gebhart/patrepeval huggingface dataset:
Lack of involvement of capsaicin-sensitive primary afferents in nerve-ligation injury induced tactile allodynia in rats (1999)

Tactile allodynia and thermal hyperalgesia, two robust signs of neuropathic pain associated with experimental nerve injury, have been hypothesized to be mechanistically distinguished based on (a) fiber types which may be involved in the afferent input, (b) participation of spinal and supraspinal circuitry in these responses, and (c) sensitivity of these endpoints to pharmacological agents. Here, the possibility that nerve-injury induced tactile allodynia and thermal hyperalgesia may be mediated via different afferent fiber input was tested by evaluating these responses in sham-operated or nerve-injured (L5/L6) rats before or after a single systemic injection of resiniferatoxin (RTX), an ultrapotent analogue of the C-fiber specific neurotoxin, capsaicin. Tactile allodynia, and three measures of thermal nociception, tail-flick, paw-flick and hot-plate responses, were determined before and at various intervals for at least 40 days after RTX injection. Nerve-injured, but not sham-operated, rats showed a long-lasting tactile allodynia and thermal hyperalgesia (paw-flick) within 2-3 days after surgery; responses to other noxious thermal stimuli (i.e., tail-flick and hot-plate tests) did not distinguish the two groups at the stimulus intensities employed. RTX treatment resulted in a significant and long-lasting (i.e. essentially irreversible) decrease in sensitivity to thermal noxious stimuli in both sham-operated and nerve-injured rats; thermal hyperalgesia was abolished and antinociception produced by RTX. In contrast, RTX treatment did not affect the tactile allodynia seen in the same nerve-injured rats. These data support the concept that thermal hyperalgesia seen after nerve ligation, as well as noxious thermal stimuli, are likely to be mediated by capsaicin-sensitive C-fiber afferents. In contrast, nerve-injury related tactile allodynia is insensitive to RTX treatment which clearly desensitizes C-fibers and, therefore such responses are not likely to be mediated through C-fiber afferents. The hypothesis that tactile allodynia may be due to inputs from large (i.e. A beta) afferents offers a mechanistic basis for the observed insensitivity of this endpoint to intrathecal morphine in this nerve-injury model. Further, these data suggest that clinical treatment of neuropathic pains with C-fiber specific agents such as capsaicin are unlikely to offer significant therapeutic benefit against mechanical allodynia.
Transcriptional mapping of the anti-viral T cell response shows that impaired memory differentiation causes T cell dysfunction (2006)

Human T cells responding to viral pathogens after HSCT can be dysfunctional and ineffective even when present in adequate numbers. The basis for this qualitative, rather than quantitative, T cell defect is not known. We hypothesized that impaired differentiation of naive T cells into memory T cells causes a qualitative T cell defect. We, therefore, studied CD8 T cell memory differentiation in 2 murine models of LCMV infection: an acute infection in which virus-specific T cells are fully functional and a chronic infection model in which T cells are present in normal numbers but are dysfunctional. In order to define how the differentiation state of dysfunctional T cells in chronic infection differ from those in acute infection, we generated gene expression profiles from naive (day 0), effector (day 7 [d7]), and memory (day 30 [d30]) T cells using oligonucleotide microarrays. In acute infection, T cell states were so distinct that 100% of naive, effector, and memory samples could be correctly classified, using a k-Nearest-Neighbor prediction classifier (kNN). Next, we hypothesized that the signature of normal memory T cells would contain gene-sets known to be important in memory differentiation. We found that Stat-5 target genes were the most enriched gene-sets in memory cells relative to naive cells of >400 gene-sets tested (P = .004 by permutation testing). This is consistent with the central role of Stat-5 signaling in memory development. Lastly, we determined where dysfunctional d30 T cells from chronic infection lie relative to the “differentiation-space” of acute infection. None of the chronic d30 T cell samples were classified as memory by kNN prediction; all were misclassified as effectors. However, chronic d30 T cells were not simply persistent effectors because chronic d30 T cells showed marked differences in gene expression pattern compared to d7 effectors. Thus, dysfunctional T cells in chronic viral infection fail to complete normal memory differentiation and are arrested in a distinct, effector-like phase. Our results show that the disruption of memory differentiation causes qualitative T cell dysfunction, and that this altered differentiation can be detected by gene-expression profiling. We are now generating a global map of antigen-specific T cell differentiation in humans. This gene-expression-based approach to evaluating immune reconstitution will identify the mechanisms limiting the recovery of T cell memory after HSCT.
Classification of ballpoint pen inks based on selective extraction and subsequent digital color and cluster analyses (2022)

Here, we propose a novel approach to the classification of blue ballpoint pen inks based on a combination of selective extraction of coloring components from a paper carrier, digital color analysis (DCA) of the remaining traces, and hierarchical cluster analysis of DCA results. Since most documents of high importance are still produced in hard copies, the proposed method, being highly time- and cost-efficient, could be a significant contribution to forensic science in the field of authenticating handwritten documents. Several commonly used solvents were applied in parallel as extractants to the replicate strokes produced by each pen. It turned out to be possible to limit the number of extractants required for an unambiguous classification to three. We have shown that the optimal descriptor for agglomerative clustering is the colorimetric distance between the original and extracted ink traces in the RGB color space. Five separate clusters of inks that are independent of sample storage temperature were obtained from a set of 16 different pens. This conclusion was further confirmed by the analysis of principal components. The developed DCA-based data processing pipeline outperformed the clustering based on the data of high-performance liquid chromatography in terms of versatility providing a more informative analysis with respect to the inks based on the phthalocyanine dyes.
Causal and Strictly Causal Estimation for Jump Linear Systems: An LMI Analysis (2006)

Jump linear systems are linear state-space systems with random time variations driven by a finite Markov chain. These models are widely used in nonlinear control, and more recently, in the study of communication over lossy channels. This paper considers a general jump linear estimation problem of estimating an unknown signal from an observed signal, where both signals are described as outputs of a jump linear system. A bound on the minimum achievable estimation error in terms of linear matrix inequalities (LMIs) is presented, along with a simple jump linear estimator that achieves this bound. While previous analysis has considered only the strictly causal estimation problem, this work presents both strictly causal and causal solutions.
The causal effects of flooding on infectious diarrheal diseases during and after flood and the related social modifiers in Anhui province, China (2019)

OPS 11: Health effects of climate change in low- and middle-income countries, Room 114, Floor 1, August 27, 2019, 10:30 AM - 12:00 PM Background: The frequency and intensity of flooding are projected to increase in a changing climate, which may have great implications for diarrhea. Yet the causal relationship between flood and diarrhea remains uncertainties and very limited study had detected its modifiers. Methods: Daily number of diarrheal cases and meteorological data from June 18th 2013 to August 31th 2017 and background data of flood in Anhui province were obtained. The differences-in-differences (DID) approach with propensity score matching were applied to examined the causal effects of the 2016 flood in Anhui during flooding and in post-flood period. The difference-in-difference-in-difference (DDD) analysis was deployed to detect the modifiers of flood’s impacts, including gender, age, occupation and community health resource. Results: During the study period, 359,580 cases of diarrhea occurred in Anhui province, with an average of 258.6 cases per day. The adjusted DID model estimated that the flood had immediately increased the risk of dysentery (RR: 1.29, 95% CI: 1.14 – 1.46) and have caused 21% increase of all-cause diarrhea in post-flood period, with 49%, 36%, 9% of risk increasing for Typhoid and Paratyphoid, Dysentery, Other Infectious Diarrhea. The DDD model showed that the flood had posed a higher risk to males, under 5 and 5-14-years old children, and non-farmers. People belonged to county with high density of health professionals had a significantly lower risk of diarrhea during flooding (RR: 0.81, 95% CI: 0.67 - 0.99) and in post-flood period (RR: 0.83, 95% CI: 0.74 - 0.92). Conclusions: Flooding has increased the risk of diarrhea and the effects were modified by age, gender, occupation and density of health professionals. Our findings recommended using DID design to detect causal effect of floods and other climate extremes and highlighted the protective effects of community health workforce on the health impacts posed by flooding.
Cover Picture: Top‐Down Meets Bottom‐Up: Dip‐Pen Nanolithography and DNA‐Directed Assembly of Nanoscale Electrical Circuits (Small 1/2005) (2004)

The cover picture shows a schematic representation of a nanoscale tunnel junction circuit formed when a DNA‐functionalized gold nanoparticle is directed between two metallic electrodes (a field‐emission SEM image is shown in the inset). The background displays an electron microscopy image of a device containing such junctions for potential use as a biosensor. Such a combination of biology, chemistry, engineering, and materials science serves as a model for the interdisciplinary character that Small exemplifies. For more information, please refer to the Communication by C. A. Mirkin and co‐workers on page 64 ff. The authors thank Yeechi Chen for the cover design.
Molecular Rectification in a Metal−Insulator−Metal Junction Based on Self-Assembled Monolayers (2002)

An electrical junction formed by mechanical contact between two self-assembled monolayers (SAMs)--a SAM formed from an dialkyl disulfide with a covalently linked tetracyanoquinodimethane group that is supported by silver (or gold) and a SAM formed from an alkanethiolate SAM that is supported by mercury-rectifies current. The precursor to the SAM on silver (or gold) was bis(20-(2-((2,5-cyclohexadiene-1,4-diylidene)dimalonitrile))decyl)) disulfide and that for the SAM on mercury was HS(CH(2))(n-1)CH(3) (n = 14, 16, 18). The electrical properties of the junctions were characterized by current-voltage measurements. The ratio of the conductivity of the junction in the forward bias (Hg cathodic) to that in the reverse bias (Hg anodic), at a potential of 1 V, was 9 +/- 2 when the SAM on mercury was derived from HS(CH(2))(15)CH(3). The ratio of the conductivity in the forward bias to that in the reverse bias increased with decreasing chain length of the alkanethiol used to form the SAM on mercury. These results demonstrate that a single redox center asymmetrically placed in a metal-insulator-metal junction can cause the rectification of current and indicate that a fixed dipole in the insulating region of a metal-insulator-metal junction is not required for rectification.
Verifying the Performance of RTDs in Nuclear Power Plants (2003)

This paper describes a number of techniques that have been developed for nuclear power plants to ensure that optimum steady‐state and transient performance is achieved with the resistance temperature detectors (RTDs) that are used in the plant for critical temperature measurements. This includes precision laboratory calibration of RTDs, the Loop Current Step Response (LCSR) method for in‐situ response time measurements, a cross calibration technique to verify the steady‐state performance of RTDs as installed in the plant, and the Time Domain Reflectometry (TDR) test that is used to identify the location of a problem along RTD cables.
Beyond Web Search (2021)

Web search has transformed how we access all kinds of information and has become a core fabric of everyday life. It is used to find information, buy things, plan travel, understand medical conditions, monitor events, etc. Search in other domains has not received nearly the same attention so our experiences in web search shape our thinking about search more generally even when the scenarios are quite different. This is especially true for email search. Although email was initially designed to facilitate asynchronous communication, it has also become a large repository of personal information. The volume of email continues to grow in both consumer and enterprise settings, and search plays a key role in getting back to needed information. Email search is, however, very different than Web search on many dimensions -- the content being sought is personal and private, metadata such as who sent it or when it was sent is plentiful and important, search intentions are different, people know a lot about what they are looking for, etc. Given these differences, new approaches are required. In this talk I will summarize research we have done using large-scale behavioral logs and complementary qualitative methods to characterize what are people looking for, what they know about what they are looking for, and how this interacts with email management practices. I will then describe several opportunities to help people articulate their information needs and design interfaces and interaction techniques to support this. Finally, I will conclude by pointing to new frontiers in email management and search.
Determination of blood plasma fluorescence extinction coefficients for dyes used in three-compartment binding model (2011)

A three-compartment kinetic model for the binding of a ligand to its receptor in tumor tissue has been explained and the kinetic rates of the model are currently being investigated. In order to determine the plasma excretion rates of the dyes of interest, the fluorescence extinction coefficients must be determined. The fluorescence extinction coefficients of the IRDye700DX-carboxylate (IRDye700DX-C) and IRDye800CW-conjugated to EGFR (IRDye800CW-EGF) have been to be 7.98 ×10<sup>6</sup> &mu;M<sup>-1</sup> cm<sup>-1</sup> and 4.73x10<sup>6</sup> &mu;M<sup>-1</sup> cm<sup>-1</sup>, respectively. We determined that the linear range of these dyes in the blood plasma of a mouse was 0 - 0.26 &mu;M. Administration of 1 nmol of each of these dyes to a mouse weighing 25-30g (0.04 &mu;M - 0.033 &mu;M, respectively) will result in blood plasma fluorescence in the linear and readable range.
Complementary target engagement and functional assays to probe NLRP3 inflammasome pathway antagonism (2022)

Abstract Inflammasomes are critical to the innate immune system and implicated in numerous chronic and acute inflammatory diseases. Having tools to screen inflammasome modulatory drugs is critical, especially for the NLRP3 inflammasome that is triggered by a wide array of stimuli. We have developed three cell-based methods for quantifying inflammasome function: a NanoBRET™ NLRP3-specific target engagement assay, a caspase-1 activity assay and an IL-1β release assay. For the NLRP3 target engagement assay, cells are transfected with a NLRP3-Nanoluc construct and incubated with a cell-permeable, fluorescent NLRP3 binder (tracer), generating a bioluminescent resonance energy transfer (BRET) signal. The homogeneous caspase-1 and IL-1β assays can be run directly with cells in culture or with transferred culture medium, enabling application of both luminescent assays to the same cell wells via split-sample analysis. Using all three assays, we tested a series of reported NLRP3 inhibitors, including MCC950, oridonin, NBC6, NBC19, CY09, OXSi2 and OLT1177™ (dapansutrile). MCC950 inhibition of caspase-1 activity and IL-1β release was demonstrated in human and mouse cell models. We used LPS-primed THP-1 cells treated with nigericin for testing the series of inhibitors. The NLRP3 target engagement assay used HEK293 cells in suspension in non-binding plates. All three assays demonstrated good inhibition for MCC950, oridonin, NBC6, NBC19 and CY09 with rank order potency consistent with published results. We did not detect inhibition with OxSi2 or OLT1177™. These three assays enable screening for inflammasome antagonists and provide a mechanistic platform for characterizing NLRP3 inflammasome inhibitors.
Multi-criteria analysis of detoxification alternatives: Techno-economic and socio-environmental assessment (2021)

The transformation of fermentable sugars provided from lignocellulosic wastes into biofuels or bioproducts is a key point at second-generation biorefineries. Spent sulfite liquor is a xylose-rich hydrolysate constituting the main residue of sulfite mills producing dissolving cellulose. Due to the presence of the inhibitors in the spent liquor, the most promising valorization options require detoxification before sugars bioconversion. In this work, a multi criteria analysis was implemented to select techno-economic and socio-environmental feasible detoxification alternatives that can be adapted to a wide variety of fermenting scenarios. Total inhibitors removal, phenolics removal, acetic acid removal, lignosulfonates removal, total sugar losses, fixed capital invested, manufacturing costs, waste toxicity, social acceptance, and employment were chosen as the most relevant criteria. The maximum allowable concentration of undesirable inhibitors cannot be established with a general character, and thereby decision-making tools result in feasible and efficient solutions. From a technical viewpoint best solution was anionic resins with a score of 0.68; the most economical alternative was the overliming with a score of 0.76; finally, from a socio-environmental perspective, overliming reached the highest score of 0.78. In addition, three spent liquor biorefinery models were proposed. Based on the multi-criteria analysis and based on the inhibitor's concentration affecting fermentation yields and productivity, the best detoxification alternatives were (1) anionic resins for polyhydroxyalkanoate production; (2) activated carbon for ethanol biorefinery; (3) overliming for xylitol biorefinery.
Genome-Based Infection Tracking Reveals Dynamics ofClostridium difficileTransmission and Disease Recurrence (2015)

Genome-based infection tracking to monitor the persistence and spread of C. difficile within healthcare facilities could inform infection control and patient management.
A 3.6pW/frame·pixel 1.35V PWM CMOS Imager with Dynamic Pixel Readout and no Static Bias Current (2008)

Low-power operation of CMOS imagers using a low voltage (around IV or less) compatible with deep submicron logic circuits enables new imager applications, such as disposable medical cameras and autonomous wireless security cameras on a chip. Pulse width modulation (PWM) is promising for this purpose. A PWM pixel can convert light intensity to a digital pulse width by using an in-pixel comparator with a low power-supply voltage without any degradation of signal-to-noise ratio (SNR). In this paper, we propose and demonstrate a low-power dynamic pixel readout in-pixel comparators(DPR) scheme with CGA PWM pixels based on dynamic operation of in-pixel comparators. DPR requires no static bias current even in the pixel readout. The power dissipation of the pixel array is dramatically reduced by 1 to 2 orders of magnitude compared with using normal static pixel readout (SPR).
Supramammillary regulation of locomotion and hippocampal activity (2021)

Locomotor speed is a basic input used to calculate one’s position, but where this signal comes from is unclear. We identified neurons in the supramammillary nucleus (SuM) of the rodent hypothalamus that were highly correlated with future locomotor speed and reliably drove locomotion when activated. Robust locomotion control was specifically identified in <i>Tac1</i> (substance P)–expressing (SuM<sup>Tac1+</sup>) neurons, the activation of which selectively controlled the activity of speed-modulated hippocampal neurons. By contrast, <i>Tac1</i>-deficient (SuM<sup>Tac1−</sup>) cells weakly regulated locomotion but potently controlled the spike timing of hippocampal neurons and were sufficient to entrain local network oscillations. These findings emphasize that the SuM not only regulates basic locomotor activity but also selectively shapes hippocampal neural activity in a manner that may support spatial navigation.
Channel Correlation Diversity in MU-MIMO Systems – Analysis and Measurements (2019)

In multiuser multiple-input multiple-output (MU-MIMO) systems, channel correlation is detrimental to system performance. We demonstrate that widely used, yet overly simplified, correlation models that generate identical correlation profiles for each terminal tend to severely underestimate the system performance. In sharp contrast, more physically motivated models that capture variations in the power angular spectra across multiple terminals, generate diverse correlation patterns. This has a significant impact on the system performance. Assuming correlated Rayleigh fading and downlink zero-forcing precoding, tight closed-form approximations for the average signal- to-noise-ratio, and ergodic sum spectral efficiency are derived. Our expressions provide clear insights into the impact of diverse correlation patterns on the above performance metrics. Unlike previous works, the correlation models are parameterized with measured data from a recent 2.53 GHz urban macrocellular campaign in Cologne, Germany. Overall, results from this paper can be treated as a timely re-calibration of performance expectations from practical MU-MIMO systems.
Structure−Activity Relationships in 1,4-Benzodioxan-Related Compounds. 6. Role of the Dioxane Unit on Selectivity for α1-Adrenoreceptor Subtypes (1999)

WB 4101-related benzodioxans 3-9 were synthesized, and their biological profiles at alpha(1)-adrenoreceptor subtypes and 5-HT(1A) serotoninergic receptors were assessed by binding assays in CHO and HeLa cells membranes expressing the human cloned receptors. Furthermore, receptor selectivity of selected benzodioxan derivatives was further determined in functional experiments in isolated rat vas deferens (alpha(1A)) and aorta (alpha(1D)) and guinea pig spleen (alpha(1B)), in additional receptor binding assays in rat cortex membranes containing alpha(2)-adrenoreceptors and 5-HT(2) serotoninergic receptors, and in rat striatum membranes containing D(2) dopaminergic receptors. An analysis of the results of receptor binding experiments for benzodioxan-modified derivatives 3-9 showed high affinity and selectivity toward the alpha(1a)-adrenoreceptor subtype for compounds 3-5 and 7 and a reversed selectivity profile for 9, which was a selective alpha(1d) antagonist. Furthermore, the majority of structural modifications performed on the prototype 1 (WB 4101) led to a marked decrease in the affinity for 5-HT(1A) serotoninergic receptors, which may have relevance in the design of selective alpha(1A)-adrenoreceptor antagonists. The exception to these findings was the chromene derivative 8, which exhibited a 5-HT(1A) partial agonist profile.