gebhart/patrepeval huggingface dataset:
Operating Characteristics of the Male Hypothalamo-Pituitary-Gonadal Axis: Pulsatile Release of Testosterone and Follicle-Stimulating Hormone and Their Temporal Coupling with Luteinizing Hormone* (1987)

To appraise the physiological pattern(s) of episodic testosterone and FSH release in man, we withdrew blood samples at 10-min intervals for 24-36 h in a total of 15 normal men. We subjected the resulting FSH (15 men) and testosterone (5 men) time series to 3 statistically based and mathematically independent procedures for detecting hormone pulsatility, viz. Cluster analysis, the Detect program, and Fourier transformation. The Cluster technique disclosed discrete testosterone and FSH peaks occurring at mean (+/- SEM) interpulse intervals of 112 +/- 14 and 85 +/- 3.4 min, respectively. These values were not significantly different from the mean LH interpulse interval of 95 +/- 11 min. The average durations of the testosterone and FSH pulsations were 90 +/- 11 and 59 +/- 3 min, respectively. The mean testosterone pulse amplitude reached a maximal value of 910 +/- 92 ng/dL (31.5 +/- 3.2 nmol/L), which represented a mean increase of 242 +/- 26 ng/dL (8.4 +/- 0.9 nmol/L) above the preceding nadir. FSH pulses had a maximum of 7.2 +/- 0.3 IU/L, and an incremental amplitude of 1.3 +/- 0.1 IU/L. An independent pulse detection procedure. Detect, yielded a testosterone pulse frequency of 12.3 +/- 0.8 pulses/day [P = NS vs. Cluster program (13 +/- 1.9 pulses/day)]. The Cluster and Detect estimates of FSH pulse frequency were also similar, viz. 16 +/- 1.9 and 16 +/- 0.6 pulses/day. Further analysis by Fourier transformation revealed significant circadian periodicities for serum testosterone, FSH, and LH, which had mean nyctohemeral amplitudes of 185 ng/dL (6.4 nmol/L), 0.38 IU/L, and 1.3 IU/L, respectively. Cross-correlation analyses disclosed significantly positive uncorrected cross-correlations between LH and testosterone that were maximal at a testosterone lag of 60 min (range, 50-70 min). To eliminate high intrinsic autocorrelations within the testosterone and LH time series, stepwise autoregressive fitting was employed. The resulting partial cross-correlation matrices indicated that LH concentrations at any given instant were significantly positively correlated to testosterone concentrations lagged by 10 and 20 min. Similarly, contemporaneous LH and FSH concentrations were significantly positively correlated (r = 0.40-0.89; P less than 0.001). Moreover, autoregressive modeling disclosed significantly positive partial cross-correlations between LH and FSH at a FSH lag of 10 min. In summary, we have identified significant pulsatile as well as circadian (24-h) patterns of testosterone and FSH release in normal men.(ABSTRACT TRUNCATED AT 400 WORDS)
Complexity and performance in parallel programming languages (2002)

Several parallel programming languages, libraries and environments have been developed to ease the task of writing programs for multiprocessors. Proponents of each approach often point out various language features that are designed to provide the programmer with a simple programming interface. However, virtually no data exists that quantitatively evaluates the relative ease of use of different parallel programming languages. The paper borrows techniques from the software engineering field to quantify the complexity of three predominate programming models: shared memory, message passing and High-Performance Fortran. It is concluded that traditional software complexity metrics are effective indicators of the relative complexity of parallel programming languages. The impact of complexity on run-time performance is also discussed in the context of message passing versus HPF on an IBM SP2.
How Biofuels Can Help End America's Oil Dependence (2004)

Contributing Authors Fuat E. Celik, Princeton University Bruce Dale, Michigan State University Michael Jackson, NRDC Kemantha Jayawardhana, Dartmouth College Haiming Jin, Dartmouth College Eric D. Larson, Princeton University Mark Laser, Dartmouth College Lee Lynd, Dartmouth College Don MacKenzie, Union of Concerned Scientists Jason Mark, Union of Concerned Scientists John McBride, Dartmouth College Samuel McLaughlin, Oak Ridge National Laboratory Daniel Saccardi, NRDC
PHOTO‐OXIDATION OF LYSOZYME IN THE PRESENCE OF METHYLENE BLUE: A PROBABLE MECHANISM (1973)

Abstract— In order to elucidate the mechanism of the photo‐oxidation of lysozyme sensitized by methylene blue this enzyme was oxidized by singlet oxygen generated by a high–frequency discharge in gaseous oxygen. The action of singlet oxygen on lysozyme gives products identical with those obtained upon dye‐sensitized oxidation with respect to their affinity to chitin, their amino acid content, their UV spectra and their enzymic activity. It is concluded that photo‐oxidation of lysozyme in the presence of methylene blue proceeds according to the singlet‐oxygen mechanism.
Merkel Cell Polyomavirus-Infected Merkel Cell Carcinoma Cells Require Expression of Viral T Antigens (2010)

Merkel cell carcinoma (MCC) is the most aggressive skin cancer. Recently, it was demonstrated that human Merkel cell polyomavirus (MCV) is clonally integrated in approximately 80% of MCC tumors. However, direct evidence for whether oncogenic viral proteins are needed for the maintenance of MCC cells is still missing. To address this question, we knocked down MCV T-antigen (TA) expression in MCV-positive MCC cell lines using three different short hairpin RNA (shRNA)-expressing vectors targeting exon 1 of the TAs. The MCC cell lines used include three newly generated MCV-infected cell lines and one MCV-negative cell line from MCC tumors. Notably, all MCV-positive MCC cell lines underwent growth arrest and/or cell death upon TA knockdown, whereas the proliferation of MCV-negative cell lines remained unaffected. Despite an increase in the number of annexin V-positive, 7-amino-actinomycin D (7-AAD)-negative cells upon TA knockdown, activation of caspases or changes in the expression and phosphorylation of Bcl-2 family members were not consistently detected after TA suppression. Our study provides the first direct experimental evidence that TA expression is necessary for the maintenance of MCV-positive MCC and that MCV is the infectious cause of MCV-positive MCC.
Lateral diffusion and retrograde movements of individual cell surface components on single motile cells observed with Nanovid microscopy. (1991)

A recently introduced extension of video-enhanced light microscopy, called Nanovid microscopy, documents the dynamic reorganization of individual cell surface components on living cells. 40-microns colloidal gold probes coupled to different types of poly-L-lysine label negative cell surface components of PTK2 cells. Evidence is provided that they bind to negative sialic acid residues of glycoproteins, probably through nonspecific electrostatic interactions. The gold probes, coupled to short poly-L-lysine molecules (4 kD) displayed Brownian motion, with a diffusion coefficient in the range 0.1-0.2 micron2/s. A diffusion coefficient in the 0.1 micron2/s range was also observed with 40-nm gold probes coupled to an antibody against the lipid-linked Thy-1 antigen on 3T3 fibroblasts. Diffusion of these probes is largely confined to apparent microdomains of 1-2 microns in size. On the other hand, the gold probes, coupled to long poly-L-lysine molecules (240 kD) molecules and bound to the leading lamella, were driven rearward, toward the boundary between lamelloplasm and perinuclear cytoplasm at a velocity of 0.5-1 micron/min by a directed ATP-dependent mechanism. This uniform motion was inhibited by cytochalasin, suggesting actin microfilament involvement. A similar behavior on MO cells was observed when the antibody-labeled gold served as a marker for the PGP-1 (GP-80) antigen. These results show that Nanovid microscopy, offering the possibility to observe the motion of individual specific cell surface components, provides a new and powerful tool to study the dynamic reorganization of the cell membrane during locomotion and in other biological contexts as well.
Enhanced photodesorption from near- and mid-infrared plasmonic nanocrystal thin films (2018)

The authors show that the desorption rate of two model molecules, indole and benzoic acid, from thin films of indium tin oxide nanocrystals supporting near- and mid-infrared (0.33–0.48 eV) localized surface plasmon resonances (LSPRs) is enhanced by as much as 60% upon illumination with broadband infrared light. The desorption rate increases linearly with light intensity. No increase in the desorption rate is detected for undoped In2O3 nanocrystal thin films or when photons resonant with the LSPR are blocked. The authors study the desorption rate enhancement as a function of illumination intensity, LSPR energy, and isotopic substitution. Importantly, the authors demonstrate the accelerated desorption via in-coupling of light to LSPRs with energies well within the mid-infrared. Their work opens the door to using these low energy photons as choreographers of chemical processes and sets the stage for future mechanistic studies.
A Novel Multipath Light Signal Dispersion Reduction Technique Based on Controlled-Polarization Optical Wireless Link Setup (2005)

The detection characteristics of an indoor-optical communication system, which utilizes infrared radiation as carrier, has been explored and enhanced for telemedicine and wireless local area network applications. The novelty of the presented technique consists of the fact that multipath dispersion can be reduced under controlled polarization link setup. The design of such a network is based on the specifications set by the IEEE 802.11 standard.
Protection of densely populated excited triplet state ensembles against deactivation by molecular oxygen (2016)

This critical review discusses different approaches towards protection of photoactive materials based on triplet excited state ensembles against deactivation by molecular oxygen though quenching and photooxidation mechanisms. Passive protection, based on the application of barrier materials for packaging, sealing, or encapsulation of the active substances, which prevent oxygen molecules from penetration and physical contact with excited states and active protection, based on the application of oxygen scavenging species are compared. Efficiencies of different approaches together with examples and prospects of their applications are outlined.
A Metropolis random walk algorithm to estimate a lower bound of the star discrepancy (2023)

Abstract In this paper, we introduce a new algorithm for estimating the lower bounds for the star discrepancy of any arbitrary point sets in <m:math xmlns:m="http://www.w3.org/1998/Math/MathML"> <m:msup> <m:mrow> <m:mo stretchy="false">[</m:mo> <m:mn>0</m:mn> <m:mo>,</m:mo> <m:mn>1</m:mn> <m:mo stretchy="false">]</m:mo> </m:mrow> <m:mi>s</m:mi> </m:msup> </m:math> [0,1]^{s} . Computing the exact star discrepancy is known to be an NP-hard problem, so we have been looking for effective approximation algorithms. The star discrepancy can be thought of as the maximum of a function called the local discrepancy, and we will develop approximation algorithms to maximize this function. Our algorithm is analogous to the random walk algorithm described in one of our previous papers [M. Alsolami and M. Mascagni, A random walk algorithm to estimate a lower bound of the star discrepancy, Monte Carlo Methods Appl. 28 (2022), 4, 341–348.]. We add a statistical technique to the random walk algorithm by implementing the Metropolis algorithm in random walks on each chosen dimension to accept or reject this movement. We call this Metropolis random walk algorithm. In comparison to all previously known techniques, our new algorithm is superior, especially in high dimensions. Also, it can quickly determine the precise value of the star discrepancy in most of our data sets of various sizes and dimensions, or at least the lower bounds of the star discrepancy.
Long-circulating Janus nanoparticles made by electrohydrodynamic co-jetting for systemic drug delivery applications (2015)

EHD co-jetting is a versatile method for the fabrication of nanoparticles for drug delivery. Circulation of the nanoparticles for 24 h is a pre-requisite for subsequent studies to explore defined targeting of the nanoparticles to a specific anatomic site.
Exploring the Binding of Barbital to a Synthetic Macrocyclic Receptor. A Charge Density Study (2018)

Experimental charge density distribution studies, complemented by quantum mechanical theoretical calculations, of a host-guest system composed of a macrocycle (1) and barbital (2) in a 1:1 ratio (3) have been carried out via high-resolution single-crystal X-ray diffraction. The data were modeled using the conventional multipole model of electron density according to the Hansen-Coppens formalism. The asymmetric unit of macrocycle 1 contained an intraannular ethanol molecule and an extraannular acetonitrile molecule, and the asymmetric unit of 3 also contained an intraannular ethanol molecule. Visual comparison of the conformations of the macrocyclic ring shows the rotation by 180° of an amide bond attributed to competitive hydrogen bonding. It was found that the intraannular and extraannular molecules inside were orientated to maximize the number of hydrogen bonds present, with the presence of barbital in 3 resulting in the greatest stabilization. Hydrogen bonds ranging in strength from 4 to 70 kJ mol<sup>-1</sup> were the main stabilizing force. Further analysis of the electrostatic potential among 1, 2, and 3 showed significant charge redistribution when cocrystallization occurred, which was further confirmed by a comparison of atomic charges. The findings presented herein introduce the possibility of high-resolution X-ray crystallography playing a more prominent role in the drug design process.
Compartmentalized Devices as Tools for Investigation of Human Brain Network Dynamics (2018)

Neuropsychiatric disorders have traditionally been difficult to study due to the complexity of the human brain and limited availability of human tissue. Induced pluripotent stem (iPS) cells provide a promising avenue to further our understanding of human disease mechanisms, but traditional 2D cell cultures can only provide a limited view of the neural circuits. To better model complex brain neurocircuitry, compartmentalized culturing systems and 3D organoids have been developed. Early compartmentalized devices demonstrated how neuronal cell bodies can be isolated both physically and chemically from neurites. Soft lithographic approaches have advanced this approach and offer the tools to construct novel model platforms, enabling circuit‐level studies of disease, which can accelerate mechanistic studies and drug candidate screening. In this review, we describe some of the common technologies used to develop such systems and discuss how these lithographic techniques have been used to advance our understanding of neuropsychiatric disease. Finally, we address other in vitro model platforms such as 3D culture systems and organoids and compare these models with compartmentalized models. We ask important questions regarding how we can further harness iPS cells in these engineered culture systems for the development of improved in vitro models. Developmental Dynamics 248:65–77, 2019. © 2018 Wiley Periodicals, Inc.
Optimization problems for plasma-induced damage - A concept for plasma-induced damage design (2012)

This article demonstrates optimization problems for plasma-induced physical damage (PPD) in MOSFET. Since plasma-induced Si substrate damage (one of PPD mechanisms) degrades MOSFET performance such as drain current (I <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">on</sub> ) and off-state leakage current (I <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">off</sub> ), an implementation of PPD impact on MOSFET specifications is quite important in developing plasma processes. However, as presented, the degradation of I <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">on</sub> and I <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">off</sub> by PPD is in a tradeoff relationship. Therefore, one can not minimize I <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">on</sub> - and I <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">off</sub> -degradation independently by tuning process parameters - one can only optimize the process parameters (ex. maximize a plasma-process performance) to satisfy given MOSFET specifications (I <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">on</sub> and I <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">off</sub> ). A methodology of optimization problems is demonstrated by focusing on PPD in the source / drain extension region of MOSFET.
Performance of a diode-pumped 1.4 W Tm:GdVO4 microchip laser at 1.9μm. (1998)

GdVO 4 as a host for Thulium has several advantages for diode pumping in comparison with YAG. The absorption cross section of Thulium in GdVO 4 is considerably stronger and broader than in YAG and the spectrum is shifted closer to the emission wavelength of commercially available AlGaAs laser diodes. The broad emission spectrum (1.9 μm - 2.1 μm) allows for tuning the laser wavelength. Furthermore, the large thermal conductivity of GdVO 4 (10 W/mK) is very favourable for efficient cooling of the crystal.
Influence of sprint training on human skeletal muscle purine nucleotide metabolism (1994)

To examine the effect of sprint training on human skeletal muscle purine nucleotide metabolism, eight active untrained subjects completed a maximal 30-s sprint bout on a cycle ergometer before and after 7 wk of sprint training. Resting muscle ATP and total adenine nucleotide content were reduced (P < 0.05) by 19 and 18%, respectively, after training. Training resulted in a 52% attenuation (P < 0.05) in the magnitude of ATP depletion after exercise and a similar reduction (P < 0.05) in the accumulation of inosine 5'-monophosphate and ammonia. During recovery, muscle inosine 5'-monophosphate (P < 0.05) and inosine (P < 0.01) content were reduced after training, as was the accumulation of inosine (P < 0.05). Plasma ammonia was higher (P < 0.05) after training early in recovery; in contrast, plasma hypoxanthine concentrations were reduced (P < 0.05) during the latter stages of recovery. The attenuated resting ATP and total adenine nucleotide contents after training probably result from the acute effects of prior training sessions. The reduction in the magnitude of ATP depletion during a 30-s sprint bout after training must reflect an improved balance between ATP hydrolysis and resynthesis. It is unclear which mechanism(s) is responsible for the reduction in the magnitude of ATP degradation after training.
Identification of novel circulating human embryonic blood stem cells (2000)

Using murine models, primitive hematopoietic cells capable of repopulation have been shown to reside in various anatomic locations, including the aortic gonad mesonephros, fetal liver, and bone marrow. These sites are thought to be seeded by stem cells migrating through fetal circulation and would serve as ideal targets for in utero cellular therapy. In humans, however, it is unknown whether similar stem cells exist. Here, we identify circulating hematopoeitic cells present during human in utero development that are capable of multilineage repopulation in immunodeficient NOD/SCID (nonobese diabetic/severe combined immunodeficient) mice. Using limiting dilution analysis, the frequency of these fetal stem cells was found to be 1 in 3.2 x 10(5), illustrating a 3- and 22-fold enrichment compared with full-term human cord blood and circulating adult mobilized-peripheral blood, respectively. Comparison of in vivo differentiation and proliferative capacity demonstrated that circulating fetal stem cells are intrinsically distinct from hematopoietic stem cells found later in human development and those derived from the fetal liver or fetal bone marrow compartment at equivalent gestation. Taken together, these studies demonstrate the existence of unique circulating stem cells in early human embryonic development that provide a novel and previously unexplored source of pluripotent stem cell targets for cellular and gene-based fetal therapies. (Blood. 2000;96:1740-1747)
Short-Time Antibacterial Effects of Dimethylaminododecyl Methacrylate on Oral Multispecies Biofilm In Vitro (2019)

Quaternary ammonium compounds constitute a large group of antibacterial chemicals with a potential for inhibiting dental plaque. The aims of this study were to evaluate short-time antibacterial and regulating effects of dimethylaminododecyl methacrylate (DMADDM) on multispecies biofilm viability, reformation, and bacterial composition in vitro. DMADDM, chlorhexidine (CHX), and sodium fluoride (NaF) were chosen in the present study. <i>Streptococcus mutans</i>, <i>Streptococcus sanguinis,</i> and <i>Streptococcus gordonii</i> were used to form multispecies biofilm. Cytotoxicity assay was used to determine the optimal tested concentration. 3-(4,5-dimethyl-thiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay and resazurin test of biofilm were conducted to study the biomass changes and metabolic changes of controlled multispecies biofilm. Scanning electron microscopy (SEM) was used to observe biofilm images. TaqMan real-time polymerase chain reaction was performed to evaluate the proportion change in multispecies biofilm of different groups. Cytotoxicity assay showed that there existed a certain concentration application range for DMADDM, CHX, and NaF. MTT assay and resazurin test results showed that DMADDM and CHX groups decreased multispecies biofilm growth and metabolic activity (<i>p</i> < 0.05), no matter after 1 min or 5 min direct contact killing or after 24 h regrowth. The proportion of <i>S. mutans</i> decreased steadily in DMADDM and CHX groups after 1 min and 5 min direct contact killing and 24 h regrowth, compared to control groups. A novel DMADDM-containing solution was developed, achieving effective short-time antibacterial effects and regulation ability of biofilm formation.
One-pass multi-layer rate-distortion optimization for quality scalable video coding (2009)

In this paper, a one-pass multi-layer rate-distortion optimization algorithm is proposed for quality scalable video coding. To improve the overall coding efficiency, the MB mode in the base layer is selected not only based on its rate-distortion performance relative to this layer but also according to its impact on the enhancement layer. Moreover, the optimization module for residues is also improved to benefit inter-layer prediction. Simulations show that the proposed algorithm outperforms the most recent SVC reference software. For eight test sequences, a gain of 0.35 dB on average and 0.75 dB at maximum is achieved at a cost of less than 8% increase of the total coding time.