gebhart/patrepeval huggingface dataset:
Orthogonal programming of heterogeneous micro-mechano-environments and geometries in three-dimensional bio-stereolithography (2018)

Engineering heterogeneous micro-mechano-microenvironments of extracellular matrix is of great interest in tissue engineering, but spatial control over mechanical heterogeneity in three dimensions is still challenging given the fact that geometry and stiffness are inherently intertwined in fabrication. Here, we develop a layer-by-layer three-dimensional (3D) printing paradigm which achieves orthogonal control of stiffness and geometry by capitalizing on the conventionally adverse effect of oxygen inhibition on free-radical polymerization. Controlled oxygen permeation and inhibition result in photo-cured hydrogel layers with thicknesses only weakly dependent to the ultraviolet exposure dosage. The dosage is instead leveraged to program the crosslink density and stiffness of the cured structures. The programmable stiffness spans nearly an order of magnitude (E ~ 2-15 kPa) within the physiologically relevant range. We further demonstrate that extracellular matrices with programmed micro-mechano-environments can dictate 3D cellular organization, enabling in vitro tissue reconstruction.
Electron Donors Supporting Growth and Electroactivity of Geobacter sulfurreducens Anode Biofilms (2011)

ABSTRACT Geobacter bacteria efficiently oxidize acetate into electricity in bioelectrochemical systems, yet the range of fermentation products that support the growth of anode biofilms and electricity production has not been thoroughly investigated. Here, we show that Geobacter sulfurreducens oxidized formate and lactate with electrodes and Fe(III) as terminal electron acceptors, though with reduced efficiency compared to acetate. The structure of the formate and lactate biofilms increased in roughness, and the substratum coverage decreased, to alleviate the metabolic constraints derived from the assimilation of carbon from the substrates. Low levels of acetate promoted formate carbon assimilation and biofilm growth and increased the system's performance to levels comparable to those with acetate only. Lactate carbon assimilation also limited biofilm growth and led to the partial oxidization of lactate to acetate. However, lactate was fully oxidized in the presence of fumarate, which redirected carbon fluxes into the tricarboxylic acid (TCA) cycle, and by acetate-grown biofilms. These results expand the known ranges of electron donors for Geobacter -driven fuel cells and identify microbial constraints that can be targeted to develop better-performing strains and increase the performance of bioelectrochemical systems.
Assessment ofE. coli andSalmonella viability and starvation by confocal laser microscopy and flow cytometry using rhodamine 123, DiBAC4(3), propidium iodide, and CTC (1997)

Assessment of cell viability using methods which do not require cell culture is essential in the field of aquatic microbiology, since many bacteria known to be present in aquatic environments cannot be grown in culture. The study of bacterial biofilms, which previously needed an epifluorescent microscope, has recently been enhanced by the use of flow cytometry and confocal scanning laser microscopy (CSLM). A method based on the combination of several membrane potential related dyes, a membrane integrity dye and a redox probe was used to measure cell viability by flow cytometry and confocal laser microscopy. Rhodamine-propidium iodide (PI) double staining was used to discriminate viable from nonviable cells in CSLM observations. Membrane depolarization during E. coli and Salmonella starvation measured by DiBAC4(3) incorporation (flow cytometry and CSLM) was found to be in concordance with respiratory activity as detected by a tetrazolium salt (CTC) reduction.
Neuropathogenesis of Zika Virus in a Highly Susceptible Immunocompetent Mouse Model after Antibody Blockade of Type I Interferon (2017)

Animal models are needed to better understand the pathogenic mechanisms of Zika virus (ZIKV) and to evaluate candidate medical countermeasures. Adult mice infected with ZIKV develop a transient viremia, but do not demonstrate signs of morbidity or mortality. Mice deficient in type I or a combination of type I and type II interferon (IFN) responses are highly susceptible to ZIKV infection; however, the absence of a competent immune system limits their usefulness for studying medical countermeasures. Here we employ a murine model for ZIKV using wild-type C57BL/6 mice treated with an antibody to disrupt type I IFN signaling to study ZIKV pathogenesis. We observed 40% mortality in antibody treated mice exposed to ZIKV subcutaneously whereas mice exposed by intraperitoneal inoculation were highly susceptible incurring 100% mortality. Mice infected by both exposure routes experienced weight loss, high viremia, and severe neuropathologic changes. The most significant histopathological findings occurred in the central nervous system where lesions represent an acute to subacute encephalitis/encephalomyelitis that is characterized by neuronal death, astrogliosis, microgliosis, scattered necrotic cellular debris, and inflammatory cell infiltrates. This model of ZIKV pathogenesis will be valuable for evaluating medical countermeasures and the pathogenic mechanisms of ZIKV because it allows immune responses to be elicited in immunologically competent mice with IFN I blockade only induced at the time of infection.
Cardiac MRI biomarkers for Duchenne muscular dystrophy (2018)

Duchenne muscular dystrophy (DMD) is a fatal inherited genetic disorder that results in progressive muscle weakness and ultimately loss of ambulation, respiratory failure and heart failure. Cardiac MRI (MRI) plays an increasingly important role in the diagnosis and clinical care of boys with DMD and associated cardiomyopathies. Conventional cardiac MRI biomarkers permit measurements of global cardiac function and presence of fibrosis, but changes in these measures are late manifestations. Emerging MRI biomarkers of myocardial function and structure include the estimation of rotational mechanics and regional strain using MRI tagging; T1-mapping; and T2-mapping, a marker of inflammation, edema and fat. These emerging biomarkers provide earlier insights into cardiac involvement in DMD, improving patient care and aiding the evaluation of emerging therapies.
Vaccination of calves with a diaminopimelic acid mutant of Salmonella typhimurium. (1987)

The purpose of this study was to evaluate the safety and efficacy of a diaminopimelic acid mutant of Salmonella typhimurium as a vaccine for calves. Transposon techniques were used to create a stable nonreverting diaminopimelic acid mutant of a virulent S. typhimurium strain. Calves were vaccinated at weekly intervals with the diaminopimelic acid mutant given as an oral dose of 10(10) organisms, followed by two subcutaneous doses of 10(9) organisms. The calves tolerated vaccination well and the vaccine strain was eliminated from the feces within four days. Of five vaccinated calves, three survived challenge with 5 X 10(9) organisms of the parent strain whereas all five unvaccinated calves that were challenged died. The surviving calves eliminated the challenge organism from the feces within three weeks.
Talent Management and Workers’ Commitment (2019)

Purpose: This investigates the relationship between talent management and workers’ commitment to oil and gas firms in Nigeria using a cross-sectional survey. Ten oil and gas servicing firms were surveyed using simple random sampling. Design/Methodology: A population of 125 managers and supervisors were surveyed from ten oil and gas firms in Rivers state while a sample of 95 was ascertained from the population using Krejcie and Morgan sample size determination table. Reliability of the instrument was determined using Cronbach Alpha. Face and content validity was employed. 95 copies of the questionnaire were administered to managers and supervisors but 74 copies were correctly filled and returned. Pearson Product Moment Correlation Coefficient (rs) was used to analyze the hypotheses with the aid of statistical package for social sciences (SPSS 20.0) while respondents’ characteristics were analyzed using frequency distribution. Findings: The study found that talent management has a positive significant relationship with workers commitment. It concluded that talent management measured in terms of talent attraction, talent development and talent retention promotes workers commitment in oil and gas firms in Nigeria. Practical Implications: This study recommends that managers of oil and gas firms should endeavor to employ all compensation plans necessary to retain talents in the industry as this will enhance their commitment towards achieving organizational goals.
HomeProxy (2013)

HomeProxy is a research prototype that uses a physical proxy to support video messaging at home among distributed family members. A physical artifact dedicated to remote family members makes it easier to chat with them over video. HomeProxy combines a form factor designed for the home environment with a "no-touch" user experience and an interface that quickly transitions between recorded and live video communication. We designed and implemented a prototype and our early experiences with it indicate the promise of offering quick video messaging at home and the challenges of a no-touch interface.
MHC-Binding Peptides as Immunotherapeutics for Cancer (2000)

(2000). MHC-Binding Peptides as Immunotherapeutics for Cancer. Immunological Investigations: Vol. 29, No. 2, pp. 105-110.
Analysis of regiospecific distribution of FA of TAG using the lipase‐catalyzed ester‐exchange (2003)

Abstract A very simple and versatile GC method has been developed that can be utilized for quick analysis, in many samples, of the FA compositions at the sn ‐2‐ and sn ‐1,3‐positions of TAG. By using the lipase‐catalyzed, sn ‐1,3‐regioselective esterexchange reaction of TAG with ethyl acetate, followed by direct injection of the crude reaction mixture into the GC apparatus without any pretreatment, the FA located at the sn ‐2‐position could accurately be analyzed as a TAG derivative in which the sn ‐1,3‐positions were substituted by an acetate residue. Furthermore, the FA located at the sn ‐1,3‐positions could simultaneously be analyzed as the corresponding ethyl ester derivatives using this method. The reliability of the analytical method was compared with conventional methods by analyzing the TAG consisting of caprylic acid (C) at the sn ‐2‐position and oleic acid (O) at the sn ‐1,3‐positions, giving comparable analytical results. The present method was applied to the analysis of the structured lipids CCD and CCE, consisting of TAG as a major component in which C and the highly unsaturated FA, DHA (D) or EPA (E), were specifically bound at the sn ‐2‐ and the sn ‐1,3‐positions, respectively.
Identification of glypican-3-derived long peptides activating both CD8<sup>+</sup>and CD4<sup>+</sup>T cells; prolonged overall survival in cancer patients with Th cell response (2015)

In a recent phase I clinical trial, a vaccine consisting of glypican-3 (GPC3)-derived CTL epitopes was found to be safe and induced measurable immune and clinical responses in patients with hepatocellular carcinoma (HCC). The aim of this study was to identify GPC3-derived long peptides (GPC3-LPs) carrying promiscuous HLA class II-restricted T helper (Th) cell epitopes. Using a computer algorithm, we predicted GPC3-LPs that can bind to promiscuous HLA class II molecules. Their antigenicity for induction of specific CD4<sup>+</sup> T cells in healthy donors or patients with HCC, before and after vaccination with GPC3-SPs, was proven by IFNγ enzyme-linked immunospot assays. Natural processing of these epitopes was confirmed by the immune response of helper T cells to dendritic cells (DCs) loaded with GPC3 proteins. Cross-presentation capacity was assessed <i>in vitro</i> using human DCs and LPs encapsulated in liposomes and <i>in vivo</i> in HLA-A2 transgenic mice (Tgm). All five LPs could induce Th1 cells and were presented by several frequently occurring HLA class II molecules <i>in vitro</i>. Four of them were likely to be naturally processed. One of the LPs encapsulated in liposomes was well cross-presented <i>in vitro</i>; it cross-primed CTLs in HLA-A2 Tgm. LP-specific and HLA class II-restricted CD4<sup>+</sup> T-cell responses were observed in 14 of 20 HCC patients vaccinated with GPC3-SPs. Repeated vaccinations enhanced GPC3-LP-specific responses in 8 of 13 patients with HCC. Moreover, the presence of the specific Th cell was correlated with prolonged overall survival (OS). GPC3-LPs can be useful for cancer immunotherapy.
Meta-optics achieves RGB-achromatic focusing for virtual reality (2021)

Virtual and augmented realities are rapidly developing technologies, but their large-scale penetration will require lightweight optical components with small aberrations. We demonstrate millimeter-scale diameter, high-NA, submicron-thin, metasurface-based lenses that achieve diffraction-limited achromatic focusing of the primary colors by exploiting constructive interference of light from multiple zones and dispersion engineering. To illustrate the potential of this approach, we demonstrate a virtual reality system based on a home-built fiber scanning near-eye display.
Non-destructive, non-invasive, in-line real-time phase-based reflectance for quality monitoring of fruit (2020)

Abstract Food quality monitoring in the production process is essential. The control of food quality and freshness is of growing interest for both consumer and food industry. Near infrared (NIR) spectroscopy is popular as it does not need any sample preparation. However, NIR spectroscopy is costly and needs reliable calibration. A non-contact, non-destructive optical process is proposed in this work to monitor the quality of the food. It is shown that the reflected phase information can be used to detect the quality of the fruits. The color and the spectral reflectance change with storage. The changes in the spectral feature due to ripening or decay of apples are used to non-destructively monitor the quality of the fruit. A closed relationship between the reflected phase information and degradation is obtained. The developed model is simple, low cost, and does not need extensive calibration as compared to conventional technologies currently used like NIR besides being robust to skin color or appearances of the fruit. The phase-based reflectance spectroscopy could revolutionize the on/inline quality monitoring of the fruits.
Imaging synthetic aperture radar (2023)

A linear-FM SAR imaging radar method and apparatus to produce a real-time image by first arranging the returned signals into a plurality of subaperture arrays, the columns of each subaperture array having samples of dechirped baseband pulses, and further including a processing of each subaperture array to obtain coarse-resolution in azimuth, then fine-resolution in range, and lastly, to combine the processed subapertures to obtain the final fine-resolution in azimuth. Greater efficiency is achieved because both the transmitted signal and a local oscillator signal mixed with the returned signal can be varied on a pulse-to-pulse basis as a function of radar motion. Moreover, a novel circuit can adjust the sampling location and the A/D sample rate of the combined dechirped baseband signal which greatly reduces processing time and hardware. The processing steps include implementing a window function, stabilizing either a central reference point and/or all other points of a subaperture with respect to doppler frequency and/or range as a function of radar motion, sorting and compressing the signals using a standard fourier transforms. The stabilization of each processing part is accomplished with vector multiplication using waveforms generated as a function of radar motion wherein these waveforms may be synthesized in integrated circuits. Stabilization of range migration as a function of doppler frequency by simple vector multiplication is a particularly useful feature of the invention; as is stabilization of azimuth migration by correcting for spatially varying phase errors prior to the application of an autofocus process.
An entropy conservation law for testing the completeness of covert channel analysis (1994)

Covert channel analysis typically involves study of individual covert channels in isolation, and determining the thoroughness of such case-by-case analysis can be difficult. To help address this problem, this paper formally defines the notion of a “complete” set of covert channels. Informally, a set of covert channels is “complete” when those channels in the set can operate in tandem to produce the maximum possible covert information flow out of a system. More formally, a “complete” set of covert channels is defined as a solution to an equation called the Maximum Information Flow Equation. An alternate way of expressing “completeness” for sets of covert channels is that all “complete” convert channel sets, and only “complete” sets, always satisfy a certain Entropy Conservation Law, which is given in different forms. One form of the Entropy Conservation Law is that any “complete” set of covert channels can be used to represent overall system behavior in what the author calls Covert Channel Normal Form. Although this paper is mainly theoretical in nature, the author also discusses some possible ways of using the theory, along with open issues.
The gem5 Simulator: Version 20.0+ (2020)

The open-source and community-supported gem5 simulator is one of the most popular tools for computer architecture research. This simulation infrastructure allows researchers to model modern computer hardware at the cycle level, and it has enough fidelity to boot unmodified Linux-based operating systems and run full applications for multiple architectures including x86, Arm, and RISC-V. The gem5 simulator has been under active development over the last nine years since the original gem5 release. In this time, there have been over 7500 commits to the codebase from over 250 unique contributors which have improved the simulator by adding new features, fixing bugs, and increasing the code quality. In this paper, we give and overview of gem5's usage and features, describe the current state of the gem5 simulator, and enumerate the major changes since the initial release of gem5. We also discuss how the gem5 simulator has transitioned to a formal governance model to enable continued improvement and community support for the next 20 years of computer architecture research.
DEUS EX MACHINA. SOBRE DESPOLITIZACIÓN Y CLAUSURA DE DILEMAS EN LA ENSEÑANZA DE LA GEOGRAFÍA (2011)

Algunas currículas jurisdiccionales de la Argentina actual se caracterizan por la habilitación de una mirada politizada de los temas de la agenda geográfica. La posibilidad de desplazar el tratamiento de los mismos de la esfera de la moral hacia la de la política abre el espacio para la construcción de problematizaciones alejadas del escándalo o la indignación. Además de desnaturalizar lo social, la mirada politizada reconoce a los problemas como encerrados en una trama conflictiva no agotable en proposiciones binarias excluyentes. En tal sentido, se orienta a definir los contornos del dilema a considerar, más que a resolver los problemas atrapados en el mismo. El objetivo de esta ponencia, por lo tanto, se orienta a exponer el carácter de las preocupaciones y resistencias de algunos profesores de Geografía frente a esta habilitación política. Una de las conclusiones centrales de este trabajo refiere a que, en ocasiones, en forma explícita o no, la apelación a los presupuestos de una Geografía clásica de corte empirista y pre político se torna un deus ex machina omnipresente el cual termina cancelando en el aula, de manera forzada y artificial, la reflexión sobre los problemas construidos o los temas de la agenda geográfica propuestos.
Soft x-ray (97-eV) phase retardation using transmission multilayers (1992)

Phase retardation as a function of incidence angle of 97-eV soft x rays from a laser plasma source on transmission through a free-standing molybdenum/silicon multilayer was measured using a multilayer polarizer and a polarization analyzer. The maximum retardation of 49° between σ and π components is over 2/3 that calculated for an ideal structure. At maximum retardation the transmittance ratio of σ- to π-amplitudes was 0.66 and the intensity transmittance, averaged for both components, was 20%. These multilayer structures will be useful in soft x-ray polarization applications.
The cell biology of the plasminogen system (1995)

The plasminogen system plays a pivotal role in maintaining vascular patency and in cell migration. Binding of plasminogen to surfaces (i.e., fibrin or cells) is of crucial importance in regulating the function of this system. Plasmin(ogen) binds to cells with low affinity and high capacity via its lysine binding sites, which are associated with its kringle domains and recognize carboxy-terminal lysines of cell surface proteins. Upon binding to cellular receptors, plasminogen is more readily activated; bound plasmin has increased enzymatic activity and is protected from inactivation by inhibitors. Plasminogen receptors are modulated by numerous factors, including proteases, steroid hormones, cytokines and the adhesive state of the cells. The apoprotein(a) moiety of lipoprotein(a) is remarkably similar in amino acid sequence to plasminogen. Shared binding sites for lipoprotein(a) and plasmin(ogen) on cell surfaces and in the subendothelial matrix may contribute to the pathogenetic risks associated with elevated levels of lipoprotein(a).
Biodynamic Imaging: Rethinking Cancer Care using Light-Scattering Theranostics (2014)

Personalized cancer care holds significant potential for the selection of more effective cancer treatments with major improvements in the quality of life for cancer patients. For instance, the development of new chemotherapeutics with much wider ranges of anti-cancer action is now providing oncologist with broad choices to tailor therapy to specific patients. However, matching therapy to individual patients has remained an obstacle because of reliance on outdated cell culture techniques [1].
Methodology for finger gesture control of mechatronic systems (2012)

This paper proposes a methodology for the real-time finger gesture following and control of mechatronic systems based on computer vision and machine learning techniques. The goal of this research is to develop a human-machine interface that could be able to control a mechatronic system by performing finger gestures in space or on a surface without the use of any kind of keyboard neither a joystick. The finger gestures will be continuously followed and directly mapped with commands of mechatronic systems such as start moving, stop moving, forward moving, backward moving etc. The proposed methodology relies on the finger gesture data acquisition, hand segmentation, fingertips localization/ identification, high-level feature extraction, early recognition and prediction using machine learning techniques and its integration into a mechatronic system. The LEGO MINDSTORMS NXT robotics platform controlled by matlab software could be used in the proposed methodology.