gebhart/patrepeval huggingface dataset:
Fluorescence energy transfer between Cys-10 residues in F-actin filaments. (1986)

Fluorescence energy transfer was measured between Cys-10 residues in an F-actin filament using 5-[2-((iodoacetyl)amino)-ethyl]aminonaphthalene-1-sulphonic acid (1,5-IAEDANS) as a fluorescence energy donor and 4-dimethylaminophenylazophenyl-4'-maleimide (DABMI) as the acceptor. Both labels were covalently attached to Cys-10 residues in an F-actin filament. Taking the helical structure of the F-actin filament into consideration, the radial coordinate of Cys-10 was calculated to be 23 A. This corresponds to a distance between adjacent sites along the long pitch helix of 56.1 A and along the genetic helix of 53.3 A.
Supplementary Methods from Identification of Alternative Splicing Events Regulated by the Oncogenic Factor SRSF1 in Lung Cancer (2023)

&lt;p&gt;PDF file - 96K, Description of the ExonPointer algorithm.&lt;/p&gt;
Mutual coupling calibration using the Reiterative Superresolution (RISR) algorithm (2014)

An integral element of a blind array calibration routine is an estimate of the direction of arriving signals. The work herein integrates the Reiterative Superresolution (RISR) algorithm into a calibration framework suitable for estimating the array mutual coupling. The RISR algorithm is a recursive minimum mean-squared error (RMMSE) Direction of Arrival (DoA) estimator that does not require a Sample Covariance Matrix (SCM) be computed. In addition, the RISR algorithm directly estimates the spatial spectrum, rather than just the angle measurement, making it well suited for assessing the array mutual coupling. Here a calibration method is derived using RISR to estimate mutual coupling. The effectiveness of the approach is via simulation.
The study of Friedel-Crafts type reaction mechanisms (1987)

In recent years the role of pi and delta complexes in electrophilic aromatic substitutions has aroused much controversy. Olah has argued that the transition state in electrophilic aromatic substitution is not a fixed one. With strong electrophiles it can occur early along the reaction coordinate resembling a pi complex, with weak electrophiles the tranistion state occures late, resembling a pi complex. This argument is based on a number of benzoylations and benzylations on benzene and toluene in which the electrophilicity of the electrophile has been varied. These conclusions have come under strong criticism and in order to shed light on the exact mechanism the following research was undertaken. This study is centered around the Friedel-Crafts acid catalysed cyclodehydration of 2-benzylbenzoic acids although the cyclodehydration of 2-naphthoylbenzoic acid and 2-benzoylbenzoic acids were also studied. The cyclodehydrations were effected mainly with methanesulphonic acid, but sulphuric acid, polyphosphoric acid and trifluoromethanesulphonic acid were also employed. Rate constants were measured and products of cyclodehydration were identified for all model compounds. The cyclodehydration was investigated by varying the electrophilicity on both the substrate and the electrophile. Consequently many new substituted 2-benzylbenzoic acids were synthesised. Hammett plots were also made and p values calculated. In addition to this the deuterium isotope effect was also investigated, but none was observed. Acidity function work (HR) was also carried out on methanesulphonic acid to try to extend the range to 100% acidity. Analysis of the rate constants and product distributions shows that the transition state resembles a delta complex rather than a pi complex. Hammett and acidity function studies do, however, indicate that the rate limiting step in the reaction is variable. This is dependent on whether there are electron withdrawing or electron donating groups present in the substrate. With electron donating groups the loss of water in the formation of the electrophile is the rate limiting step whereas with electron withdrawing groups the formation of the delta complex is rate limiting.
Reproducing Sound Fields Using MIMO Acoustic Channel Inversion (2011)

Sound fields are essentially band-limited phenomena, both temporally and spatially. This implies that a spatially sampled sound field respecting the Nyquist criterion is effectively equivalent to its continuous original. We describe Sound Field Reconstruction (SFR)---a technique that uses the previously stated observation to express the reproduction of a continuous sound field as an inversion of the discrete acoustic channel from a loudspeaker array to a grid of control points. The acoustic channel is inverted using truncated singular value decomposition (SVD) in order to provide optimal sound field reproduction subject to a limited effort constraint. Additionally, a detailed procedure for obtaining loudspeaker driving signals that involves selection of active loudspeakers, coverage of the listening area with control points, and frequency domain FIR filter design is described. Extensive simulations comparing SFR with Wave Field Synthesis show that on average, SFR provides higher sound field reproduction accuracy.
Wearable body sensor network towards continuous cuff-less blood pressure monitoring (2008)

We present a wearable IEEE 802.15.4-based Body Sensor Network (BSN) that enables continuous cuff-less blood pressure monitoring, opening up new perspectives for hypertension diagnosis and treatment, cardio-vascular event detection, and stress monitoring. Arterial blood pressure is estimated based on the Pulse Arrival Time (PAT), which is measured using a single lead electrocardiogram (ECG) patch on the chest and a photoplethysmogram (PPG) sensor at the finger or ear. Measurement context information—user posture and activity level—is extracted using a 3-D acceleration sensor. Since precise PAT measurements require the synchronization of the BSN devices’ clocks, the Flooding Time Synchronization Protocol (FTSP) was implemented. The acquired data are stored and displayed on a PDA or a wristwatch. Our BSN can currently operate for up to eight hours and perform PAT measurements under moderate activity conditions. Future work includes higher motion tolerance, posture-corrected blood pressure estimation and on-sensor data processing and storage.
Loss concentration based Controlled Delay: An Active Queue Management algorithm for enhanced Quality of Experience for video telephony (2015)

This paper presents an Active Queue Management (AQM) algorithm for improving the Quality of Experience (QoE) of video telephony over packet switched networks. The algorithm exploits the characteristics of the video coding structure, and builds on the Controlled Delay (Codel) active queue management algorithm recently proposed by Nichols and Jacobson to address the prevalent ‘bufferbloat’ problem in the current Internet. The proposed algorithm, Loss Concentration based controlled Delay (LC-Codel), maintains low queuing delay which is essential for video telephony, while using loss concentration to improve video QoE. Simulation results show significant gains in QoE with negligible impact on cross traffic.
Delay-Adaptive Distributed Stochastic Optimization (2020)

In large-scale optimization problems, distributed asynchronous stochastic gradient descent (DASGD) is a commonly used algorithm. In most applications, there are often a large number of computing nodes asynchronously computing gradient information. As such, the gradient information received at a given iteration is often stale. In the presence of such delays, which can be unbounded, the convergence of DASGD is uncertain. The contribution of this paper is twofold. First, we propose a delay-adaptive variant of DASGD where we adjust each iteration's step-size based on the size of the delay, and prove asymptotic convergence of the algorithm on variationally coherent stochastic problems, a class of functions which properly includes convex, quasi-convex and star-convex functions. Second, we extend the convergence results of standard DASGD, used usually for problems with bounded domains, to problems with unbounded domains. In this way, we extend the frontier of theoretical guarantees for distributed asynchronous optimization, and provide new insights for practitioners working on large-scale optimization problems.
Fundamental limitations on multiple-antenna wireless links in Rayleigh fading (2002)

Multiple-antenna wireless links have been shown theoretically to sustain enormous data rates in Rayleigh flat-fading, provided that the propagation coefficients between pairs of transmitter and receiver antennas are statistically independent and known to the receiver. It is not always possible for the receiver to learn the coefficients. Without assuming any knowledge of the fading coefficients and without imposing any ad hoc training schemes, we examine the capacity of the link as a function of the fading rate and SNR. We first look at piecewise constant fading processes where we compute the capacity at high SNRs. We then look at continuous fading processes, and it is shown that the capacity cannot be increased by increasing the number of transmitter antennas beyond a certain fading coherence time. This is radically different from the case when the fading coefficients are known, where the capacity increases indefinitely by increasing the number of transmitter and receiver antennas.
Triple Threat: Three Primary Malignancies Simultaneously Involving Three Genitourinary Organs (2023)

Statistically, the chance of having concurrent renal cell carcinoma (RCC), urothelial carcinoma of the bladder (UC), and a neuroendocrine tumor (NET) of the renal parenchyma is less than one in a trillion. Herein, we describe an unusual case of a 67-year-old female who presented with bilateral flank pain and severe gross hematuria. Cross-sectional imaging revealed two large heterogeneous, endophytic renal masses with a single enlarged paracaval lymph node. Diagnostic cystoscopy was performed for completion of gross hematuria evaluation and revealed a concurrent papillary bladder tumor. Percutaneous biopsies of bilateral renal masses revealed clear cell RCC involving the left kidney and well-differentiated NET involving the right kidney, and transurethral resection of the bladder tumor revealed high-grade nonmuscle invasive urothelial carcinoma. The patient elected to undergo bilateral nephroureterectomy, radical cystectomy, and retroperitoneal and pelvic lymphadenectomy. Final pathology confirmed the presence of three different malignancies: noninvasive high-grade papillary UC of the bladder (pTaN0), left renal clear cell RCC (pT2bN0), right renal well-differentiated NET, and a single paracaval lymph nodes positive for metastatic NET (pT2aN1).
Host cell factor CD59 restricts complement lysis of Plasmodium falciparum‐infected erythrocytes (1997)

Here we demonstrate that components of the entire complement cascade are fixed on the surface of erythrocytes infected with the human malarial parasite Plasmodium falciparum. Despite the activation of lytic complement factors, no complement-mediated lysis of P. falciparum-infected erythrocytes occurred only in the absence of functional intrinsic CD59. These data suggest that the restriction of the complement attack of P. falciparum-infected erythrocytes is principally mediated by intrinsic host cell factors, in particular CD59.
Time Course and Site(s) of Cytochrome c Tyrosine Nitration by Peroxynitrite (2005)

Cytochrome c-dependent electron transfer and apoptosome activation require protein-protein binding, which are mainly directed by conformational and specific electrostatic interactions. Cytochrome c contains four highly conserved tyrosine residues, one internal (Tyr67), one intermediate (Tyr48), and two more accessible to the solvent (Tyr74 and Tyr97). Tyrosine nitration by biologically-relevant intermediates could influence cytochrome c structure and function. Herein, we analyzed the time course and site(s) of tyrosine nitration in horse cytochrome c by fluxes of peroxynitrite. Also, a method of purifying each (nitrated) cytochrome c product by cation-exchange HPLC was developed. A flux of peroxynitrite caused the time-dependent formation of different nitrated species, all less positively charged than the native form. At low accumulated doses of peroxynitrite, the main products were two mononitrated cytochrome c species at Tyr97 and Tyr74, as shown by peptide mapping and mass spectrometry analysis. At higher doses, all tyrosine residues in cytochrome c were nitrated, including dinitrated (i.e., Tyr97 and Tyr67 or Tyr74 and Tyr67) and trinitrated (i.e., Tyr97, Tyr74, and Tyr67) forms of the protein, with Tyr67 well represented in dinitrated species and Tyr48 being the least prone to nitration. All mono-, di-, and trinitrated cytochrome c species displayed an increased peroxidase activity. Nitrated cytochrome c in Tyr74 and Tyr67, and to a lesser extent in Tyr97, was unable to restore the respiratory function of cytochrome c-depleted mitochondria. The nitration pattern of cytochrome c in the presence of tetranitromethane (TNM) was comparable to that obtained with peroxynitrite, but with an increased relative nitration yield at Tyr67. The use of purified and well-characterized mono- and dinitrated cytochrome c species allows us to study the influence of nitration of specific tyrosines in cytochrome c functions. Moreover, identification of cytochrome c nitration sites in vivo may assist in unraveling the chemical nature of proximal reactive nitrogen species.
Control of Hepatic Nuclear Superoxide Production by Glucose 6-Phosphate Dehydrogenase and NADPH Oxidase-4 (2011)

Redox-regulated signal transduction is coordinated by spatially controlled production of reactive oxygen species within subcellular compartments. The nucleus has long been known to produce superoxide (O(2)(·-)); however, the mechanisms that control this function remain largely unknown. We have characterized molecular features of a nuclear superoxide-producing system in the mouse liver. Using electron paramagnetic resonance, we investigated whether several NADPH oxidases (NOX1, 2, and 4) and known activators of NOX (Rac1, Rac2, p22(phox), and p47(phox)) contribute to nuclear O(2)(·-) production in isolated hepatic nuclei. Our findings demonstrate that NOX4 most significantly contributes to hepatic nuclear O(2)(·-) production that utilizes NADPH as an electron donor. Although NOX4 protein immunolocalized to both nuclear membranes and intranuclear inclusions, fluorescent detection of NADPH-dependent nuclear O(2)(·-) predominantly localized to the perinuclear space. Interestingly, NADP(+) and G6P also induced nuclear O(2)(·-) production, suggesting that intranuclear glucose-6-phosphate dehydrogenase (G6PD) can control NOX4 activity through nuclear NADPH production. Using G6PD mutant mice and G6PD shRNA, we confirmed that reductions in nuclear G6PD enzyme decrease the ability of hepatic nuclei to generate O(2)(·-) in response to NADP(+) and G6P. NOX4 and G6PD protein were also observed in overlapping microdomains within the nucleus. These findings provide new insights on the metabolic pathways for substrate regulation of nuclear O(2)(·-) production by NOX4.
SYNTHETIC PROCEDURE FOR THE PREPARATION OF NOVEL POTENT AND SELECTIVE A3ADENOSINE RECEPTOR RADIOLIGANDS (2001)

2-Phenylethynyladenosine and its N6-methyl derivative were synthesized and evaluated in binding assays at human adenosine receptors stably transfected on CHO cells. Results showed that the N6-methyl-2-phenylethynyladenosine is endowed with very high affinity and selectivity at A3 receptor subtype. Hence, an alternative procedure for the synthesis of tritiated N6-methyl-2-phenylethynyladenosine was set up to introduce tritiated methylamine in the final step.
Laser Optics: Low Timing Jitter Mode-Locked Semiconductor Diode Lasers (2002)

Low timing jitter mode-locked semiconductor diode lasers was discussed. Optical linewidth of the individual comb components within the mode-locked laser optical spectrum was measured using heterodyne method. Results showed that the longitudinal mode linewidth determines the phase noise corner frequency.
Étude de la mouillabilité des roches réservoir à l'échelle du pore par cryomicroscopie électronique à balayage (1992)

Le but de cette étude est de caractériser, à l'échelle du pore, la mouillabilité des roches réservoir, en relation avec leur géométrie et/ou leur minéralogie. Cette caractérisation se fait, après congélation des échantillons, par l'observation de la distribution des fluides au sein du milieu poreux (saumure et huile brute), en microscopie électronique à balayage. Les expériences ont d'abord été effectuées sur des roches modèles parfaitement mouillables à l'eau, verre fritté et grès naturels. Certains de ces minéraux ont été rendus hydrophobes par greffage de silane. L'étude de ces systèmes a mis en évidence une corrélation entre la mouillabilité et la distribution des fluides. Puis, une roche réservoir (grès argileux de la formation de Brent, de mer du Nord) connue comme étant de mouillabilité intermédiaire a été étudiée. Un travail précédent (étude de déplacements eau/huile par tomographie X) avait abouti à la conclusion que si ces roches présentaient des hétérogénéités de mouillabilité, l'échelle de ces hétérogénéités devait être inférieure au millimètre. Les études de cryomicroscopie ont montré le caractère hydrophobe de la kaolinite, tandis que les illites, le quartz et les feldspaths sont préférentiellement mouillables à l'eau. L'imbibition spontanée d'huile pourrait ainsi être attribuée à l'existence au sein de la roche d'un réseau de kaolinite, tandis que l'imbibition spontanée de saumure serait due à l'existence d'un second réseau plus ou moins imbriqué avec le premier et constitué des autres minéraux. Un autre cas de roche réservoir a été étudié, à savoir un carbonate du Moyen-Orient. Les mésopores intergranulaires y ont été observés comme étant mouillables à l'huile tandis que les micropores restaient mouillables à l'eau. Dans ce cas, la mouillabilité intermédiaire de ces échantillons s'explique par la géométrie plutôt que par la minéralogie qui est plutôt homogène.
Über den Effekt der Kathodothermolumineszenz (1958)

Während der Einfluß der Temperatur auf die mit Ultraviolett (UV) angeregte Lumineszenz schon häufig untersucht wurde [1, 2], liegt wenig experimentelles Material für den Fall der Kathodenstrahlanregung von Phosphoren vor. Es soll daher über den Einfluß der Temperatur auf die Kathodolumineszenz, insbesondere im Bereich von 100 bis 300 °K berichtet werden. Bei ständiger Kathodenstrahlanregung der Phosphore zeigen sich im Falle der Erwärmung, genau wie bei der Anregung durch elektrische Felder [3, 4], Maxima, die an die Glowmaxima der Thermolumineszenz erinnern, während bei der Abkühlung die Kurven völlig monoton verlaufen.
SIMULATION OF COLD-TEST DISPERSION AND INTERACTION IMPEDANCES FOR COUPLED-CAVITY TUBE SLOW-WAVE CIRCUITS (1992)

The cold-test dispersion and interaction impedance characteristics for three types of coupled-cavity slow-wave circuits were simulated with the frequencydomain algorithm of Micro-SOS, a threedimensional electromagnetic simulation code. The results agree very closely with experimental data and show the utility of the simulation code for eliminating the need for expensive and time-consuming experimental coldtesting procedures.
Neuroinflammatory profiles of the human female brain in midlife resembles the human male late‐life Alzheimer's brain (2022)

Abstract Nicole Delatorre &amp; Hannah Van Rossum are co‐first authors Background Neuroinflammation is a well‐documented feature of Alzheimer’s Disease (AD). Two important questions in defining the role of the neuroimmune system in AD remain unaddressed: 1) the initiation phase of inflammation and 2) sex differences in the inflammatory cascade. Previous preclinical findings from our group demonstrated elevated inflammatory and immune transcripts including CD3, CD4, and MHCII. With this work, we extend and translate our preclinical discoveries to test the hypotheses that the inflammatory phenotype of LOAD is initiated in midlife of the human aging process and sex differences are prevalent. Method Both fixed and frozen human tissue samples were obtained from NIH NeuroBioBank (University of Maryland, University of Miami, and Mt. Sinai) that included the corpus callosum, hippocampus, and hypothalamus of 40 brain donors that were sex and age matched. For the purposes of this study, samples were sub‐classified into 3 groups: healthy aging 40‐49 years‐old, healthy aging 50‐59 years‐old, and AD age 60‐80 years‐old. Transcriptomic analyses were conducted to determine neuroinflammatory gene expression and to identify common signaling profiles. Neuroinflammatory markers were visualized using 3,3’‐diaminobenzidine immunohistochemistry and included microglia (IBA‐1), activated microglia (HLA), and T‐cells (CD3, CD4, CD8). Result Gene expression change was determined by comparing each group to the young male. The profiles were compared using fisher exact tests and revealed region‐specific and sex‐specific transcript regulation. Midlife females exhibited significant differences in genes involved in hypothalamic adaptive immune response (p=0.0054), hippocampal astrocyte function p=0.007, and hypothalamic inflammatory signaling p=0.028). AD males exhibited altered gene expression in corpus callosum neurotransmission (p=0.0355), hippocampal innate immune response, and hypothalamic adaptive and innate immune response (p=0.0496, p=0.0208). Both midlife female and AD male showed hippocampal upregulation of innate immune transcripts and hypothalamic upregulation of adaptive and innate immune response genes. Conclusion These results provide evidence of early activation of the immune response in brain as a potential sex‐dependent risk factor for AD. Outcomes of these analyses support future studies that identify neuroimmune biomarkers of the AD prodrome and present an early opportunity for intervention in order to reduce risk and/or delay AD. NIH: R01AG057931, R01AG057931‐02S1, T32AG061897, R01AG057931‐01A1
Synthesis of novel sugar-lactam conjugates using the Aubé reaction (2010)

An efficient and convenient method for the synthesis of sugar-lactam conjugates is reported starting from readily available sugar azides using the Aubé reaction. Cyclic azido alcohols are used in the Aubé reaction for the first time in a carbohydrate setting. The resulting glycoconjugates could be further used to increase the chemical diversity on the sugar backbone, and may find potential applications as glycomimetics, peptidomimetics, in glycotargeting and in CNS drug delivery.
Modelling and prediction of the effect of cutting strategy on surface generation in ultra-precision raster milling (2016)

This paper studies the effect of cutting strategy on surface generation in ultra-precision raster milling (UPRM). By adding the influences of shift length and tool-interference on surface generation, a holistic surface roughness prediction model is built which takes into account the effect of cutting parameters, tool path generation, geometry parameters of diamond tool, the size of the workpiece and machine characteristics. The optimal shift ratio can be achieved by changing factors involved in developing cutting strategy to improve surface quality without decreasing machining efficiency. Conditions for the presence of tool-interference in UPRM are presented. Based on the holistic surface generation model, an integrated system is developed to automatically generate the numerical control program, and predict surface quality and machining efficiency. A series of cutting experiments has been conducted to verify the proposed surface generation model and test the performance of the integrated system. The experimental results agree well with the predicted results from the model and the integrated system.