gebhart/patrepeval huggingface dataset:
CSMA/CN (2010)

A wireless transmitter learns of a packet loss, infers collision, only after completing the entire transmission. If the transmitter could detect the collision early (such as with CSMA/CD in wired networks), it could immediately abort its transmission, freeing the channel for useful communication. There are two main hurdles to realize CSMA/CD in wireless networks. First, a wireless transmitter cannot simultaneously transmit and listen for a collision. Second, any channel activity around the transmitter may not be an indicator of collision at the receiver. This paper attempts to approximate CSMA/CD in wireless networks with a scheme called CSMA/CN (collision notification). Under CSMA/CN, the receiver uses PHY layer information to detect a collision and immediately notifies the transmitter. The collision notification consists of a unique signature, sent on the same channel as the data. The transmitter employs a listener antenna and performs signature correlation to discern this notification. Once discerned, the transmitter immediately aborts transmission. We show that the notification signature can be reliably detected at the listener antenna, even in the presence of a strong self-interference from the transmit antenna. A prototype testbed of 10 USRP/GNURadios demonstrates the feasibility and effectiveness of CSMA/CN
Working Supramolecular Machines Trapped in Glass and Mounted on a Film Surface (2001)

Zwei oberflächengebundene Nanomotoren wurden konstruiert: Bei beiden dient das π-elektronenarme tetrakationische Cyclophan Cyclobis(paraquat-p-phenylen) als Zylinder (blau), in dem sich die Bewegung des Kolbens (π-elektronenreiche Dioxynaphthalin-Einheiten; rot und rosa) induzieren lässt, wenn Reduktionsmittel entweder durch Chemikalien zur Verfügung gestellt werden oder durch eine Lichtquelle, wobei dann 9-Anthracencarbonsäure (gelb) als Photosensibilisator dient und Ethylendiamintetraacetat (grün) als „Opferreagens“.
Potentiation of diethylstilbestrol‐induced alterations in the female mouse reproductive tract by transforming growth factor‐α transgene expression (1996)

Neonatal estrogen exposure causes numerous abnormalities in the female reproductive tract, including carcinogenesis. One mechanism by which neonatal estrogen elicits teratogenic and carcinogenic effects is epigenetic and involves the modulation of a number of estrogen-regulated genes including epidermal growth factor (EGF). Because of the evidence that there is an integral relationship between the EGF family, estrogen action, and the regulation of the growth and differentiation of the reproductive tract, we used transforming growth factor-α (TGFα) transgenic mice to investigate the interaction of constitutive TGFα expression with the potent estrogen diethylstilbestrol (DES) in the induction of reproductive-tract alterations. Our study was designed to determine whether TGFα expression could modulate DES-induced carcinogenesis of the female mouse reproductive tract. The animals were homozygous TGFα transgenic female mice from the MT42 line and the parental CD-1 outbred mice. The presence of the TGFα transgene significantly increased the incidence of DES-induced vaginal adenosis, uterine endometrial hyperplasia, uterine polyps, hypospadia, benign ovarian cysts, and pituitary adenomas. However, constitutive TGFα expression did not promote reproductive-tract neoplasia. This study demonstrates that TGFα participates in the regulation of developmental and morphogenic events in the Müllerian duct and urogenital sinus, suggesting a role for TGFα in the pathogenesis of reproductive-tract diseases. Furthermore, we showed that although constitutive expression of the TGFα transgene did have an effect on the reproductive tract, TGFα overexpression alone could not substitute for DES as a reproductive-tract carcinogen or as a promoter of uterine neoplasia, indicating that DES-induced carcinogenesis requires events in addition to the overexpression of this single peptide growth factor. © 1996 Wiley-Liss, Inc. 1 This article is a US Government work and, as such, is in the public domain in the United States of America.
Enhancement of room-temperature photoluminescence in InAs quantum dots (2003)

We report pronounced enhancement of room-temperature photoluminescence up to 80-fold induced by proton implantation and the rapid thermal annealing process in a multilayer InAs/GaAs quantum-dot structure. This effect is studied by a combination of material methods and resulted from both proton passivation and carrier capture enhancement effects. The maximum photoluminescence peak shift is about 23 meV, resulting from the intermixing of quantum dots. Linear dependence behavior as observed for both the nonradiative recombination time and carrier relaxation time on the ion-implantation dose. Maximum enhancement of the photoluminescence is observed for a proton implantation dose of 1.0×1014 cm−2 followed by rapid thermal annealing at 700 °C. These effects will be useful for quantum dot optoelectronic devices.
A High Voltage Power Supply That Mitigates Current Reversals in Capillary Zone Electrophoresis-Electrospray Mass Spectrometry (2016)

Capillary electrophoresis coupled with electrospray ionization typically employs two power supplies, one at each end of the capillary. One power supply is located at the proximal (injection) end of the capillary. The power supply located at the distal (detector) end of the capillary drives the electrospray. Electrophoresis is driven by the difference in potential between these power supplies. Separations that employ large capillary inner diameter, high conductivity background electrolyte, and high separation potentials generate higher current than that produced by the electrospray. Excess current flows through the electrospray power supply. Most power supplies are not designed to sink current, and the excess current will cause the electrospray voltage to deviate from its set point. We report a simple circuit to handle this excess current, allowing separations under a wide range of electrophoretic conditions. Graphical Abstract ᅟ.
Current View on the Mechanism of Action of Perifosine in Cancer (2014)

Perifosine treatment exhibits a complex molecular response including the inhibition of Akt or the induction of apoptosis via clustering of death receptors in lipid rafts. However, the molecular response can vary between different tumor entities and the contribution of each target pathway to the activity of Perifosine might be distinct depending on the tumor entity or the agent combined with Perifosine. In this review we discuss the current view on the mechanism of action of perifosine in cancer and the contribution of the molecular targets of Perifosine to its activity.
Temperature-Aware Distributed Run-Time Optimization on MP-SoC Using Game Theory (2008)

With forecasted hundreds of processing elements (PE), future embedded systems will be able to handle multiple applications with very diverse running constraints. In order to avoid hot-spots and control the temperature of the tiles, dynamic voltage-frequency scaling (DVFS) can be applied at PE level. At system level, it implies to dynamically manage the different voltage-frequency couples of each PE in order to obtain a global optimization. In this article we present an approach based on game theory, which adjusts at run-time the frequency of each PE. It aims at reducing the tile temperature while maintaining the synchronization between the tasks of the application graph. A fully distributed scheme is assumed in order to build a scalable mechanism. Results show that the proposed run-time algorithm find solutions in few calculation cycles achieving temperature reductions of about 23%.
ALS-linked misfolded SOD1 species have divergent impacts on mitochondria (2016)

Approximately 20 % of familial Amyotrophic Lateral Sclerosis (ALS) is caused by mutations in superoxide dismutase (SOD1), which leads to misfolding of the SOD1 protein, resulting in a toxic gain of function. Several conformation-restricted antibodies have been generated that specifically recognize misfolded SOD1 protein, and have been used as therapeutics in pre-clinical models. Misfolded SOD1 selectively associates with spinal cord mitochondria in SOD1 rodent models. Using the SOD1(G93A) rat model, we find that SOD1 conformational specific antibodies AMF7-63 and DSE2-3H1 labeled a fibrillar network concentrated in the anterior horn; while A5C3, B8H10, C4F6 and D3H5 labeled motor neurons as well as puncta in the neuropil. There is a time-dependent accumulation of misfolded SOD1 at the surface of spinal cord mitochondria with AMF7-63-labeled mitochondria having increased volume in contrast to a mitochondrial subset labeled with B8H10. In spinal cord homogenates and isolated mitochondria, AMF7-63, DSE2-3H1 and B8H10 detect misfolded SOD1 aggregates. SOD1 that lacks its metal cofactors has an increased affinity for naïve mitochondria and misfolded SOD1 antibodies B8H10 and DSE2-3H1 readily detect demetalated mutant and wild-type SOD1. Together, these data suggest that multiple non-native species of misfolded SOD1 may exist, some of which are associated with mitochondrial damage. Conformational antibodies are invaluable tools to identify and characterize the variation in misfolded SOD1 species with regards to biochemical characteristics and toxicity. This information is highly relevant to the further development of these reagents as therapeutics.
Supplementary Figure 4 from Dual-specific Chimeric Antigen Receptor T Cells and an Indirect Vaccine Eradicate a Variety of Large Solid Tumors in an Immunocompetent, Self-antigen Setting (2023)

&lt;p&gt;ACTIV therapy induces cytokine secretion and apoptosis of tumor cells.&lt;/p&gt;
Atrial Septostomy for Left Ventricular Unloading During Extracorporeal Membrane Oxygenation for Cardiogenic Shock (2021)

In acute CS supported by VA ECMO, atrial septostomy is an effective LV unloading tool. LV pressure is a key component of LV work load, so whenever LV work reduction is a priority, arterial pressure should carefully be titrated low while maintaining organ perfusion.
Poled electro-optic photolime gel polymer doped with chlorophenol red and bromomethyl blue chromophores (1995)

An electro-optic polymer with chlorophenol red dye and type-A photolime gel was demonstrated. The electro-optic coefficient γ33 in the direction of the poling field was measured to be 28 pm/V. Chlorophenol red in polymer showed a 1/e relaxation time constant of 820 h, which is more stable than other dye demonstrated previously to be electro-optic in the same polymer.
Analytical performance of a single epitope B-type natriuretic peptide sandwich immunoassay on the Minicare platform for point-of-care diagnostics (2019)

Point-of-care B-type natriuretic peptide (BNP) testing with adequate analytical performance has the potential to improve patient flow and provide primary care givers with easy-to-use advanced diagnostic tools in the management of heart failure. We present the analytical evaluation of the Minicare BNP immunoassay under development on the Minicare I-20 platform for point-of-care testing. Analytical performance was evaluated using EDTA venous whole blood, EDTA plasma and capillary whole blood. Method comparison with a lab-testing system was performed using samples from 187 patients. Normal values were determined based on 160 healthy adults, aging from 19 to 70 years. Limit of blank (LoB), limit of detection (LoD) were determined to be 3.3 ng/L, 5.8 ng/L. Limit of quantitation (LoQ) in whole blood at 20% and 10% coefficient of variation (CV) was found < 9 ng/L and <30 ng/L respectively without significant differences between EDTA whole blood and EDTA plasma. Total CV was found to be from 6.7% to 9.7% for BNP concentrations between 92.6 and 3984 ng/L. The sample type comparison study demonstrated correlation coefficients between 0.97 and 0.99 with slopes between 1.03 and 1.09 between the different samples. Method comparison between Minicare BNP and Siemens ADVIA Centaur BNP demonstrated a correlation coefficient of 0.92 with a slope of 1.06. The 97.5% URL of a healthy population was calculated to be 72.6 ng/L. The Minicare BNP assay is a robust, easy-to-use and sensitive test for rapid determination of BNP concentrations that can be used in a near-patient setting.
Supplementary Figure 2 from Immunotargeting of Antigen xCT Attenuates Stem-like Cell Behavior and Metastatic Progression in Breast Cancer (2023)

&lt;p&gt;qPCR analysis of xCT expression in tumorspheres&lt;/p&gt;
One-microsecond molecular dynamics simulation of channel gating in a nicotinic receptor homologue (2010)

Recently discovered bacterial homologues of eukaryotic pentameric ligand-gated ion channels, such as the Gloeobacter violaceus receptor (GLIC), are increasingly used as structural and functional models of signal transduction in the nervous system. Here we present a one-microsecond-long molecular dynamics simulation of the GLIC channel pH stimulated gating mechanism. The crystal structure of GLIC obtained at acidic pH in an open-channel form is equilibrated in a membrane environment and then instantly set to neutral pH. The simulation shows a channel closure that rapidly takes place at the level of the hydrophobic furrow and a progressively increasing quaternary twist. Two major events are captured during the simulation. They are initiated by local but large fluctuations in the pore, taking place at the top of the M2 helix, followed by a global tertiary relaxation. The two-step transition of the first subunit starts within the first 50 ns of the simulation and is followed at 450 ns by its immediate neighbor in the pentamer, which proceeds with a similar scenario. This observation suggests a possible two-step domino-like tertiary mechanism that takes place between adjacent subunits. In addition, the dynamical properties of GLIC described here offer an interpretation of the paradoxical properties of a permeable A13'F mutant whose crystal structure determined at 3.15 A shows a pore too narrow to conduct ions.
Nicotinamide adenine dinucleotide is transported into mammalian mitochondria (2018)

Mitochondrial NAD levels influence fuel selection, circadian rhythms, and cell survival under stress. It has alternately been argued that NAD in mammalian mitochondria arises from import of cytosolic nicotinamide (NAM), nicotinamide mononucleotide (NMN), or NAD itself. We provide evidence that murine and human mitochondria take up intact NAD. Isolated mitochondria preparations cannot make NAD from NAM, and while NAD is synthesized from NMN, it does not localize to the mitochondrial matrix or effectively support oxidative phosphorylation. Treating cells with nicotinamide riboside that is isotopically labeled on the nicotinamide and ribose moieties results in the appearance of doubly labeled NAD within mitochondria. Analogous experiments with doubly labeled nicotinic acid riboside (labeling cytosolic NAD without labeling NMN) demonstrate that NAD(H) is the imported species. Our results challenge the long-held view that the mitochondrial inner membrane is impermeable to pyridine nucleotides and suggest the existence of an unrecognized mammalian NAD (or NADH) transporter.
Analiza możliwości wykorzystania geofizycznych metod sejsmiki powierzchniowej do oceny stanu technicznego wałów przeciwpowodziowych (2012)

W artykule przedstawiono wyniki badań geologiczno-inżynierskich wybranych odcinków wałów przeciwpowodziowych rzeki Wisły na terenie Doliny Maciejowickiej. Wykonane prace pozwoliły na analizę zmian struktury gruntu w miejscach zaobserwowanych uszkodzeń i zjawisk filtracyjnych w rejonie wału, powstałych w wyniku wezbrania. Przeprowadzono wizje terenowe, rozpoznanie geologiczne i sondowania dynamiczne oraz badania z użyciem metod sejsmiki powierzchniowej (SASW i CSWS) wykorzystującej fale Rayleigha. Projekt badawczy został zrealizowany przez Koło Naukowe Inżynierii Wodnej w ramach grantu rektorskiego Politechniki Warszawskiej, przy współpracy z Zakładem Geologii Inżynierskiej Uniwersytetu Warszawskiego. Na podstawie zrealizowanych badań można wnioskować, że wykorzystane do badania stanu wałów przeciwpowodziowych nowoczesne metody badawcze (sejsmika inżynierska) prezentują duży potencjał do wykorzystania w dalszych pracach badawczych i wdrożeniowych.
System-Level Analysis of Transcriptional and Translational Regulatory Elements in Streptomyces griseus (2022)

Bacteria belonging to <i>Streptomyces</i> have the ability to produce a wide range of secondary metabolites through a shift from primary to secondary metabolism regulated by complex networks activated after vegetative growth terminates. Despite considerable effort to understand the regulatory elements governing gene expression related to primary and secondary metabolism in <i>Streptomyces</i>, system-level information remains limited. In this study, we integrated four multi-omics datasets from <i>Streptomyces griseus</i> NBRC 13350: RNA-seq, ribosome profiling, dRNA-seq, and Term-Seq, to analyze the regulatory elements of transcription and translation of differentially expressed genes during cell growth. With the functional enrichment of gene expression in different growth phases, one sigma factor regulon and four transcription factor regulons governing differential gene transcription patterns were found. In addition, the regulatory elements of transcription termination and post-transcriptional processing at transcript 3'-end positions were elucidated, including their conserved motifs, stem-loop RNA structures, and non-terminal locations within the polycistronic operons, and the potential regulatory elements of translation initiation and elongation such as 5'-UTR length, RNA structures at ribosome-bound sites, and codon usage were investigated. This comprehensive genetic information provides a foundational genetic resource for strain engineering to enhance secondary metabolite production in <i>Streptomyces</i>.
A possible role for cysteine proteinase and its inhibitors in motility of malignant melanoma and other tumour cells (1992)

The metastasis of malignant tumour cells depends on their rapid replication, and their ability to adhere to the matrix of a biological barrier such as basement membrane, to degrade the matrix, and to migrate through this more permeable barrier. Secreted enzymes, including the cysteine proteinases cathepsins B and L, are known to degrade basement membrane components. Using a barrier-free substratum we studied the possible role of cysteine proteinases in influencing the motility per se of metastatic cells. We found that stefins, the natural inhibitors of cysteine proteinases, markedly decreased the stimulated motility of both human melanoma cells and W256 carcinosarcoma cells at low concentrations (0.5 microM). A stefin also inhibited melanoma cell adherence, but to a lesser extent than motility. Additionally, synthetic inhibitors (E-64, diazomethyl ketones) of cysteine proteinases were found to depress stimulated motility of W256 cells. These results suggest that cysteine proteinases and their inhibitors may have a direct role in the development of a migratory response per se in tumour cells.
Complex interactions of transcription factors in mediating cytokine biology in T cells (2014)

T-helper (Th) cells play critical roles within the mammalian immune system, and the differentiation of naive CD4(+) T cells into distinct T-helper subsets is critical for normal immunoregulation and host defense. These carefully regulated differentiation processes are controlled by networks of cytokines, transcription factors, and epigenetic modifications, resulting in the generation of multiple CD4(+) T-cell subsets, including Th1, Th2, Th9, Th17, Treg, and Tfh cells. In this review, we discuss the roles of transcription factors in determining the specific type of differentiation and in particular the role of interleukin-2 (IL-2) in promoting or inhibiting Th differentiation. In addition to discussing master regulators and subset-specific transcription factors for distinct T-helper cell populations, we focus on signal transducer and activator of transcription (STAT) proteins and on the cooperative action of interferon regulatory factor 4 (IRF4) with activator protein 1 (AP-1) family proteins and STAT3 in the assembly of complexes that broadly influence T-cell differentiation.
Fine-grain DVFS and AVFS techniques for complex SoC design: An overview of architectural solutions through technology nodes (2015)

In this paper we propose to give an overview of fine-grain design techniques we demontrated past years in our lab for power reduction in complex SoCs. Those works are based on Globally Asynchronous and Locally Synchronous systems in which each IP is an independent voltage and frequency domain. After having proposed some simple DFS architectures based on GALS architectures in 130nm technology, we extended our works to fine-grain Dynamic Voltage and Frequency Scaling architectures to reduce dynamic and static power reduction at 65 nm node. Furthermore, considering 32 nm deep submicron technologies, we demonstrated an Adaptive Voltage and Frequency architecture to compensate for in-die PVT variations. Area overhead and power reduction results are discussed all along the paper.
A Belted Monofacial Ionophore Featuring High Selectivity for Lithium Ion Complexation (1999)

Despite its preferred equatorial conformation in the solid state and in solution, the cis,cis-trispiro ether 1 binds readily and strongly to lithium ions. The 2:1 sandwich complex 2 is initially formed and transformed progressively into the 1:1 species 3 upon the addition of more LiClO4.
The HMGB1 protein induces a metabolic type of tumour cell death by blocking aerobic respiration (2016)

The high-mobility group box 1 (HMGB1) protein has a central role in immunological antitumour defense. Here we show that natural killer cell-derived HMGB1 directly eliminates cancer cells by triggering metabolic cell death. HMGB1 allosterically inhibits the tetrameric pyruvate kinase isoform M2, thus blocking glucose-driven aerobic respiration. This results in a rapid metabolic shift forcing cells to rely solely on glycolysis for the maintenance of energy production. Cancer cells can acquire resistance to HMGB1 by increasing glycolysis using the dimeric form of PKM2, and employing glutaminolysis. Consistently, we observe an increase in the expression of a key enzyme of glutaminolysis, malic enzyme 1, in advanced colon cancer. Moreover, pharmaceutical inhibition of glutaminolysis sensitizes tumour cells to HMGB1 providing a basis for a therapeutic strategy for treating cancer.