gebhart/patrepeval huggingface dataset:
Differentiation of fetal liver cells in vitro. (1981)

Fetal mouse liver hepatocytes proliferate on a substrate of irradiated pigskin epidermis scored with scalpel blade slits to permit cell access to the basement membrane. At the time the cells are explanted, fetal genes, such as those responsible for production of alpha-fetoprotein (AFP) and gamma-glutamyltransferase (GGTase), are strongly expressed. The levels of GGTase decrease rapidly and become undetectable within 2 weeks. The levels of AFP decrease more gradually but become undetectable after 3-5 weeks in culture. As the AFP levels decrease, there is a concomitant increase in albumin production. Hydrocortisone prolongs production of AFP (for up to 8 weeks) but not of GGTase, and it decreases albumin production for up to 8 weeks. Once cells lose AFP expression, addition of hydrocortisone does not restart it. Based on these data, fetal mouse liver hepatocytes, cultured on pigskin, seem to be an excellent in vitro model for liver cell maturation.
Novel trihydroxamate‐containing peptides: Design, synthesis, and metal coordination (2006)

Novel trihydroxamate-containing peptides were designed to mimic desferrioxamine (Desferal(R), DFO, a naturally occurring siderophore) but possess distinct conformational restrictions and varied lipophilicity to probe structure vs. metal coordination. The synthesis was performed via fragment condensation of hydroxamate-containing oligopeptides such as Fmoc-Leu- Psi[CON(OBz)]-Phe-Ala-Pro-OH and H-Leu-Psi[CON(OBz)]-Phe-Ala-Pro-OBu(t) (Fmoc: 9-fluor enylmethoxycarbonyl; OBz: benzyl; OBu(t): tert-butyl) either in solution or on a solid support. The metal-binding properties were studied by electrospray ionization-mass spectroscopy (ESI-MS), ultraviolet (UV)-visible spectroscopy, and (1)H nuclear magnetic resonance (NMR). Similar to the dihydroxamate analogs previously explored [Biopolymers (Peptide Science), 2003, Vol. 71, pp. 489-515], the compounds with three hydroxamates arrayed at 10-atom intervals, i.e., H-[Leu-Psi[CON(OH)]-Phe-Ala-Pro](3)-OH (P1), cyclo[Leu-Psi[CON(OH)]-Phe-Ala-Pro](3) (P2), and H-[Leu-Psi(CONOH)-Phe-Ala-Pro](2)-Leu-NHOH (P7), exhibited high affinities for intramolecular coordination with Fe(III) and Ga(III). As expected, both P1 and P2 showed higher relative Fe(III)-binding affinities than the corresponding dihydroxamate-containing peptide analogs (P11 and P12). Even though both P1 and P2 did not compete with DFO in the relative metal-binding affinity in both solution and gas phases, P1, P2, and DFO exhibited similar relative binding selectivities to 11 different metal ions including Fe(III), Fe(II), Al(III), Ga(III), In(III), Zn(II), Cu(II), Co(II), Ni(II), Gd(III), and Mn(II). Compared to the other metal ions, they had higher relative binding affinities with Fe(III), Fe(II), Al(III), Ga(III), and In(III). The decreased metal-binding affinities of P1 and P2 in comparison with DFO suggested the conformational restrictions of their backbones perturb their three hydroxamate groups from optimal hexadentate orientations for metal coordination. As detected by ESI-MS, P2 was distinguished from both P1 and DFO by solvation of its Ga(III) and Fe(III) complexes (such as acetonitrile or water), thereby stabilizing the resulting complexes in the gas phase. Noteworthy, P2 led to 69% death rate in Hela cells at a concentration of 50 microM, exhibiting higher cytotoxicity than DFO in vitro despite its much lower affinity for iron. This enhanced toxicity may simply reflect the increased lipophilicity of the cyclic trihydroxamate (P2) together with the improvements in its cell penetration, and/or subsequent intracellular molecular recognition of both side chains and hydroxamate groups. The cytotoxicity was significantly suppressed by precoordination with Ga(III) or Fe(III), suggesting a mechanism of toxicity via sequestration of essential metal ions as well as the importance of curbing the metal coordination before targeting. The potential of such siderophore-mimicking peptides in oncology needs further exploration.
Fast online pointer analysis (2007)

Pointer analysis benefits many useful clients, such as compiler optimizations and bug finding tools. Unfortunately, common programming language features such as dynamic loading, reflection, and foreign language interfaces, make pointer analysis difficult. This article describes how to deal with these features by performing pointer analysis online during program execution. For example, dynamic loading may load code that is not available for analysis before the program starts. Only an online analysis can analyze such code, and thus support clients that optimize or find bugs in it. This article identifies all problems in performing Andersen's pointer analysis for the full Java language, presents solutions to these problems, and uses a full implementation of the solutions in a Java virtual machine for validation and performance evaluation. Our analysis is fast: On average over our benchmark suite, if the analysis recomputes points-to results upon each program change, most analysis pauses take under 0.1 seconds, and add up to 64.5 seconds.
New and Current Clinical Imaging Techniques to Study Chronic Obstructive Pulmonary Disease (2009)

Chronic obstructive pulmonary disease (COPD) is a heterogeneous disease characterized by both small airway and parenchymal abnormalities. There is increasing evidence to suggest that these two morphologic phenotypes, although related, may have different clinical presentations, prognosis, and therapeutic responses to medications. With the advent of novel imaging modalities, it is now possible to evaluate these two morphologic phenotypes in large clinical studies using noninvasive or minimally invasive methods such as computed tomography (CT), magnetic resonance imaging (MRI), and optical coherence tomography (OCT). In this article, we provide an overview of these imaging modalities in the context of COPD and discuss their strengths as well as their limitations for providing quantitative COPD phenotypes.
Discovering recurring anomalies in text reports regarding complex space systems (2005)

Many existing complex space systems have a significant amount of historical maintenance and problem data bases that are stored in unstructured text forms. The problem that we address in this paper is the discovery of recurring anomalies and relationships between problem reports that may indicate larger systemic problems. We illustrate our techniques on data from discrepancy reports regarding software anomalies in the Space Shuttle. These free text reports are written by a number of different people, thus the emphasis and wording vary considerably. We test four automatic methods of anomaly detection in text that are popular in the current literature on text mining. The first method that we describe is k-means or Gaussian mixture model and its application to the term-document matrix. The second method is the Sammon nonlinear map, which projects high dimensional document vectors into two dimensions for visualization and clustering purposes. The third method is based on an analysis of the results of applying a clustering method, expectation maximization on a mixture of von Mises Fisher distributions that represents each document as a point on a high dimensional sphere. In this space, we perform clustering to obtain sets of similar documents. The results are derived from a new method known as spectral clustering, where vectors from the term-document matrix are embedded in a high dimensional space for clustering. The paper concludes with recommendations regarding the development of an operational text mining system for analysis of problem reports that arise from complex space systems. We also contrast such systems with general purpose text mining systems, illustrating the areas in which this system needs to be specified for the space domain.
Changing Priorities in Vaccinology: Antibiotic Resistance Moving to the Top (2018)

Antimicrobial resistance (AMR) is currently the most alarming issue for human health. AMR already causes 700,000 deaths/year. It is estimated that 10 million deaths due to AMR will occur every year after 2050. This equals the number of people dying of cancer every year in present times. International institutions such as G20, World Bank, World Health Organization (WHO), UN General Assembly, European Union, and the UK and USA governments are calling for new antibiotics. To underline this emergency, a list of antibiotic-resistant "priority pathogens" has been published by WHO. It contains 12 families of bacteria that represent the greatest danger for human health. Resistance to multiple antibiotics is particularly relevant for the Gram-negative bacteria present in the list. The ability of these bacteria to develop mechanisms to resist treatment could be transmitted with genetic material, allowing other bacteria to become drug resistant. Although the search for new antimicrobial drugs remains a top priority, the pipeline for new antibiotics is not promising, and alternative solutions are needed. A possible answer to AMR is vaccination. In fact, while antibiotic resistance emerges rapidly, vaccines can lead to a much longer lasting control of infections. New technologies, such as the high-throughput cloning of human B cells from convalescent or vaccinated people, allow for finding new protective antigens (Ags) that could not be identified with conventional technologies. Antibodies produced by convalescent B cell clones can be screened for their ability to bind, block, and kill bacteria, using novel high-throughput microscopy platforms that rapidly capture digital images, or by conventional technologies such as bactericidal, opsono-phagocytosis and FACS assays. Selected antibodies expressed by recombinant DNA techniques can be used for passive immunization in animal models and tested for protection. Antibodies providing the best protection can be employed to identify new Ags and then used for generating highly specific recombinant Fab fragments. Co-crystallization of Ags bound to Fab fragments will allow us to determine the structure and characteristics of new Ags. This structure-based Ag design will bring to a new generation of vaccines able to target previously elusive infections, thereby offering an effective solution to the problem of AMR.
Neighboring block based disparity vector derivation for 3D-AVC (2013)

3D-AVC, being developed under Joint Collaborative Team on 3D Video Coding (JCT-3V), significantly outperforms the Multiview Video Coding plus Depth (MVC+D) which has no new macroblock level coding tools compared to Multiview video coding extension of H.264/AVC (MVC). However, for multiview compatible configuration, i.e., when texture views are decoded without accessing depth information, the performance of the current 3D-AVC is only marginally better than MVC+D. The problem is caused by the lack of disparity vectors which can be obtained only from the coded depth views in 3D-AVC. In this paper, a disparity vector derivation method is proposed by using the motion information of neighboring blocks and applied along with existing coding tools in 3D-AVC. The proposed method improves 3D-AVC in the multiview compatible mode substantially, resulting in about 20% bitrate reduction for texture coding. When enabling the so-called view synthesis prediction to further refine the disparity vectors, the performance of the proposed method is 31% better than MVC+D and even better than 3D-AVC under the best performing 3D-AVC configuration.
Dynamic Manipulation of Charged Lipids in Model Membrane for Bio-Microarrays (2016)

We describe the dynamic manipulation of the charged lipids in a confined geometry where two dispersive factors arising from the random diffusion-based Brownian motion and the field-induced drift of target lipids compete with each other. It is found that the lateral distribution of the target lipids is well controlled through a combined effect of an external electric field and the geometric restrictions by the confinement. The dynamic manipulation scheme for the charged lipids in two-dimension would be useful for understanding the spatial organization of membrane components in a supported lipid membrane mimicking a real cell membrane and for producing membrane-based microarrays.
MAGE-C2/CT10 Protein Expression Is an Independent Predictor of Recurrence in Prostate Cancer (2011)

The cancer-testis (CT) family of antigens is expressed in a variety of malignant neoplasms. In most cases, no CT antigen is found in normal tissues, except in testis, making them ideal targets for cancer immunotherapy. A comprehensive analysis of CT antigen expression has not yet been reported in prostate cancer. MAGE-C2/CT-10 is a novel CT antigen. The objective of this study was to analyze extent and prognostic significance of MAGE-C2/CT10 protein expression in prostate cancer. 348 prostate carcinomas from consecutive radical prostatectomies, 29 castration-refractory prostate cancer, 46 metastases, and 45 benign hyperplasias were immunohistochemically analyzed for MAGE-C2/CT10 expression using tissue microarrays. Nuclear MAGE-C2/CT10 expression was identified in only 3.3% primary prostate carcinomas. MAGE-C2/CT10 protein expression was significantly more frequent in metastatic (16.3% positivity) and castration-resistant prostate cancer (17% positivity; p<0.001). Nuclear MAGE-C2/CT10 expression was identified as predictor of biochemical recurrence after radical prostatectomy (p = 0.015), which was independent of preoperative PSA, Gleason score, tumor stage, and surgical margin status in multivariate analysis (p<0.05). MAGE-C2/CT10 expression in prostate cancer correlates with the degree of malignancy and indicates a higher risk for biochemical recurrence after radical prostatectomy. Further, the results suggest MAGE-C2/CT10 as a potential target for adjuvant and palliative immunotherapy in patients with prostate cancer.
Speed-based supercapacitor state of charge tracker for light railway vehicles (2011)

The paper suggests a supercapacitor control for light railway vehicles based on the tracking of the actual train speed. Different configurations in terms of storage capacity and braking resistance power are presented and compared. The proposed control algorithm evaluates analytically the supercapacitor reference current on the basis of the actual train kinetic energy, taking properly into account the efficiencies of the different subsystems. Therefore, on the basis of the size selected for the storage device, the control is capable of recovering the electrical energy during the braking of the train for recharging completely the supercapacitor units and dissipating the extra energy on the braking resistor. Realistic railway vehicle operations are presented by means of numerical simulations referring to different configurations of storage device and braking resistors. The results obtained show that the control is very effective in all the cases considered and that the final choice of the storage size is a trade-off between energy saving and equipment cost.
System level performance evaluation of spatial multiplexing with per common basis rate control (2006)

In this paper, we evaluate the system level perfor- mance of a spatial multiplexing with per common basis rate control (PCBRC) in which the active bases are selected at the receiver from the common unitary basis set known at both receiving and transmitting ends, conveyed to the transmitter using limited feedback, and assembled into a precoding matrix at the transmitter. System level capacity evaluation using spatial channel model (SCM) shows that the proposed PCBRC out- performs multi-mode antenna selection and precoder codebook design methods even with the same or lower feedback rate.
Left ventricular morphology influences mortality after the Norwood operation (2009)

These results indicate that LV hypertrophy and decreased RV function adversely effect survival after the Norwood operation. They suggest that LV morphology, especially septal hypertrophy, can influence outcomes in HLHS and should be considered when evaluating treatment options.
Nonlinearity in nanomechanical cantilevers (2013)

Euler-Bernoulli beam theory is widely used to successfully predict the linear dynamics of micro- and nanocantilever beams. However, its capacity to characterize the nonlinear dynamics of these devices has not yet been rigorously assessed, despite its use in nanoelectromechanical systems development. In this article, we report the first highly controlled measurements of the nonlinear response of nanomechanical cantilevers using an ultralinear detection system. This is performed for an extensive range of devices to probe the validity of Euler-Bernoulli theory in the nonlinear regime. We find that its predictions deviate strongly from our measurements for the nonlinearity of the fundamental flexural mode, which show a systematic dependence on aspect ratio (length/width) together with random scatter. This contrasts with the second mode, which is always found to be in good agreement with theory. These findings underscore the delicate balance between inertial and geometric nonlinear effects in the fundamental mode, and strongly motivate further work to develop theories beyond the Euler-Bernoulli approximation.
Laparoscopic Bladder Seromyotomy: Laboratory Experience (1996)

Twelve female microminipigs with normal bladder capacity underwent laparoscopic bladder seromyotomy. Three other female microminipigs were added to the study as controls. Urodynamic studies and cystograms were performed preoperatively and at 2 and 4 months after a laparoscopic bladder seromyotomy. Histologic studies of the treated bladders were performed when the animals were euthanized at 4 months. The operation was completed in all 12 test animals. There was no significant difference in bladder capacity or leak-point pressure between the 12 seromyotomy and the 3 control bladders at any time point. Histologically, over the seromyotomy site, the urothelium remained intact; however, the muscularis was attenuated, and a thin layer of fibrotic tissue replaced the normal serosal covering of the bladder. Laparoscopic bladder seromyotomy can be performed reliably in the porcine animal model. Not surprisingly, no significant changes in bladder capacity or bladder compliance were seen in our study of normal bladders. An animal model of a neuropathic contracted bladder is needed to assess more accurately the physiological impact of laparoscopic seromyotomy.
Multichannel equalization for high track density magnetic recording (2002)

We have studied single and multiple channel equalization techniques for improving detection performance at high track densities. A multichannel matched filter approach is used to bound the performance gain that can be expected from an equalizer specifically designed to reduce intertrack interference. Side reading of the head is simulated at various off-track head positions using the reciprocity integral. Significant performance improvements are predicted for a three element head detecting data on the center track. Up to a 2 dB improvement in SNR is predicted for the three element scheme while the head is on-track, and up to a 5 dB improvement as the head moves off-track.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Optical validation ofin vitroextra-cellular neuronal recordings (2011)

Simultaneous calcium imaging and extra-cellular recordings from cultured cortical rat neurons were performed to directly map the efficacy of extra-cellular recordings with microelectrodes. For the first time, we can associate extra-cellular recordings with neuronal activity of specific neurons in the vicinity of the electrode. We demonstrate that recorded cells can be identified by correlating the electrical signals and the calcium response. Our data demonstrate that in sparse cultures, microelectrodes record exclusively from cells which reside at very close proximity to the recording electrode. Moreover, we show that recording appears to be limited to only a partial subset of the cells residing in this range. We further show that even in cases of strong neuron-electrode coupling, extra-cellular signals recorded from single, well-identified neurons vary in shape over time rendering spike sorting and network activity rate analysis incongruous. As multi-electrode array technology is becoming increasingly widespread, the visualization technique we report here will help users better understand the limits of this versatile and useful method.
Imposing Hard Constraints on Deep Networks: Promises and Limitations (2017)

Imposing constraints on the output of a Deep Neural Net is one way to improve the quality of its predictions while loosening the requirements for labeled training data. Such constraints are usually imposed as soft constraints by adding new terms to the loss function that is minimized during training. An alternative is to impose them as hard constraints, which has a number of theoretical benefits but has not been explored so far due to the perceived intractability of the problem. In this paper, we show that imposing hard constraints can in fact be done in a computationally feasible way and delivers reasonable results. However, the theoretical benefits do not materialize and the resulting technique is no better than existing ones relying on soft constraints. We analyze the reasons for this and hope to spur other researchers into proposing better solutions.
The Duration of Antibiotics Prophylaxis at the Time of Catheter Removal after Radical Prostatectomy: Clinically Integrated, Cluster, Randomized Trial (2021)

A clinically integrated trial using cluster randomization accrued rapidly with no important logistical problems and negligible burden on surgeons. If surgeons choose to prescribe empiric prophylactic antibiotics after catheter removal following RP, then the duration should not exceed 1 day.
Digital correction of geometric and radiometric errors in ERTS data. (1971)

The sensor systems of the ERTS-A satellite are discussed and sources of geometric and radiometric errors in the received images are identified. Digital algorithms are presented for detection of reseau and ground control points, for rapid implementation of geometric corrections, and for radiometric correction of errors caused by shading, image motion, modulation transfer function, and quantum and systematic noise.
National Aeronautics and Space Administration Langley Research Center's Design Criteria for Small Unmanned Aerial Vehicle Development (2007)

National Aeronautics and Space Administration (NASA) Langley Research Center (LaRC) has a long, rich tradition of advanced aeronautics research using subscale aircraft. LaRC has developed detailed procedures and guidelines that set forth criteria for the design, analysis, quality assurance and documentation for wind-tunnel model systems to be tested at the LaRC. The criteria are intended to prevent model systems failure and/or facility damage. However, traditional wind tunnel experimental testing can not meet all of the aeronautics research requirements. To that end, LaRC uses free flying subscale models in large wind tunnels and small Unmanned Aerial Vehicles (UAVs) to extend traditional aeronautics research testing capability. With the absence of standardized and accepted design criteria for free flying subscale testbeds, LaRC has adapted the wind-tunnel model systems criteria to guide the development of theses free-flying vehicles and is in the process of developing unique criteria specifically for these testbeds. This paper will review LaRC's criteria and procedures for design and development of wind tunnel test articles (models). The paper will outline how this set of criteria, along with other limited but established criteria and best practices from the user community, has been applied to the development of small UAVs, giving specific examples of recent or current activities. In addition, shortcomings of the current guidelines will be discussed and recommendations will be presented.