gebhart/patrepeval huggingface dataset:
Approximation Algorithm for the Binary-Preference Capacitated Selfish Replication Game and a Tight Bound on its Price of Anarchy (2015)

We consider the capacitated selfish replication (CSR) game with binary preferences, over general undirected networks. We first show that such games have an associated ordinary potential function, and hence always admit a pure-strategy Nash equilibrium (NE). Further, when the minimum degree of the network and the number of resources are of the same order, there exists an exact polynomial time algorithm which can find a NE. Following this, we study the price of anarchy of such games, and show that it is bounded above by 3; we further provide some instances for which the price of anarchy is at least 2. We develop a quasi-polynomial algorithm O(n^2D^{ln n}), where n is the number of players and D is the diameter of the network, which can find, in a distributed manner, an allocation profile that is within a constant factor of the optimal allocation, and hence of any pure-strategy NE of the game. Proof of this result uses a novel potential function.
Supplementary Table S10 from C/EBPα Confers Dependence to Fatty Acid Anabolic Pathways and Vulnerability to Lipid Oxidative Stress–Induced Ferroptosis in &lt;i&gt;FLT3&lt;/i&gt;-Mutant Leukemia (2023)

&lt;p&gt;Table S10: EnrichR analysis of CEBPA_UP signature&lt;/p&gt;
NIME Publication Ecosystem Workshop (2020)

How can we develop an open, future-oriented, multimedia-rich, and institutionally recognised publication ecosystem for NIME practitioners and researchers? This workshop will continue previous discussions about the need for a NIME journal, and for solutions to share ideas, hardware designs, code, scores, and performances, systematically. Concerns about C19, climate change, and accessibility make these discussions urgent and demand reimagining our expectations for a publication venue. What solutions can we start implementing right away, and which goals do we have as a community? This open workshop will lay the ground for concrete experimentation in the year(s) to come.
Modulating the affinity and the selectivity of engineered calmodulin EF‐Hand peptides for lanthanides (2006)

A set of engineered peptides (33 amino acids long) corresponding to the helix-turn-helix (EF-Hand) motif of the metal-binding site I of the protein calmodulin from paramecium tetraurelia have been synthesized. A disulfide bridge has been introduced in the native sequence in order to stabilize a native-like conformation. The calcium-binding carboxylate residues in positions 20, 22, 24, and 31 were mutated into other amino acids and the influence of such mutations on the binding affinity of the peptides for calcium and lanthanides have been studied. It was shown that the binding affinity for terbium ions can be modulated with dissociation constants ranging from 40 nmolar to 40 mmolar. The study of the influence of the mutations on the terbium affinity showed that the residue in position 24 played a key role on the capability of the peptides to bind lanthanides and that the affinity could be enhanced by mutations on non-coordinating positions. Such peptides with high affinity for lanthanides may facilitate the development of new highly sensitive biosensors to monitor the metal pollution in the environment.
Estimation of Infarct Size in Man and its Relation to Prognosis (1972)

Infarct size was assessed quantitatively in 33 patients with acute myocardial infarction with a new technic based on analysis of serial serum creatine phosphokinase (CPK) changes to determine its relationship to prognosis. We have recently measured infarct size in the conscious dog with this method which takes into account CPK distribution space, fractional disappearance rate, proportion degraded in myocardium, and proportion released into the circulation, and we have validated the method by measurement of myocardial CPK depletion in the same animals. In the present study, CPK activity (determined spectrophotometrically) and isoenzyme profiles (assayed electrophoretically) were measured in patient serum samples obtained every 2 hours. Infarct size was estimated by mathematical analysis of serial CPK changes utilizing the method previously developed in the conscious dog model. CPK isoenzyme profiles demonstrated prominent anodal bands, absent from normal serum, indicating that enzyme elevations reflected CPK released from heart rather than skeletal muscle. In 19 class I-II survivors (New York Heart Association) estimated infarct size was 31 ± 4 CPK-gram-equivalents (CPK-g-Eq). It was significantly larger ( P &lt; 0.01), 103 ± 14, in nine patients who died and in four class III or IV survivors (91 ± 8). Estimation of cumulative infarct size differentiated patients with electrocardiographic changes and clinical sequelae from complications such as pericarditis from those patients with extension of infarction. Thus, infarct size can be assessed quantitatively in patients with acute myocardial infarction and provide a useful diagnostic and prognostic index based on the extent of myocardial damage.
Load Balancing in the Presence of Services in Named-Data Networking (2019)

Abstract Load balancing is a mechanism to distribute client requests among several service instances. It enables resource utilization, lowers response time, and increases user satisfaction. In Named-Data Networking (NDN) and NDN-like architectures, load balancing becomes crucial when dynamic services are present, where relying solely on forwarding strategies can overload certain service instances while others are underutilized especially with the limited benefit of on-path caching when it comes to services. To understand the challenges and opportunities of load balancing in NDN, we analyze conventional load balancing in IP networks, and three closely related fields in NDN: congestion control, forwarding strategies, and data center management. We identify three possible scenarios for load balancing in NDN: facade load balancer, controller for Interest queues, and router-based load balancing. These different solutions use different metrics to identify the load on replicas, have different compliance levels with NDN, and place the load balancing functionality in different network components. From our findings, we propose and implement a new lightweight router-based load balancing approach called the communicating vessels and experimentally show how it reduces service response time and senses server capabilities without probing.
Electrochemically Synthesized Poly(3-hexylthiophene) Nanowires as Photosensitive Neuronal Interfaces (2021)

Poly(3-hexylthiophene) (P3HT) is a hole-conducting polymer that has been intensively used to develop organic optoelectronic devices (e.g., organic solar cells). Recently, P3HT films and nanoparticles have also been used to restore the photosensitivity of retinal neurons. The template-assisted electrochemical synthesis of polymer nanowires advantageously combines polymerization and polymer nanostructuring into one, relatively simple, procedure. However, obtaining P3HT nanowires through this procedure was rarely investigated. Therefore, this study aimed to investigate the template-assisted electrochemical synthesis of P3HT nanowires doped with tetrabutylammonium hexafluorophosphate (TBAHFP) and their biocompatibility with primary neurons. We show that template-assisted electrochemical synthesis can relatively easily turn 3-hexylthiophene (3HT) into longer (e.g., 17 ± 3 µm) or shorter (e.g., 1.5 ± 0.4 µm) P3HT nanowires with an average diameter of 196 ± 55 nm (determined by the used template). The nanowires produce measurable photocurrents following illumination. Finally, we show that primary cortical neurons can be grown onto P3HT nanowires drop-casted on a glass substrate without relevant changes in their viability and electrophysiological properties, indicating that P3HT nanowires obtained by template-assisted electrochemical synthesis represent a promising neuronal interface for photostimulation.
Nuclear Factor of Activated T Cells Regulates Osteopontin Expression in Arterial Smooth Muscle in Response to Diabetes-Induced Hyperglycemia (2009)

These results identify a glucose-sensitive transcription pathway in vivo, revealing a novel molecular mechanism that may underlie vascular complications of diabetes.
The Future of Computing: Logic or Biology (2003)

In the late 60s, Bob Floyd and Tony Hoare discovered the concept of program correctness. (The idea actually goes back to von Neumann. As Fred Schneider has observed, a number of explorers discovered America before Columbus—but when Columbus discovered America, it stayed discovered. That’s why the U.S. celebrates Columbus Day, not Leif Erickson Day.) Some people initially working on program correctness thought that, in the future, everyone would prove that their programs were correct. Programming errors would then disappear. We soon learned how naive that hope was. Floyd and Hoare showed that we could, in principle, do this. But in practice, it turned out to be very hard. Today, we know that verification is economically feasible only in a small number of applications—mainly, for fairly small programs that perform lifecritical functions. Verification techniques are being used successfully to help debug programs, at Microsoft and elsewhere. But actually proving the correctness of a program is rarely done. But Floyd and Hoare did make a profound contribution to our way of thinking about programs. They taught us that a program is a mathematical object, and we could think about it using logic. This idea inspired me, in early 1977, to write a short note titled How to Tell a Program from an Automobile. Let me read part of it.
Investigations of phagosomes, mitochondria, and acidic granules in human neutrophils using fluorescent probes (2002)

The oxidative burst is frequently evaluated by the conversion of dihydrorhodamine 123 (DHR) to rhodamine 123 (R123) and hydroethidium (HE) to ethidium with the use of flow cytometry (FCM). Added R123 accumulates in mitochondria, but during phagocytosis R123 originating from DHR has been observed in neutrophil granules. The present study was designed to identify the site of reactive oxygen species (ROS) formation and the intracellular traffic of R123 in neutrophils by using mitochondrial membrane potential probes and the lysosomotropic probe LysoTracker Red, which have not previously been applied to neutrophils. Quiescent and phagocytosing human peripheral blood neutrophils were incubated with DHR, HE, R123, MitoTracker Green (MTG), MitoTracker Red (CMX-Ros), and LysoTracker Red alone and in all combinations of red and green probes, and studied by FCM and confocal laser scanning microscopy (CLSM). Phagosomes were filled with R123 originating from DHR. Phagocytosis also triggered the oxidative burst in oxidative response granules that differed from acidic granules. All the neutrophils stained with mitochondrial and lysosomotropic dyes. Added R123 and MTG selectively accumulated in mitochondria. Added R123, MTG, and DHR increased the fluorescence of CMX-Ros and LysoTracker Red. This is the first FCM and CLSM demonstration of ROS formation in phagosomes. A distinct subpopulation of neutrophil granules, termed oxidative response granules, also was identified. Neutrophil mitochondrial membrane potential may be evaluated by incubating the cells with R123 and MTG, but results with CMX-Ros should be interpreted with caution. HE and DHR seem to measure a common pathway in the oxidative burst. The simultaneous application of several probes for investigations of organelles carries the risk of probe interference.
Inertial gravity currents produced by fluid drainage from an edge (2017)

We present theoretical, numerical and experimental studies of the release of a finite volume of fluid instantaneously from an edge of a rectangular domain for high Reynolds number flows. For the cases we considered, the results indicate that approximately half of the initial volume exits during an early adjustment period. Then, the inertial gravity current reaches a self-similar phase during which approximately 40 % of its volume drains and its height decreases as $\unicode[STIX]{x1D70F}^{-2}$ , where $\unicode[STIX]{x1D70F}$ is a dimensionless time that is derived with the typical gravity wave speed and the horizontal length of the domain. Based on scaling arguments, we reduce the shallow-water partial differential equations into two nonlinear ordinary differential equations (representing the continuity and momentum equations), which are solved analytically by imposing a zero velocity boundary condition at the closed end wall and a critical Froude number condition at the open edge. The solutions are in good agreement with the performed experiments and direct numerical simulations for various geometries, densities and viscosities. This study provides new insights into the dynamical behaviour of a fluid draining from an edge in the inertial regime. The solutions may be useful for environmental, geophysical and engineering applications such as open channel flows, ventilations and dam-break problems.
Paper #224: Precision and Accuracy of Identification of Anatomical Surface Landmarks Amongst 30 Expert Hip Arthroscopists (2013)

This study evaluates the ability of 30 independent expert hip arthroscopists to identify common surface landmarks used in the hip specialty practice by comparing examiner applied landmark tags with ultrasound verified anatomic tags.
Characterization oflpr-Derived T Cell Hybridomas: Fas-Deficient Hybridomas Are Deathless, Growth-Arrested, and Cytotoxic upon Activation (1996)

T cell hybridomas that are deathless upon TCR crosslinking were generated from lpr mice. The deathless hybridomas (1.4 and 5D5) expressed extremely low Fas even after anti-CD3 activation, whereas activation-induced cell death (AICD) was observed for Fas-expressing hybridomas. The deathless hybridomas were activated to produce FasL and IL-2, indicating that the intrinsic defect in Fas expression or up-regulation resulted in AICD blockade. The deathless hybridoma cells expressed longer and stronger FasL cytotoxicity than AICD-sensitive hybridomas. Although deathless, activated 5D5 cells were arrested at the G1/S border. Growth arrest lasted for at least 5 days, but some cells eventually recovered and proliferated. The deathless 5D5 cells were used to demonstrate that AICD includes a fratricidal mechanism that kills AICD-sensitive bystanders. The deathless T cell hybridomas are useful tools for studying T cell activation-dependent functions sensitive to AICD.
Accurate quantification of apoptosis progression and toxicity using a dielectrophoretic approach (2016)

A loss of ability of cells to undergo apoptosis (programmed cell death, whereby the cell ceases to function and destroys itself) is commonly associated with cancer, and many anti-cancer interventions aim to restart the process. Consequently, the accurate quantification of apoptosis is essential in understanding the function and performance of new anti-cancer drugs. Dielectrophoresis has previously been demonstrated to detect apoptosis more rapidly than other methods, and is low-cost, label-free and rapid, but has previously been unable to accurately quantify cells through the apoptotic process because cells in late apoptosis disintegrate, making cell tracking impossible. In this paper we use a novel method based on light absorbance and multi-population tracking to quantify the progress of apoptosis, benchmarking against conventional assays including MTT, trypan blue and Annexin-V. Analyses are performed on suspension and adherent cells, and using two apoptosis-inducing agents. IC<sub>50</sub> measurements compared favourably to MTT and were superior to trypan blue, whilst also detecting apoptotic progression faster than Annexin-V.
Assessing genetic overlap and causality between blood plasma proteins and Alzheimer’s Disease (2021)

ABSTRACT Background Blood plasma proteins are modifiable and have been associated with Alzheimer’s disease (AD), but understanding which proteins are on the causal pathway remains challenging. Objective Investigate the genetic overlap between candidate proteins and AD using polygenic risk scores (PRS) and interrogate their causal relationship using bi-directional Mendelian Randomization (MR). Methods Following a literature review, 31 proteins were selected for PRS analysis. PRS were constructed for prioritised proteins with and without the apolipoprotein E region (APOE+/- PRS) and tested for association with AD status across three cohorts (n=6244). An AD PRS was also tested for association with protein levels in one cohort (n=410). Proteins showing association with AD were taken forward for MR. Results For APOE e3, apolipoprotein B-100, and C-reactive protein (CRP), protein APOE+ PRS were associated with AD below Bonferroni significance (pBonf, p-value &lt;0.00017). No protein APOE-PRS or AD PRS (APOE+/-) passed pBonf. However, vitamin D-binding protein (protein PRS APOE-, p-value=0.009) and insulin-like growth factor-binding protein 2 (AD APOE- PRS p-value=0.025, protein APOE-PRS p-value=0.045) displayed suggestive signals and were selected for MR. In bi-directional MR, none of the 5 proteins demonstrated a causal association (p-value&lt;0.05) in either direction. Conclusion Apolipoproteins and CRP PRS are associated with AD and provide a genetic signal linked to a specific, modifiable risk factor. Whilst evidence of causality was limited, this study was conducted in a moderate sample size and provides a framework for larger samples with greater statistical power.
A Practical Synthesis of SDZ WAG 994 by Selective Methylation of N<sup>6</sup>-Cyclohexyladenosine (1996)

Abstract A selective 2′-O-methylation of N6-cyclohexyladenosine (2) under phase-transfer catalysis conditions and a preferential crystallization of N6-cyclohexyl-2′-O-methyladenosine (1, SDZ WAG 994) from a mixture of by-products is described. A plausible explanation for the selective crystallization of 1 as a hydrate is presented.
The World Federation of Societies of Biological Psychiatry (WFSBP) Guidelines for the Biological Treatment of Substance Use and Related Disorders. Part 2: Opioid dependence (2011)

There is enough high quality data to formulate evidence-based guidelines for the treatment of opioid abuse and dependence. This task force report provides evidence for the efficacy of a number of medications to treat opioid abuse and dependence, particularly the opioid agonists methadone or buprenorphine. These medications have great relevance for clinical practice.
Cardiac efficiency and Starling's Law of the Heart (2022)

The formulation by Starling of The Law of the Heart states that 'the [mechanical] energy of contraction, however measured, is a function of the length of the muscle fibre'. Starling later also stated that 'the oxygen consumption of the isolated heart … is determined by its diastolic volume, and therefore by the initial length of its muscular fibres'. This phrasing has motivated us to extend Starling's Law of the Heart to include consideration of the efficiency of contraction. In this study, we assessed both mechanical efficiency and crossbridge efficiency by studying the heat output of isolated rat ventricular trabeculae performing force-length work-loops over ranges of preload and afterload. The combination of preload and afterload allowed us, using our modelling frameworks for the end-systolic zone and the heat-force zone, to simulate cases by recreating physiologically feasible loading conditions. We found that across all cases examined, both work output and change of enthalpy increased with initial muscle length; hence it can only be that the former increases more than the latter to yield increased mechanical efficiency. In contrast, crossbridge efficiency increased with initial muscle length in cases where the extent of muscle shortening varied greatly with preload. We conclude that the efficiency of cardiac contraction increases with increasing initial muscle length and preload. An implication of our conclusion is that the length-dependent activation mechanism underlying the cellular basis of Starling's Law of the Heart is an energetically favourable process that increases the efficiency of cardiac contraction. KEY POINTS: Ernest Starling in 1914 formulated the Law of the Heart to describe the mechanical property of cardiac muscle whereby force of contraction increases with muscle length. He subsequently, in 1927, showed that the oxygen consumption of the heart is also a function of the length of the muscle fibre, but left the field unclear as to whether cardiac efficiency follows the same dependence. A century later, the field has gained an improved understanding of the factors, including the distinct effects of preload and afterload, that affect cardiac efficiency. This understanding presents an opportunity for us to investigate the elusive length-dependence of cardiac efficiency. We found that, by simulating physiologically feasible loading conditions using a mechano-energetics framework, cardiac efficiency increased with initial muscle length. A broader physiological importance of our findings is that the underlying cellular basis of Starling's Law of the Heart is an energetically favourable process that yields increased efficiency.
Bevacizumab Efficacy in Metastatic Colorectal Cancer is Dependent on Primary Tumor Resection (2014)

Addition of bevacizumab to chemotherapy is associated with improvement of OS only in patients with primary tumor resection. These data support the rationale to validate prospectively the influence of primary tumor resection on bevacizumab antitumor effect in synchronous mCRC.
Design of a 3-DoF joint system with dynamic servo-adaptation in orthotic applications (2011)

Most exoskeleton designs rely on structures and mechanical joints that do not guarantee the right match between the orthosis and the user. This paper proposes a virtual joint model based on three active degrees of freedom aimed to emulate a human joint. This joint is capable of performing a dynamic servo-adaptation in real-time to avoid misalignments and to provide a flexible adjustment to different users' sizes in order to avoid undesirable interaction forces.
Passive current flow and morphology in the terminal arborizations of the posterior pituitary (1993)

1. Patch-clamp techniques were used to study the morphology and electrotonic properties of the terminal arborizations of the posterior pituitary. 2. Neurobiotin-labeling experiments revealed axons and swellings connected to the structure that was patch clamped. The large swellings were en passant and situated along axons in a topological arrangement identical to that of the small varicosities. Axons had many varicosities and few branches, reflecting a predominant architectural motif of beads on a string rather than berries on a bush. 3. Cable theory was used to analyze passive current transients produced by voltage steps under whole-cell clamp. Most charging transients were not consistent with an equivalent cylinder representation as posited by the Rall model for a motoneuron. A few charging transients were consistent with the Rall model and provided estimates for basic membrane and cable properties. 4. Some of the charging transients that violated predictions of the Rall model were consistent with an alternative model, in which the patch-clamped swelling was assumed to be coupled to another swelling by a segment of axon. This model was called the Dumbbell model, and it, together with the neurobiotin-labeling experiments, indicated that a significant number of large swellings were less than one length constant away from another large swelling. 5. Large swellings can have diameters approximately 30 times larger than the diameters of the connecting axons. These swellings lie along the axon such that action potentials must propagate through them to spread excitation through the entire terminal arborization. These large swellings could be sites where action-potential propagation is more likely to fail. 6. The information presented here about neurohypophysial nerve terminals should be useful in further investigations of how terminal arborization geometry and membrane properties influence neurosecretion and synaptic transmission.