gebhart/patrepeval huggingface dataset:
Expression of human lambda expands the repertoire of OmniChickens (2020)

Most of the approved monoclonal antibodies used in the clinic were initially discovered in mice. However, many targets of therapeutic interest are highly conserved proteins that do not elicit a robust immune response in mice. There is a need for non-mammalian antibody discovery platforms which would allow researchers to access epitopes that are not recognized in mammalian hosts. Recently, we introduced the OmniChicken®, a transgenic animal carrying human VH3-23 and VK3-15 at its immunoglobulin loci. Here, we describe a new version of the OmniChicken which carries VH3-23 and either VL1-44 or VL3-19 at its heavy and light chain loci, respectively. The Vλ-expressing birds showed normal B and T populations in the periphery. A panel of monoclonal antibodies demonstrated comparable epitope coverage of a model antigen compared to both wild-type and Vκ-expressing OmniChickens. Kinetic analysis identified binders in the picomolar range. The Vλ-expressing bird increases the antibody diversity available in the OmniChicken platform, further enabling discovery of therapeutic leads.
Effects of Thiazolidinediones on Growth and Differentiation of Human Aorta and Coronary Myocytes (1997)

Thiazolidinediones, insulin-sensitizing agents that lower insulin and lipid levels in insulin-resistant states, block agonist-induced Ca2+ entry into vascular smooth muscle (VSM) cells in vitro and lower blood pressure in animals and humans in vivo. In this study, we investigated the effects of ciglitazone and troglitazone on cell growth and DNA synthesis (as thymidine incorporation), and differentiation in cultured human aorta (haVSM) and human coronary artery (hcaVSM) VSM cells. Mitotically quiescent haVSM cells were stimulated with serum or platelet-derived growth factor (PDGF). Ciglitazone (40 micromol/L) inhibited haVSM cell proliferation by 84 +/- 16% (mean +/- SEM) (P < .05, n = 3), and serum and PDGF stimulated [3H]-thymidine incorporation by 91 +/- 18% (P < .03, n = 3) and 73 +/- 14% (P < .03, n = 4), respectively. Troglitazone (5 micromol/L) inhibited proliferation of haVSM cells by 78 +/- 14% (P < .05, n = 3) and hcaVSM cells by 91 +/- 18% (P < .05, n = 3). Proliferating VSM cells (synthetic phenotype) expressed small amounts of alpha-actin, whereas nonproliferating VSM cells (contractile phenotype) exhibited abundant alpha-actin. Exposure of proliferating haVSM cells to 40 micromol/L ciglitazone induced a marked increase in alpha-actin staining, consistent with transition to the well differentiated, contractile phenotype. To the extent that thiazolidinediones similarly affect growth factor-induced proliferation and differentiation of arterial myocytes in vivo, these agents may be useful in treating atherosclerosis and in preventing restenosis after angioplasty.
The OMEGA EP High-Energy, Short-Pulse Laser System (2008)

OMEGA EP (Extended Performance) is a petawatt-class addition to the existing 30-kJ, 60-beam OMEGA Laser Facility at the University of Rochester. Activation of the OMEGA EP Laser is complete and results will be described.
Direct evidence for three-dimensional off-axis trapping with single Laguerre-Gaussian beam (2014)

Optical tweezers are often applied to control the dynamics of objects by scanning light. However, there is a limitation that objects fail to track the scan when the drag exceeds the trapping force. In contrast, Laguerre-Gaussian (LG) beams can directly control the torque on objects and provide a typical model for nonequilibrium systems such as Brownian motion under external fields. Although stable "mid-water" trapping is essential for removing extrinsic hydrodynamic effects in such studies, three-dimensional trapping by LG beams has not yet been clearly established. Here we report the three-dimensional off-axis trapping of dielectric spheres using high-quality LG beams generated by a special holographic method. The trapping position was estimated as ~ half the wavelength behind the beam waist. These results establish the scientific groundwork of LG trapping and the technical basis of calibrating optical torque to provide powerful tools for studying energy-conversion mechanisms and the nonequilibrium nature of biological molecules under torque.
Tracing garbage collection on highly parallel platforms (2010)

The pervasiveness of multiprocessor and multicore hardware and the rising level of available parallelism are radically changing the computing landscape. Can software deal with tomorrow's potential higher parallelism? In this paper we study this issue from the garbage collection perspective. In particular, we investigate the scalability of parallel heap tracing, which stands at the core of the garbage collection activity. Heap shapes can be sequential in nature, and prevent the collector from scaling the trace. We start by proposing the idealized trace utilization as a scalability measure for evaluating the scalability of a given heap shape. We then examine standard Java benchmarks and evaluate the existence of non-scalable object-graph shapes in their execution. Next, we propose and implement a prototype of garbage collection techniques that attempt to ameliorate the object-graph shape problem. Finally, we measure and report their efficacy.
Thermodynamic, Environmental and Economic Assessment of Exhaust Gas Recirculation for NOx Reduction in Gas Turbine Based Compressor Station (1999)

A thermodynamic, environmental and economic assessment of an exhaust gas recirculation (EGR) system for NOx reduction has been carried out on an RB211 gas turbine based compressor station. The configured system was evaluated using a commercial process simulation software ASPEN PLUS® for the EGR process, along with a one dimensional model for the prediction of NOx. The assessment was focused on a realistic system of 20% gas recirculation cooled 300 °C with an aerial cooler. Detailed economic analysis based on present value cost per unit mechanical energy (kWh), showed that there is no economic advantage in implementing an EGR system in an existing gas turbine based station. Although the environmental cost was lower with the EGR system, it was offset by the cost of the EGR system itself combined with the additional incremental cost of fuel due to the decrease in the thermal efficiency.
Recent Advances in Incretin-Based Pharmacotherapies for the Treatment of Obesity and Diabetes (2022)

The incretin hormone glucagon-like peptide-1 (GLP-1) has received enormous attention during the past three decades as a therapeutic target for the treatment of obesity and type 2 diabetes. Continuous improvement of the pharmacokinetic profile of GLP-1R agonists, starting from native hormone with a half-life of ~2-3 min to the development of twice daily, daily and even once-weekly drugs highlight the pharmaceutical evolution of GLP-1-based medicines. In contrast to GLP-1, the incretin hormone glucose-dependent insulinotropic polypeptide (GIP) received little attention as a pharmacological target, because of conflicting observations that argue activation or inhibition of the GIP receptor (GIPR) provides beneficial effects on systemic metabolism. Interest in GIPR agonism for the treatment of obesity and diabetes was recently propelled by the clinical success of unimolecular dual-agonists targeting the receptors for GIP and GLP-1, with reported significantly improved body weight and glucose control in patients with obesity and type II diabetes. Here we review the biology and pharmacology of GLP-1 and GIP and discuss recent advances in incretin-based pharmacotherapies.
Comparison of monoclonal antibody (P504S) and polyclonal antibody to alpha methylacyl‐CoA racemase (AMACR) in the work‐up of prostate cancer (2005)

Differences between P504S and p-AMACR appear marginal and clinically insignificant. AMACR is negative in a subset of unequivocal minute PCa with both antibodies. However, when utilized in proper context, AMACR may offer significant advantage in converting an 'atypical' diagnosis to PCa where morphology and basal markers are less than optimal in resolving the diagnosis.
How Communicating Polygenic and Clinical Risk for Atherosclerotic Cardiovascular Disease Impacts Health Behavior: an Observational Follow-up Study (2022)

Web-based communication of personal atherosclerotic cardiovascular disease risk-data including polygenic risk to middle-aged persons motivates positive changes in health behavior and the propensity to seek care. It supports integration of genomic information into clinical risk calculators as a feasible approach to enhance disease prevention.
Crystalline Oxide Semiconductor FET/Si-FET Hybrid Structure-based In-Memory Computing Circuit for Artificial Neural Network Applications (2019)

2019 International Conference on Solid State Devices and Materials ,Crystalline Oxide Semiconductor FET/Si-FET Hybrid Structure-based In-Memory Computing Circuit for Artificial Neural Network Applications
Acute-phase administration of ivabradine supported by intra-aortic balloon pump induces myocardial recovery without significant haemodynamic worsening in a patient with acute fulminant myocarditis: a case report (2022)

Ivabradine has the potential to induce rapid cardiac recovery and haemodynamic improvement in the acute phase of heart failure if supported by intra-aortic balloon pump.
Influence of MT effects on T2 quantification with 3D balanced steady‐state free precession imaging (2010)

Signal from balanced steady-state free precession is affected by magnetization transfer. To investigate the possible effects on derived T(2) values using variable nutation steady-state free precession, magnetization transfer-effects were modulated by varying the radiofrequency pulse duration only or in combination with variable pulse repetition time. Simulations reveal a clear magnetization transfer dependency of T(2) when decreasing radiofrequency pulse duration, reaching maximal deviation of 34.6% underestimation with rectangular pulses of 300 μs duration. The observed T(2) deviation evaluated in the frontal white matter and caudate nucleus shows a larger underestimation than expected by numerical simulations. However, this observed difference between simulation and measurement is also observed in an aqueous probe and can therefore not be attributed to magnetization transfer: it is an unexpected sensitivity of derived T(2) to radiofrequency pulse modulation. As expected, the limit of sufficiently long radiofrequency pulse duration to suppress magnetization transfer-related signal modulations allows for proper T(2) estimation with variable nutation steady-state free precession.
Countries, Rooms, and Plants, but Not Mammalian Cells (2005)

In Response: We thank the author for identifying this common error. It is good to know that the rest was perfect! T. J. Gan, MD Department of Anesthesiology Duke University Medical Center Durham, NC [email protected] Michael P. W. Grocott, BSc, MRCP, FRCA Michael G. Mythen, MD, FRCA Centre for Anaesthesia University College London London, UK
Toward the Standardization of Grant-Free Operation and the Associated NOMA Strategies in 3GPP (2019)

The dramatic increase in Internet traffic to and from wireless devices poses significant challenges for network operators. While the current growth of traffic is mostly due to consumers communicating more frequently and larger amounts of data over the wireless infrastructure, much of the future growth is predicted to originate from non-human-operated devices or so-called IoT communication. The 3GPP standardization activities toward 5G cellular systems envisages two IoT-centric scenarios: mMTC and URLLC. In this article, we quantify the advantages of grant-free operation for 5G mMTC using latency, signaling overhead, and power consumption aspects. We propose the high-level design of a new grant-free state of operation and explain its interaction with the legacy LTE operating states. We also describe promising grantfree NOMA solutions with respect to synchronization and HARQ, and resource collision handling procedures. Our discussion and proposal relate closely to the current 5G standardization activities in 3GPP and highlight solutions that can easily be integrated into the current LTE framework.
Supplementary material and Supplementary table 1 from A Novel Epigenetic Signature for Early Diagnosis in Lung Cancer (2023)

&lt;p&gt;Study design participants, supplementary figure legends and List of cancer-related differentially methylated CpGs&lt;/p&gt;
Malaria incidence and prevalence during the first year of life in Nanoro, Burkina Faso: a birth-cohort study (2018)

These findings indicate high and marked age and seasonal-dependency of malaria infections and disease during the first year of life in Nanoro, calling for intensified efforts to control malaria in rural Burkina Faso.
THE OCCURRENCE OF A NOTCH IN REVERSE SHOULDER ARTHROPLASTY: A PROSPECTIVE STUDY ABOUT THE ROLE OF THE RELATIONSHIP BETWEEN GLENOID AND HUMERUS (2011)

Background: The orientation and the position of glenoid are two factors which have been pointed out as a cause of notch in case of reverse shoulder arthroplasty (RSA). Our hypothesis is that the notch is mostly depending on the relationship between the humerus and the glenoid. Material and method: The inclusion criteria of this prospective study were: RSA with a 2 years minimum follow up, pre and post op x-rays of good quality to allow accurate measurements, a minimum of 3 x-rays regularly separated in the first 2 years. On these x-rays, done at rest, we have analyzed: the vertical orientation of the glenoid, the degree of abduction of the humerus, the gleno-metaphyseal angle (GMA) which represents the relationship between glenoid and humerus. Sixty one shoulders in 60 patients (57 females, 7 males) have been included. The mean age was 74,6 y.o (56–82) and the mean body mass index (BMI) was 25,4 (16–36). Results: The patients with a notch had a significant correlation with a lower BMI (p Discussion: The occurrence of a notch is strongly increased in patients with a lower BMI because of a less degree of abduction of the humerus, mostly if the glenoid is orientated upward. So the relationship between humerus and glenoid is more important to analyse than position of glenoid alone. The BMI is another important factor to take into account in case of indication of RSA because the risk of occurrence of a notch is quite higher.
Manufacturing of lab-on-a-chip devices : characterizing seals for on-board reagent delivery (2013)

Thesis (M. Eng. in Manufacturing)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, 2013.
Minimizing the Age of Incorrect Information for Real-time Tracking of Markov Remote Sources (2021)

The age of Incorrect Information (AoII) has been introduced to address the shortcomings of the standard Age of information metric (AoI) in real-time monitoring applications. In this paper, we consider the problem of monitoring the states of remote sources that evolve according to a Markovian Process. A central scheduler selects at each time slot which sources should send their updates in such a way to minimize the Mean Age of Incorrect Information (MAoII). The difficulty of the problem lies in the fact that the scheduler cannot know if the information at side of the monitor is correct or not before receiving the updates and it has then to estimate it. We show that the problem can be modeled as a partially Observable Markov Decision Process Problem framework. We develop a new scheduling scheme based on Whittles index policy. The scheduling decision is made by updating a belief value of the states of the sources, which is to the best of our knowledge has not been considered before in the Age of Information area. To that extent, we proceed by using the Lagrangian Relaxation Approach, and prove that the dual problem has an optimal threshold policy. Building on that, we show that the problem is indexable and compute the expressions of the Whittles indices. Finally, we provide some numerical results to highlight the performance of our derived policy compared to the classical AoI metric.
Rethinking Data-driven Networking with Foundation Models: Challenges and Opportunities (2022)

Foundational models have caused a paradigm shift in the way artificial intelligence (AI) systems are built. They have had a major impact in natural language processing (NLP), and several other domains, not only reducing the amount of required labeled data or even eliminating the need for it, but also significantly improving performance on a wide range of tasks. We argue foundation models can have a similar profound impact on network traffic analysis, and management. More specifically, we show that network data shares several of the properties that are behind the success of foundational models in linguistics. For example, network data contains rich semantic content, and several of the networking tasks (e.g., traffic classification, generation of protocol implementations from specification text, anomaly detection) can find similar counterparts in NLP (e.g., sentiment analysis, translation from natural language to code, out-of-distribution). However, network settings also present unique characteristics and challenges that must be overcome. Our contribution is in highlighting the opportunities and challenges at the intersection of foundation models and networking.
Disulfiram produces potent anxiolytic-like and antinociceptive effects in rodents (2022)

Disulfiram (DSF) is an FDA approved drug for the treatment of alcoholism. The drug acts by inhibiting aldehyde dehydrogenase, an enzyme essential to alcohol metabolism. However, a recent study has demonstrated that DSF also potently inhibits the cytoplasmic protein FROUNT, a common regulator of chemokine receptor CCR2 and CCR5 signaling. Several studies have reported that chemokine receptors are associated with the regulation of emotional and pain behaviors in rodents. Therefore, this study was performed to clarify these effects of DSF in rodents. The anxiolytic-like and antinociceptive effects of DSF were investigated using an elevated plus-maze (EPM) test and a formalin test, respectively. DSF significantly increased the amount of time spent in the open arms of the maze without affecting the total open arms entries in the EPM test. Moreover, DSF decreased the duration of pain-related behaviors in the formalin test. However, no effect in both EPM and formalin tests was seen following administration of the selective aldehyde dehydrogenase inhibitor cyanamide. These results suggested that DSF produces anxiolytic-like and antinociceptive effects in rodents. We propose that the inhibitory activity of DSF against FROUNT function provides an effective therapeutic option in anxiety accompanied with pain.
Concentration dependent effects of hydrogen peroxide on lens epithelial cells (1999)

Hydrogen peroxide in cooperation with some growth factors plays an important role in the proliferation of lens epithelial cell.
CCD-Chip (2011)

Der CCD-Chip ist ein Lichtdetektor, der in fast allen Bereichen den konventionellen Film und das Magnetband verdrängt hat. Mit dem CCD-Chip begann der Siegeszug der Digitalfotografie und der digitalen Videokameras. CCD ist eine Abkürzung und steht für Charge Coupled Device, das bedeutet „ladungsgekoppeltes Gerät“. Das sagt scheinbar noch nicht viel, aber im Prinzip doch schon eine Menge. Das wird bei den physikalischen Grundlagen gleich im Anschluss näher geklärt. Dann folgt ein Unterkapitel mit Problemen von CCD-Chips und deren Lösungsmöglichkeiten. Den Abschluss bildet schließlich ein Überblick über verschiedene Anwendungsmöglichkeiten von CCD-Chips.
Melting Point Depression of the Surface Layer in n-Alkane Emulsions and Its Implications for Fat Destabilization in Ice Cream (2005)

Evidence of phase changes occurring at the surface of droplets but not in the bulk is presented for n-alkane emulsions. It is postulated that these phase changes are the result of the formation of a monolayer thick solid solution of the oil phase and surfactant. The role of surfactant is shown to extend to controlling the rate of collision between crystallized and uncrystallized droplets and a secondary nucleation mechanism due to droplet collision. Ultrasound velocity methods for the study of emulsion crystallization are shown capable of giving quantitative data regarding nucleation kinetics such as Gibbs free energy, concentration of catalytic impurities, size of catalytic impurities, and nucleation rates. We show that destabilization of a stabilizing protein film at the surface of a droplet can occur through crystallization of an oil droplet and does not require competitive absorption processes at the droplet surface involving small molecule surfactants. This destabilization process may be an important factor in the “aging” of ice cream emulsions.
Anti-fusion targeted nanomicellar theranostics: Novel antiviral strategies for respiratory syncytial virus infection-induced lung diseases (2021)

The respiratory syncytial virus (RSV), is an important pathogen that infects an estimated 64 million people and causes ~200,000 deaths globally every year. Despite progress in the biology of RSV, there is no effective treatment or vaccine against RSV infection. Currently, only high-risk infants receive antibody-based prophylaxis, which is expensive and moderately effective in reducing hospitalization. Therefore, a broadly applicable, effective and inexpensive approach to prevent or treat RSV-bronchiolitis or pneumonia remains an urgent unmet need. We have been investigating nanomedical approaches against RSV infection and have reported on a variety of different strategies including genome vaccine, and siRNA based nanoparticles. More recently, we have developed a novel prophylaxis and/or therapy against RSV infection was inspired by the following discoveries: (1) A platform of phospholipid micellar nanoparticles (PMN) was developed, which when given intranasally delivers payload predominantly to the lung, (2) A decoy short heptad repeat (HR)2 peptide was identified, which effectively inhibits the RSV-cell fusion. iii) Human mesenchymal cells were found to be highly susceptible to RSV. The latter aided in establishing a novel 3D scaffold for anti-RSV drug screens, which consisted of creating a completely naked mouse lung scaffold (nMLS) by completely decellularizing and recellularizing the nMLS with desired human cells such as including hMSCs and epithelial cells and then infecting the cells in scaffold with RSV with or without drugs. (4) A robust immunocompromised mouse model was created by combining cyclophosphamide treatment with infection by a highly mucogenic strain, RSV-L19F. These developments have led to the hypothesis that a RSV-targeted PMN (RTPMN), combining HR2D anti-fusion peptide and plasmid encoded siRNAs against RSV-NS1 can provide a safe, effective and inexpensive anti-RSV prophylaxis and/or therapy. The completion of preclinical formulation of antiRSV PMN-based prophylactics and therapeutics is expected to pave the way to IND-driven studies and clinical trials.