gebhart/patrepeval huggingface dataset:
Design and Synthesis of 3‐Carbamoylbenzoic Acid Derivatives as Inhibitors of Human Apurinic/Apyrimidinic Endonuclease 1 (APE1) (2012)

Apurinic/apyrimidinic (AP) endonuclease 1 (APE1) is a multifaceted protein with an essential role in the base excision repair (BER) pathway. Its implication in tumor development, progression, and resistance has been confirmed in multiple cancers, making it a viable target for intensive investigation. In this work, we designed and synthesized different classes of small-molecule inhibitors of the catalytic endonuclease function of APE1 that contain a 3-carbamoylbenzoic acid scaffold. Further structural modifications were made with the aim of increasing the activity and cytotoxicity of these inhibitors. Several of our compounds were shown to inhibit the catalytic endonuclease function of APE1 with potencies in the low-micromolar range in vitro, and therefore represent novel classes of APE1 inhibitors worthy of further development.
Limitations on threshold adjustment by backgating in fully depleted silicon-on-insulator metal-oxide-semiconductor field effect transistors (1998)

Fully depleted silicon-on-insulator metal-oxide-semiconductor field effect transistors with junction-isolated back gate electrodes formed by implanting boron through the silicon film and buried oxide into lightly doped n-type separation by implantation of oxygen substrates have been studied experimentally and through numerical device simulation. The useful range of threshold adjustment by back gate biasing is shown to be approximately ±300 mV for typical structures, irrespective of silicon film or buried oxide thickness, and is limited primarily by accumulation or inversion of the back surface of the silicon film for extreme values of back gate bias.
Chloride Diffusion Models for Type V and Silica Fume Cement Concretes (2020)

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Iron‐Catalyzed Intramolecular Arene C(sp<sup>2</sup>)−H Amidations under Mechanochemical Conditions (2022)

In a ball mill, FeBr<sub>3</sub> -catalyzed intramolecular amidations lead to 3,4-dihydro-2(1H)-quinolinones in good to almost quantitative yields. The reactions do not require a solvent and are easy to perform. No additional ligand is needed for the iron catalyst. Both 4-substituted aryl and β-substituted dioxazolones provide products with high selectivity. Mechanistically, an electrophilic spirocyclization followed by C-C migration explains the formation of rearranged products.
Personal imaging (1997)

In this thesis, I propose a new synergy between humans and computers, called “Humanistic Intelligence” (HI), and provide a precise definition of this new form of human-computer interaction. 
I then present a means and apparatus for reducing this principle to practice. The bulk of this thesis concentrates on a specific embodiment of this invention, called Personal Imaging, most notably, a system which I show attains new levels of creativity in photography, defines a new genre of documentary video, and goes beyond digital photography/video to define a new renaissance in imaging, based on simple principles of projective geometry combined with linearity and superposition properties of light. 
I first present a mathematical theory of imaging which allows the apparatus to measure, to within a single unknown constant, the quantity of light arriving from each direction, to a fixed point in space, using a collection of images taken from a sensor array having a possibly unknown nonlinearity. Within the context of personal imaging, this theory is a contribution in and of itself (in the sense that it was an unsolved problem previously), but when also combined with the proposed apparatus, it allows one to construct environment maps by simply looking around. 
I then present a new form of connected humanistic intelligence in which individuals can communicate, across boundaries of time and space, using shared environment maps, and the resulting computer-mediated reality that arises out of long-term adaptation in a personal imaging environment. 
Finally, I present a new philosophical framework for cultural criticism which arises out of a new concept called ‘humanistic property’. This new philosophical framework has two axes, a ‘reflectionist’ axis and a ‘diffusionist’ axis. In particular, I apply the new framework to personal imaging, thus completing a body of work that lies at the intersection of art, science, and technology. (Copies available exclusively from MIT Libraries, Rm. 14-0551, Cambridge, MA 02139-4307. Ph. 617-253-5668; Fax 617-253-1690.)
Optically Transparent Recombinant Silk-Elastinlike Protein Polymer Films (2011)

Recombinant protein polymers, evaluated extensively as biomaterials for applications in drug delivery and tissue engineering, are rarely reported as being optically transparent. Here we report the notable optical transparency of films composed of a genetically engineered silk-elastinlike protein polymer SELP-47K. SELP-47K films of 100 μm in thickness display a transmittance of 93% in the wavelength range of 350-800 nm. While covalent cross-linking of SELP-47K via glutaraldehyde decreases its transmittance to 77% at the wavelength of 800 nm, noncovalent cross-linking using methanol slightly increases it to 95%. Non- and covalent cross-linking of SELP-47K films also influences their secondary structures and water contents. Cell viability and proliferation analyses further reveal the excellent cytocompatibility of both non- and covalently cross-linked SELP-47K films. The combination of high optical transparency and cytocompatibility of SELP-47K films, together with their previously reported outstanding mechanical properties, suggests that this protein polymer may be useful in unique, new biomedical applications.
Non-Linear Ordered Precoding with Limited Feedback for Multiuser MIMO Systems (2019)

Using of quantized channel state information on transmitter (CSIT) side for adaptive signal processing on base station (BS) side also called as precoding provides to reduce feedback channel bandwidth in comparison with full CSIT. There are many solutions for feedback channel quantization but the aim of this paper is to note the performance of grassmannian manifold for codebook design.
Noninvasive Prenatal Test for β-Thalassemia and Sickle Cell Disease Using Probe Capture Enrichment and Next-Generation Sequencing of DNA in Maternal Plasma (2021)

This probe capture NGS assay demonstrates the potential of NIPT for β-hemoglobinopathies.
Comparison of Experiments and Simulation of Joule Heating in ac Electrokinetic Chips (2010)

ac electrokinetic manipulations of particles and fluids are important techniques in the development of lab-on-a-chip technologies. Most of these systems involve planar micro-electrode geometries, generating high strength electric fields. When these fields are applied to a dielectric medium, Joule heating occurs. Understanding electrothermal heating and monitoring the temperature in these environments are critical for temperature-sensitive investigations including biological applications. Additionally, significant changes in fluid temperature when subjected to an electric field will induce electrohydrodynamic flows, potentially disrupting the intended microfluidic profile. This work investigates heat generated from the interaction of ac electric fields and water at various electrical conductivities (from 0.92 mS/m to 390 mS/m). The electrode geometry is an indium tin oxide (ITO) electrode strip 20 μm wide and a grounded, planar ITO substrate separated by a 50 μm spacer with microfluidic features. Laser-induced fluorescence is used to measure the experimental changes in temperature. A normalization procedure that requires a single temperature-sensitive dye, Rhodamine B (RhB), is used to reduce uncertainty. The experimental electrothermal results are compared with theory and computer simulations.
Integrated tracking with vision and sound (2002)

The research summarised here is working towards automatic control systems for cameras, in support of remote meetings. Progress is reported on several fronts: use of active contours to track heads, stereo sound analysis applying particle filtering to handle both visual and aural clutter, and the use of exemplars for stabilisation of inter-frame matching.
Pd-Catalyzed Selective Synthesis of Cyclic Sulfonamides and Sulfinamides Using K<sub>2</sub>S<sub>2</sub>O<sub>5</sub> as a Sulfur Dioxide Surrogate (2017)

A variety of cyclic sulfonamides and sulfinamides could be selectively synthesized under Pd catalysis using haloarenes bearing amino groups and a sulfur dioxide (SO<sub>2</sub>) surrogate. The amount of base was key in determining the selectivity. Mechanistic studies revealed that sulfinamides were initially formed via an unprecedented formal insertion of sulfur monoxide and were oxidized to sulfonamides in the presence of an iodide ion and DMSO.
Submucosal Endoscopic Myotomies for Esophageal Lengthening: A Novel Minimally Invasive Technique with Feasibility Study (2012)

BSELM is feasible and allows significant esophageal lengthening. Unlike surgical myotomies, BSELM enables selective division of circular fibers to potentially preserve perfusion near the anastomosis and prevent long-term dilatation. Studies are ongoing to characterize the ideal pattern of selective endoscopic myotomy and long-term effects.
C-MCMA: a new multiple access protocol for centralized wireless local networks (2002)

The development of wireless local area networks depends, to a large extent, on the availability of flexible and efficient multiple access techniques that cope with the constraints imposed by the wireless propagation environment. In this paper we consider centralized network topologies, with a base station exchanging data packets with a set of portable terminals. We propose a new multiple access protocol whereby the portable terminals compete for the uplink access to the channel with minipackets in response to controlling commands, issued by the base station. Accordingly, the protocol is called centralized minipacket competition multiple access (C-MCMA). In order to judge on the efficiency of C-MCMA its performance is compared with that of the busy channel multiple access protocol with collision detection (BCMA/CD), taking into account receiver capture effects and downlink traffic. It is concluded that for a wide range of values for the parameters of the models considered C-MCMA outperforms BCMA/CD.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Monoliths for fast bioseparation and bioconversion and their applications in biotechnology (2004)

Monoliths have consolidated their position in bioseparation. More than 200 different applications have been reported in the past two decades and their advantages compared to conventional chromatography demonstrated. These include the high mass transfer efficiency due to the convective flow enabled by the macroporous character of the matrix. Recently plasmid DNA and viruses were separated with high efficiency and cryogels and monolithic superporous agarose were developed for capture of proteins from crude homogenates and separation of microorganisms or lymphocytes. Currently four companies manufacture monoliths mainly for analytical applications although monoliths with a volume of 0.8 liter are commercially available and 8 L are available as prototypes. A book entitled "Monolithic materials: preparation, properties and applications" was published in 2003 and became standard reference of the status of this area. This review focuses on the progress in monoliths that goes beyond the scope of this reference book. Less progress has been made in the field of bioconversions in spite of the fact that monolithic supports exhibit better performance than beads in enzymatic processing of macromolecules. It appears that the scientific community has not yet realized that supports for these applications are readily available. In addition, monoliths will further substantially advance bioseparations of both small and large molecules in the future.
Polyarylenealkenylenes and polyheteroarylenealkenylenes, 15. Syntheses and electrical conductivities of alkoxylated poly(2,5‐thiophenediylvinylene‐1,4‐phenylenevinylene)s (1983)

Abstract Poly(2,5‐thiophenediylvinylene‐1,4‐phenylenevinylene)s with one or two alkoxy groups as side chains of variable lenghts (8a, b and 9a – c) were prepared by Wittig‐reaction of 2,5‐thiophenedicarbaldehyde with the corresponding “bis(Wittig‐salt)s”. To establish the structure of the polymers, model compounds 10 and 11 were synthesized. Charge‐transfer (donor‐acceptor) complexes were prepared by iodine doping of the polyvinylenes 8 and 9 . The room temperature conductivity, σ 298K , of the original polymers was found to be increased by several orders of magnitude upon doping. It was not possible to remove all the iodine from the charge‐transfer complexes in vacuum.
An evaluation of open set recognition for FLIR images (2015)

Typical supervised classification algorithms label inputs according to what was learned in a training phase. Thus, test inputs that were not seen in training are always given incorrect labels. Open set recognition algorithms address this issue by accounting for inputs that are not present in training and providing the classifier with an option to &#114;eject" unknown samples. A number of such techniques have been developed in the literature, many of which are based on support vector machines (SVMs). One approach, the 1-vs-set machine, constructs a &#115;lab" in feature space using the SVM hyperplane. Inputs falling on one side of the slab or within the slab belong to a training class, while inputs falling on the far side of the slab are rejected. We note that rejection of unknown inputs can be achieved by thresholding class posterior probabilities. Another recently developed approach, the Probabilistic Open Set SVM (POS-SVM), empirically determines good probability thresholds. We apply the 1-vs-set machine, POS-SVM, and closed set SVMs to FLIR images taken from the Comanche SIG dataset. Vehicles in the dataset are divided into three general classes: wheeled, armored personnel carrier (APC), and tank. For each class, a coarse pose estimate (front, rear, left, right) is taken. In a closed set sense, we analyze these algorithms for prediction of vehicle class and pose. To test open set performance, one or more vehicle classes are held out from training. By considering closed and open set performance separately, we may closely analyze both inter-class discrimination and threshold effectiveness.
Buprenorphine Analogs to Treat Relapse (2020)

Substance use disorders (SUDs) – the overuse and dependence on at least one substance – have a lifetime prevalence of ~10% in the U.S. While buprenorphine (BUP) treatment reduces relapse rates, it is only marginally effective, as 70% of SUD patients relapse within a year. Due to BUP’s marginal effectiveness and abuse potential, there is a need to improve SUD therapies that prevent relapse to multiple drugs of abuse after exposure to stress, drug‐associated context and drug priming. Here we evaluate BUP and two analogs for their ability to inhibit cocaine‐ and stress‐induced relapse using a conditioned place preference (CPP) paradigm. Pharmacologically, BUP is a potent (sub nM) partial agonist at the m‐opioid receptor (MOR) with potent antagonist activity at the k‐(KOR), and d‐opioid receptors (DOR). In vitro BUP can act as a weak (mM) partial agonist at the nociceptin/OrphaninFQ (NOP) receptor with uncertain in vivo consequences. We measured in vitro potency and efficacy using [ 35 S]GTPgS functional assays in CHO cells separately expressing DOR, KOR, MOR or NOP. Since NOP receptor agonists reduce relapse in animal models, we compared BU10119 with NOP agonist activity (EC 50 = 120 nM ± 20; E MAX = 44% ± 5%) or BU12004 with NOP antagonist activity (K B = 190 nM ±30) to BUP (EC 50 = 1300 nM ± 320; E MAX = 39% ± 7%). Furthermore, BU12004 and BU10119 were MOR antagonists (K B = 0.42 nM ± 0.08 and K B = 1.1 nM ± 0.2, respectively) with less abuse liability than the MOR partial agonist BUP (EC 50 = 0.79 nM ± 0.31; E MAX = 34% ± 6%). BUP, BU10119, and BU12004 were all potent antagonists at DOR and KOR. BU10119 (1.0 mg/kg) attenuated cocaine‐primed reinstatement in CPP, but 10 mg/kg BU12004 did not. BUP trended toward reduced drug‐primed reinstatement. The in vivo rank order of BU10119 &gt;BUP &gt;BU12004 matches the rank order for NOP agonism in vitro. Additionally, 1.0 mg/kg of either BU10119 or BU12004 blocked swim stress‐primed reinstatement, ostensibly due to their KOR antagonist activity. Taken together, BU10119 provides a promising lead to treat SUDs with better effectiveness and reduced abuse potential compared to BUP. Support or Funding Information Supported by NIDA R01 DA07315 and 035316.
End-to-side portocaval shunting for a small-for-size graft in living donor liver transplantation (2004)

In the development of adult-to-adult living donor liver transplantation (LDLT), the small-for-size graft has been associated with poor clinical outcome. Persistent portal hypertension or portal venous overperfusion are considered to be causative factors, and partial diversion of portal flow to systemic circulation may be effective for avoiding injuries that occur in the small-for-size (SFS) graft. Recently, we constructed an end-to-side portocaval shunting using 1 of the portal branches and anastomosed the other branch with the portal vein of the graft in 2 cases of LDLT recipients transplanted with a SFS graft. With the suppression of portal hypertension, as well as sufficient portal flow to the graft, the recipients recovered successfully with favorable graft function. This new and simple technique may be able to be used as a feasible and effective method to attenuate the SFS syndrome. (Liver Transpl 2004;10:807-810.)
Value of serology in predicting Pseudomonas aeruginosa infection in young children with cystic fibrosis (2010)

<h3>Background</h3> Early detection of <i>Pseudomonas aeruginosa</i> is essential for successful eradication. The accuracy of serum antibodies against specific and multiple <i>P aeruginosa</i> antigens at predicting lower airway infection in young children with cystic fibrosis (CF) was investigated. <h3>Methods</h3> A commercial <i>P aeruginosa</i> multiple antigen (MAg) ELISA and an in-house exotoxin A (ExoA) ELISA were compared in two populations: a discovery population of 76 children (0.1–7.1 years) undergoing annual bronchoalveolar lavage (BAL)-based microbiological surveillance and a test population of 55 children (0.1–5.6 years) participating in the Australasian CF Bronchoalveolar Lavage Trial. <h3>Results</h3> In the discovery population, <i>P aeruginosa</i> was cultured from BAL fluid (≥10<sup>5</sup> colony-forming units (cfu)/ml) in 15/76 (19.7%) children (median age 1.88 years). Positive MAg and ExoA serological results were found in 38 (50.0%) and 30 (39.5%) children, respectively. Positive (PPV) and negative (NPV) predictive values for serology at diagnosing <i>P aeruginosa</i> infection (≥10<sup>5</sup> cfu/ml) were 0.14 and 0.99 respectively (MAg assay) and 0.11 and 0.98 (ExoA assay). In the test population, <i>P aeruginosa</i> was cultured from BAL fluid (≥10<sup>5</sup> cfu/ml) in 16/55 (29.1%) children (median age 1.86 years) and from oropharyngeal swabs in 32/36 (88.9%). Positive MAg and ExoA serology was detected in 19 (34.5%) and 33 (60.0%) children, respectively. The PPV and NPV of serology were 0.26 and 0.94 respectively (MAg assay) and 0.19 and 0.98 (ExoA assay) and were marginally higher for oropharyngeal cultures. <h3>Conclusions</h3> Measuring serum antibody responses against <i>P aeruginosa</i> is of limited value for detecting early <i>P aeruginosa</i> infection in young children with CF.
183 Explaining Research to Children and Adolescents (2023)

OBJECTIVES/GOALS: By establishing a youth-centric web-app as a central hub of information and inspiration in an attempt to engage a young demographic, this project aims to increase community awareness and reduce misconceptions surrounding clinical trials, in hopes of fairly representing marginalized communities among future clinical trial participants. METHODS/STUDY POPULATION: We designed a children’s web-app to host a collection of child-friendly educational materials (such as picture books, games, and age-appropriate articles about advances in clinical research) explaining clinical research and its process. An emphasis was put on ensuring the web-app and its contents were understandable and appealing to children. The effectiveness of this tool will be tested through a focus group study. Children ages 7-10 will be given a preliminary survey measuring their knowledge and opinions about clinical research, and then given time to explore the web-app. Afterwards, they will be given a secondary survey to gauge their acquired knowledge from the website and asked about their opinion on the design and usability of the web-app and its materials, as well as how likely they were to revisit the site. RESULTS/ANTICIPATED RESULTS: We anticipate a very positive response from the children regarding the design and usability of the web-app and its materials. By using an adolescent-focused design methodology at every step of the design process, we will ensure that all materials are attractive and engaging to our younger target audience. Exposing children to accessible information about clinical trials at a young age allows us to build their trust in the research process prior to the possible internalization and acceptance of cultural misconceptions. Over time, we hope to see a change in attitudes toward clinical research as well as increased participation, whether from under-represented groups or a younger demographic, and positively contribute to T3 and onwards in the translational continuum. DISCUSSION/SIGNIFICANCE: In a rapidly changing world, the best approach to making change is through targeting the younger demographic, the leaders of tomorrow. Our project will allow adolescents to foster a more well-rounded opinion of clinical research, increasing their participation and better paving a more positively received future for translational science as a whole.
New ent-Kaurene-Type Diterpenoids Possessing Cytotoxicity from the New Zealand Liverwort Jungermannia Species (2003)

Two new ent-kaurene-type and a new rearranged ent-kaurene-type diterpenoids possessing cytotoxicity against a human leukemia cell line have been isolated from the New Zealand liverwort Jungermannia species, together with previously known ent-kaurene-type diterpenoids. Their structures were established based on extensive NMR techniques.
Recapitulating tumour microenvironment in chitosan–gelatin three-dimensional scaffolds: an improved<i>in vitro</i>tumour model (2012)

Owing to the reduced co-relationship between conventional flat Petri dish culture (two-dimensional) and the tumour microenvironment, there has been a shift towards three-dimensional culture systems that show an improved analogy to the same. In this work, an extracellular matrix (ECM)-mimicking three-dimensional scaffold based on chitosan and gelatin was fabricated and explored for its potential as a tumour model for lung cancer. It was demonstrated that the chitosan-gelatin (CG) scaffolds supported the formation of tumoroids that were similar to tumours grown in vivo for factors involved in tumour-cell-ECM interaction, invasion and metastasis, and response to anti-cancer drugs. On the other hand, the two-dimensional Petri dish surfaces did not demonstrate gene-expression profiles similar to tumours grown in vivo. Further, the three-dimensional CG scaffolds supported the formation of tumoroids, using other types of cancer cells such as breast, cervix and bone, indicating a possible wider potential for in vitro tumoroid generation. Overall, the results demonstrated that CG scaffolds can be an improved in vitro tool to study cancer progression and drug screening for solid tumours.