decreased but did not eliminate the ability of serum, FGF, and PDGF to cause increases in ornithine decarboxylase activity. Similarly, pretreatment with PMA abolished the ability of additional PMA to increase ornithine decarboxylase mRNA levels but did not prevent the increases in these mRNA levels caused by FGF or serum. These data suggest that the increases in ornithine decarboxylase activity and mRNA levels that occur in quiescent fibroblasts in response to serum, FGF, or PDGF are due to activation of at least two separate pathways, one involving protein kinase C and the other independent of protein kinase C.
MLi2Ti6O14 (M = Sr, Ba, 2Na) Lithium Insertion Titanate Materials: A Comparative Study (2010)

MLi(2)Ti(6)O(14) (M = Sr, Ba, 2Na) titanates have been investigated as lithium insertion materials for lithium-ion batteries. A comparative study has been undertaken based on the structure, morphology, and electrochemical properties of the titanate materials, which were prepared by sol-gel synthesis. Their lithium insertion behavior was analyzed by crystallographic considerations. While Na(2)Li(2)Ti(6)O(14) can reversibly host two Li(+) ions, SrLi(2)Ti(6)O(14) and BaLi(2)Ti(6)O(14) can reversibly insert almost four lithium ions per unit formula. Among the three materials, SrLi(2)Ti(6)O(14) showed superior capacity and rate capability. It was concluded that this class of materials could be of practical use in high-power lithium batteries for transportation applications.
Oligodendrocytes Are Targets of HIV-1 Tat: NMDA and AMPA Receptor-Mediated Effects on Survival and Development (2015)

Over 33 million individuals are currently infected by HIV. Among these individuals, ∼60% develop HIV-associated neurocognitive disorders. Myelin damage and white matter injury have been frequently reported in HIV patients but not extensively studied. Clinical studies using combined antiretroviral therapy (cART) together with adjunctive "anti-inflammatory" drugs show no improvement over cART alone, suggesting existence of injury mechanisms in addition to inflammation. In our studies, oligodendrocytes exhibited rapid increases in intracellular Ca(2+) level upon HIV-1 transactivator of transcription (Tat) exposure. Thus, immature and mature oligodendrocytes can be direct targets of Tat. Since ionotropic glutamate receptor antagonists can partially or fully reverse the detrimental effects of Tat, glutamate receptors could be a potential therapeutic target for white matter damage in HIV patients.
Normal visual fields as assessed by computerized static threshold perimetry in patients with untreated primary hypothyroidism (1989)

In this prospective study, 25 consecutive patients with untreated primary hypothyroidism were tested with a highly sensitive perimetric technique, since a high prevalence of visual field defects has been described in this condition. All patients had clinical hypothyroidism, a serum TSH value greater than 20 mU/l (reference range 0.4-4.0) and decreased/low normal serum total T4 concentration. Visual fields were tested with fully automated threshold-measuring computerized perimetry of the central 30 degrees field. Interpretation of fields included computer-assisted analysis provided by a perimetric statistical programme package. In 23 patients, conventional inspection and computer-assisted analysis showed no visual field defects. Two patients were excluded from the latter analysis: one patient who did not respond adequately at computerized perimetry and in whom manual field tests were entirely normal: one patient who had low sensitivity values in the uppermost parts of both visual fields owing to markedly swollen upper eye lids. In conclusion, although pituitary hyperplasia has been well documented in primary hypothyroidism, the present prospective study clearly indicates that visual field defects are not a common finding in patients with this disease.
A 3.3 V 6-Bit 100 kS/s Current-Steering Digital-to-Analog Converter Using Organic P-Type Thin-Film Transistors on Glass (2011)

A 3.3 V 6-bit binary-weighted current-steering digital-to-converter converter (DAC) using low-voltage organic p-type thin-film transistors (OTFTs) is presented. The converter marks records in speed and compactness owing to an OTFT fabrication process that is based on high-resolution silicon stencil masks. The chip has been fabricated on a glass substrate and consumes an area of 2.6× 4.6 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> . The converter has a maximum update rate of 100 kS/s and a maximum output voltage swing of 2 V. The measured DNL and INL at an update rate of 1 kS/s are - 0.69 and 1.16 LSB, respectively. A spurious-free dynamic range (SFDR) of 32 dB has been measured for output sinusoids at 31 Hz (update rate of 1 kS/s) and 3.1 kHz (update rate of 100 kS/s).
An optoelectronic implementation of the adaptive resonance neural network (1993)

A solution to the problem of implementation of the adaptive resonance theory (ART) of neural networks that uses an optical correlator which allows the large body of correlator research to be leveraged in the implementation of ART is presented. The implementation takes advantage of the fact that one ART-based architecture, known as ART1, can be broken into several parts, some of which are better to implement in parallel. The control structure of ART, often regarded as its most complex part, is actually not very time consuming and can be done in electronics. The bottom-up and top-down gated pathways, however, are very time consuming to simulate and are difficult to implement directly in electronics due to the high number of interconnections. In addition to the design, the authors present experiments with a laboratory prototype to illustrate its feasibility and to discuss implementation details that arise in practice. This device can potentially outperform alternative implementations of ART1 by as much as two to three orders of magnitude in problems requiring especially large input fields.
Antimicrobial Cellulose: Preparation and Application of 5-Methyl-5-Aminomethylhydantoin (2006)

A new N-halamine precursor, 5-methyl-5-aminomethylhydantoin (AH), was synthesized. This N-halamine precursor can be coated onto cotton surfaces with the addition of the crosslinking agent butanetetracarboxylic acid (BTCA) and rendered biocidal by exposure to halogen solutions either before or after curing the coating or material. Standard washing tests show that covalently bound AH/BTCA on the cotton swatches can survive repeated washing cycles. After 50 washing cycles, chlorinated cotton swatches had lost 98.7 % of oxidative Cl + , but after rechlorination, almost 43.5 % of Cl + was regained. Biocidal tests indicated that the cotton swatches coated with chlorinated AH/BTCA were effective against Gram positive Staphylococcus aureus and Gram negative Escherichia coli .
Human Fertility Impact Factor Editorial (2012)

I am delighted to say that Human Fertility now has its first Impact factor; a highly respectable 1.377. This represents a wonderful achievement and I would like to thank all those who have contribu...
The novel persistent sodium current inhibitor PRAX‐562 has potent anticonvulsant activity with improved protective index relative to standard of care sodium channel blockers (2022)

PRAX-562 demonstrated robust preclinical anticonvulsant activity similar to CBZ but improved compared to LTG. PRAX-562 exhibited significantly improved preclinical tolerability compared with standard Na<sub>V</sub> blockers (CBZ and LTG), potentially due to the preference for persistent I<sub>Na</sub> . Preferential targeting of persistent I<sub>Na</sub> may represent a differentiated therapeutic option for diseases of hyperexcitability, where standard Na<sub>V</sub> blockers have demonstrated efficacy but poor tolerability.
Roboscope: A flexible and bendable surgical robot for single portal Minimally Invasive Surgery (2017)

Minimally Invasive Surgery (MIS) can reduce iatrogenic injury and decrease the possibility of surgical complications. This paper presents a novel flexible and bendable endoscopic device, “Roboscope”, which delivers two instruments, two miniature scanning fiber endoscopes, and a suction/irrigation port to the operation site through a single portal. Compared with existing bendable and steerable robotic surgical systems, Roboscope provides two bending degrees of freedom for its outer sheath and two insertion degrees of freedom, while simultaneously delivering two instruments and two endoscopes to the surgical site. Each bending axis and insertion freedom of Roboscope is independently controllable via an external actuation pack. Surgical tools can be changed without retracting the robot arm. This paper presents the design of the Roboscope mechanical system, electrical system, and control and software systems, design requirements and prototyping validation as well as analysis of Roboscope workspece.
A Double Robust Approach to Causal Effects in Case-Control Studies (2014)

In a recent issue of the Journal, VanderWeele and Vansteelandt (Am J Epidemiol. 2011;174(10):1197-1203) discussed an inverse probability weighting method for case-control studies that could be used to estimate an additive interaction effect, referred to as the "relative excess risk due to interaction." In this article, we reinforce the well-known disadvantages of inverse probability weighting and comment on the desirability of the described parameter. Further, we review an existing double robust estimator not considered by VanderWeele and Vansteelandt, the case-control-weighted targeted maximum likelihood estimator, which has improved properties in comparison with a previously described inverse-probability-weighted estimator. This targeted maximum likelihood estimator can be used to target various parameters of interest, and its implementation has been described previously for the risk difference, relative risk, and odds ratio.