gebhart/patrepeval huggingface dataset:
Jeev: A Low-Cost Cell Phone Application for Tracking the Vaccination Coverage of Children in Rural Communities (2013)

Immunization saves millions of lives against vaccine-preventable diseases. Yet, 24 million children born every year do not receive proper immunization during their first year. UNICEF and WHO have emphasized the need to strengthen the immunization surveillance and monitoring in developing countries to reduce childhood deaths. In this regard, we present a software application called Jeev to track the vaccination coverage of children in rural communities. Jeev synergistically combines the power of smart phones and the ubiquity of cellular infrastructure, QR codes, and national identification cards. We present the design of Jeev and highlight its unique features along with a preliminary evaluation of its performance. We plan to pilot test Jeev in a rural population to study its effectiveness and identify socio-cultural issues that may arise in a large-scale deployment.
Effectiveness and safety of protease inhibitor‐based regimens in HIV‐infected Thai children failing first‐line treatment (2012)

PI-based regimens are safe and effective for HIV-infected Thai children who have failed first-line NNRTI-based regimens. However, long-term follow-up is warranted in order to ascertain the feasibility and sustainability of these new regimens.
Supramolecular Injectable Hyaluronate Hydrogels for Cartilage Tissue Regeneration (2020)

Mesenchymal stem cells (MSCs) have been widely investigated to repair injured cartilage tissues for the treatment of arthritis. Despite these great efforts, the difficulty in the spatiotemporal control of delivered cells has limited the further clinical development with rapid clearance. Here, we developed injectable hyaluronate (HA) hydrogels to encapsulate MSCs for controlled cartilage tissue regeneration based on the supramolecular chemistry between β-cyclodextrin-modified HA (HA-CD) and adamantane (Ad)-modified HA (HA-Ad). Supramolecular HA hydrogels exhibited remarkable mechanical characteristics such as shear thinning and self-healing with a high cell viability of encapsulated MSCs. The spatiotemporally controlled delivery of MSCs from the supramolecular HA hydrogels resulted in the statistically significant chondrogenic differentiation and extracellular matrix deposition <i>in vitro</i> and <i>in vivo</i>. We could confirm the notable cartilage tissue regeneration in cartilage defect model rats after treatment with supramolecular HA hydrogels encapsulating MSCs for 28 days. Taken together, supramolecular HA hydrogels would be successfully harnessed as an injectable delivery system of MSCs for cartilage tissue regeneration and other tissue engineering applications.
Color model comparative analysis for breast cancer diagnosis using H and E stained images (2015)

Digital cancer diagnosis is a research realm where signal processing techniques are used to analyze and to classify color histopathology images. Different from grayscale image analysis of magnetic resonance imaging or X-ray, colors in histopathology images convey large amount of histological information and thus play significant role in cancer diagnosis. Though color information is widely used in histopathology works, as today, there is few study on color model selections for feature extraction in cancer diagnosis schemes. This paper addresses the problem of color space selection for digital cancer classification using H and E stained images, and investigates the effectiveness of various color models (RGB, HSV, CIE L*a*b*, and stain-dependent H and E decomposition model) in breast cancer diagnosis. Particularly, we build a diagnosis framework as a comparison benchmark and take specific concerns of medical decision systems into account in evaluation. The evaluation methodologies include feature discriminate power evaluation and final diagnosis performance comparison. Experimentation on a publicly accessible histopathology image set suggests that the H and E decomposition model outperforms other assessed color spaces. For reasons behind various performance of color spaces, our analysis via mutual information estimation demonstrates that color components in the H and E model are less dependent, and thus most feature discriminate power is collected in one channel instead of spreading out among channels in other color spaces.
Development of an In Vivo Probe to Track SARS-CoV-2 Infection in Rhesus Macaques (2021)

Infection with the novel coronavirus, SARS-CoV-2, results in pneumonia and other respiratory symptoms as well as pathologies at diverse anatomical sites. An outstanding question is whether these diverse pathologies are due to replication of the virus in these anatomical compartments and how and when the virus reaches those sites. To answer these outstanding questions and study the spatiotemporal dynamics of SARS-CoV-2 infection a method for tracking viral spread <i>in vivo</i> is needed. We developed a novel, fluorescently labeled, antibody-based <i>in vivo</i> probe system using the anti-spike monoclonal antibody CR3022 and demonstrated that it could successfully identify sites of SARS-CoV-2 infection in a rhesus macaque model of COVID-19. Our results showed that the fluorescent signal from our antibody-based probe could differentiate whole lungs of macaques infected for 9 days from those infected for 2 or 3 days. Additionally, the probe signal corroborated the frequency and density of infected cells in individual tissue blocks from infected macaques. These results provide proof of concept for the use of <i>in vivo</i> antibody-based probes to study SARS-CoV-2 infection dynamics in rhesus macaques.
IL-4 and IL-13 upregulate ornithine decarboxylase expression by PI3K and MAP kinase pathways in vascular smooth muscle cells (2008)

Ornithine decarboxylase (ODC) is the first and rate-controlling enzyme in the synthesis of polyamines, which are essential for normal cell growth. We have previously demonstrated that IL-4 and IL-13 can stimulate rat aortic smooth muscle cell (RASMC) proliferation. The objective of this study was to determine whether IL-4 and IL-13 induce cell proliferation by upregulating ODC expression in RASMC. The results revealed that incubation of RASMC with IL-4 and IL-13 for 24 h caused four- to fivefold induction of ODC catalytic activity. The increased ODC catalytic activity was attributed to the increased expression of ODC mRNA. Moreover, these observations were paralleled by increased production of polyamines. We further investigated the signal transduction pathways responsible for ODC induction by IL-4 and IL-13. The data illustrated that PD-98059, a MEK (MAPK kinase) inhibitor, LY-294002, a phosphatidylinositol 3-kinase (PI3K) inhibitor, and H-89, a protein kinase A (PKA) inhibitor, substantially decreased the induction of ODC catalytic activity and ODC mRNA expression induced by IL-4 and IL-13, suggesting positive regulation of the ODC gene by ERK, PI3K, and PKA pathways. Interestingly, dexamethasone, a known inhibitor of cell proliferation, completely abrogated the response of RASMC to IL-4 and IL-13. Furthermore, the inhibition of ODC by these inhibitors led to the reduced production of polyamines and decreased DNA synthesis as monitored by [(3)H]thymidine incorporation. Our data indicate that upregulation of ODC by IL-4 and IL-13 might play an important role in the pathophysiology of vascular disorders characterized by excessive smooth muscle growth.
Industrial chemistry program at a small undergraduate college (1986)

Recent estimates show that 70-90% of students graduating from chemistry programs will enter the chemical industry but the typical chemistry curriculum does not adequately prepare students for either industrial careers or for understanding real world problems.
Turbulence to turbulence transition in homeotropically aligned nematic liquid crystals (1999)

In this paper, a study of the electrically driven turbulent-turbulent transition in a homeotropically oriented nematic sample is reported. The transition has the characteristics of a nucleation process, and its threshold has been experimentally determined. The nucleation rate and the growth velocity of the new turbulent nuclei are also reported.
Randomized numerical linear algebra: Foundations and algorithms (2020)

This survey describes probabilistic algorithms for linear algebraic computations, such as factorizing matrices and solving linear systems. It focuses on techniques that have a proven track record for real-world problems. The paper treats both the theoretical foundations of the subject and practical computational issues. Topics include norm estimation, matrix approximation by sampling, structured and unstructured random embeddings, linear regression problems, low-rank approximation, subspace iteration and Krylov methods, error estimation and adaptivity, interpolatory and CUR factorizations, Nyström approximation of positive semidefinite matrices, single-view (‘streaming’) algorithms, full rank-revealing factorizations, solvers for linear systems, and approximation of kernel matrices that arise in machine learning and in scientific computing.
Stable and sensitive stimuli-responsive anisotropic hydrogels for sensing ionic strength and pressure (2018)

Stimuli-responsive hydrogels that respond to pressure and ionic strength were prepared with large mono-domain, nematic organization of cellulose nanocrystals (CNCs).
MATCH for the Prosumer Smart Grid The Algorithmics of Real-Time Power Balance (2016)

Prosumers or proactive consumers are steadily on the rise in emerging Smart Grid systems. These consumers, apart from their traditonal role of using energy from the grid, also are actively involved in individually transferring stored energy from renewable sources such as wind and solar, to the grid. The large-scale integration of renewable generation in the emerging grid will re-define ways of meeting consumer energy demands, and more importantly drive greener and cost-effective utility operations. In this paper, we investigate the problem of matching consumer demand with the grid supply in real-time, and in the presence of renewables. We formulate this problem as a stochastic optimization problem and propose MATCH, a fast distributed real-time algorithm that accounts for the uncertainties in (i) renewable generation, (ii) the latter's transmission through the grid network, (iii) loads, and (iv) energy prices, and balances power in the Smart Grid at all times. MATCH is based on the Lyapunov stochastic optimization framework and scales to localities with a large number of networked renewable generation sources. We validate the efficacy of MATCH through experiments conducted using data modelled on proprietary data obtained from two public utilities. As part of the main results of this work, we show that (a) MATCH outputs unique approximate-optimal grid parameter configuration vectors in real-time that ensure perennial supplydemand balance in the grid at a minimum cost, and (b) mesh transmission network topologies lead to better MATCH outputs when compared to other existing transmission network topologies.
Improvement in Scoliosis Research Society-22R Pain Scores After Surgery for Adolescent Idiopathic Scoliosis (2016)

2.
Broadband High-Density Development Wide Azimuth - Application in the Gulf of Mexico (2013)

Broadband acquisition and processing can yield stronger signal at both high and low frequencies, for improved resolution and signal penetration. These benefits of broadband data can be combined with wide-azimuth survey design to gain the additional benefits of higher signal-to-noise ratio and better illumination of complex structures. For this field development survey in the southern Gulf of Mexico, a broadband, high-density, wide azimuth acquisition was designed to improve the imaging of faulted Cretaceous reservoirs under a complex overburden. The data were then processed through a broadband processing flow, and results were compared to the legacy images from conventional data.
431. The chemistry of carcinogenic nitrogen compounds. Part V. Angular hydroxybenzacridines and hydroxydibenzacridines (1950)

Ng. Ph. Buu-Hoï, J. Chem. Soc., 1950, 2096 DOI: 10.1039/JR9500002096
New derivatives of kanamycin B obtained by combined modifications in positions 1 and 6". Synthesis, microbiological properties, and in vitro and computer-aided toxicological evaluation (1991)

Substitution of the C-1 atom in the 2-deoxystreptamine moiety of gentamicin C2, a broad-spectrum aminoglycoside antibiotic, by an axial hydroxymethyl group has been reported to confer protection against most clinically important bacterial enzymes inactivating aminoglycosides, while simultaneously reducing the nephrotoxic potential of this drug. We report here on a similar modification of kanamycin B. Microbiological evaluation, however, revealed no useful protection, as established by the almost complete lack of activity of 1-C-(hydroxymethyl)kanamycin B against an array of organisms producing defined types of aminoglycoside-inactivating enzymes and against which 1-C-(hydroxymethyl)gentamicin C2 and amikacin (1-N-[(S)-2-hydroxy-4-aminobutyryl]kanamycin A) are active. Moreover, toxicological evaluation, based on the in vitro measurement of the drug inhibitory potential toward lysosomal phospholipases, a predictive test of the intrinsic nephrotoxic potential of aminoglycosides, showed not decreased but rather increased toxicity. Comparative conformational analysis of the interactions of the drug with a phosphatidylinositol monolayer explained the lack of protective effect, since no significant change of the mode of insertion of the derivative in this monolayer was detected compared to that of kanamycin B. Combination of a 1-C-(hydroxymethyl) substituent with a 6"-chloro, 6"-acetamido substituent resulted in a partial improvement of the toxicological behavior with no loss of activity for the 6"-chloro and the 6"-azido derivatives, but not to the extent of obtaining better derivatives than kanamycin B itself. We, therefore, suggest that the advantages of an axial hydroxymethyl substituent at C-1 are probably restricted to the gentamicin family and do not extend to kanamycins. It might be concluded that the structural differences between gentamicins and kanamycins play an important, still undescribed role both in their effective recognition by aminoglycoside-inactivating enzymes, which are responsible for most of the clinically important cases of resistance to aminoglycosides, and also in the interactions with phospholipids, which in turn cause nephrotoxicity.
Supplementary Table S2 from Mechanisms and Antitumor Activity of a Binary EGFR/DNA–Targeting Strategy Overcomes Resistance of Glioblastoma Stem Cells to Temozolomide (2023)

&lt;p&gt;Table S2 summarizes IC50s of TMZ, gefitinib or ZR2002 for various GSCs.&lt;/p&gt;
5,6-Dihydroxyindoles in the Fenton Reaction:  A Model Study of the Role of Melanin Precursors in Oxidative Stress and Hyperpigmentary Processes (1999)

Increasing evidence supports the view that diffusible melanin-related metabolites do not serve merely as pigment precursors, but may also act as modulators of the responses of the pigmentary cell melanocyte to external stimuli, especially to inflammation. In this study, the effect of melanin precursors 5, 6-dihydroxyindole (DHI) and 5,6-dihydroxyindole-2-carboxylic acid (DHICA) on the Fenton-induced oxidation of deoxyribose was investigated as a model of the oxidative stress processes triggered by the release of iron during inflammation. DHICA caused a powerful inhibition of the H(2)O(2)-Fe(II)/EDTA oxidation under both aerobic and anaerobic conditions, proving to be more efficient than typical hydroxyl radical (HO(*)) scavengers even at low concentrations with respect to deoxyribose. Conversely, DHI in air was a prooxidant at low indole:Fe(II) ratios, but shifted to an antioxidant at higher ratios (>6). The magnitude of the prooxidant effect increased by lowering the pH of the medium or by replacing Fe(II) with Fe(III), but was suppressed by exclusion of oxygen. Both the indoles retained their effects on the Fenton reaction in the absence of EDTA, as a result of their ability to chelate iron ions as evidenced by spectrophotometric experiments. Investigation of the reaction of DHI and DHICA with the Fenton reagent led to the conclusion that the indoles interact efficiently with HO(*), yielding indolesemiquinone species which are then converted to melanin pigments by self-coupling or disproportionation. At low DHI:iron molar ratios, the ability of semiquinones, generated by autoxidation of indoles, to recycle Fe(II) ions prevails, accounting for the observed prooxidant effect. Collectively, the results of this study provide new evidence for melanogenic 5,6-dihydroxyindoles as a novel class of biological antioxidants and point to these compounds as the key to interpreting the response of melanocytes to oxidative injuries. Moreover, the rapid formation of melanin following the exposure of 5, 6-dihydroxyindoles to the Fenton oxidation suggests new mechanisms of skin hyperpigmentation associated with inflammation.
Structures of Helical β-Tapes and Twisted Ribbons:  The Role of Side-Chain Interactions on Twist and Bend Behavior (2003)

Molecular Dynamics (MD) simulations have been used to obtain a molecular insight into the origins of the twist, bend, and helix pitch of the tape-like and ribbon (double tape)-like β-sheet aggregates formed by the self-assembling peptides P11-I (CH3CO-QQRQQQQQEQQ-NH2) and P11-II (CH3CO-QQRFQWQFEQQ-NH2). P11-II differs from P11-I in that glutamines at positions 4, 6, and 8 have been substituted for F, W, and F, and this gives rise to left-handed helicoidal tapes having a significantly shorter helix pitch. The presence of these hydrophobic residues also enhances the cross-tape attractive forces in P11-II ribbons, which foreshortens the helix pitch.
Resource-Constrained Adaptive Search for Sparse Multi-Class Targets with\n Varying Importance (2014)

In sparse target inference problems it has been shown that significant gains\ncan be achieved by adaptive sensing using convex criteria. We generalize\nprevious work on adaptive sensing to (a) include multiple classes of targets\nwith different levels of importance and (b) accommodate multiple sensor models.\nNew optimization policies are developed to allocate a limited resource budget\nto simultaneously locate, classify and estimate a sparse number of targets\nembedded in a large space. Upper and lower bounds on the performance of the\nproposed policies are derived by analyzing a baseline policy, which allocates\nresources uniformly across the scene, and an oracle policy which has a priori\nknowledge of the target locations/classes. These bounds quantify analytically\nthe potential benefit of adaptive sensing as a function of target frequency and\nimportance. Numerical results indicate that the proposed policies perform close\nto the oracle bound (&lt;3dB) when signal quality is sufficiently high\n(e.g.~performance within 3 dB for SNR above 15 dB). Moreover, the proposed\npolicies improve on previous policies in terms of reducing estimation error,\nreducing misclassification probability, and increasing expected return. To\naccount for sensors with different levels of agility, three sensor models are\nconsidered: global adaptive (GA), which can allocate different amounts of\nresource to each location in the space; global uniform (GU), which can allocate\nresources uniformly across the scene; and local adaptive (LA), which can\nallocate fixed units to a subset of locations. Policies that use a mixture of\nGU and LA sensors are shown to perform similarly to those that use GA sensors\nwhile being more easily implementable.\n
Evolution of Enzymatic Activity in the Enolase Superfamily:  Structure of o-Succinylbenzoate Synthase from Escherichia coli in Complex with Mg2+ and o-Succinylbenzoate, (2000)

The X-ray structures of the ligand free (apo) and the Mg(2+)*o-succinylbenzoate (OSB) product complex of o-succinylbenzoate synthase (OSBS) from Escherichia coli have been solved to 1.65 and 1.77 A resolution, respectively. The structure of apo OSBS was solved by multiple isomorphous replacement in space group P2(1)2(1)2(1); the structure of the complex with Mg(2+)*OSB was solved by molecular replacement in space group P2(1)2(1)2. The two domain fold found for OSBS is similar to those found for other members of the enolase superfamily: a mixed alpha/beta capping domain formed from segments at the N- and C-termini of the polypeptide and a larger (beta/alpha)(7)beta barrel domain. Two regions of disorder were found in the structure of apo OSBS: (i) the loop between the first two beta-strands in the alpha/beta domain; and (ii) the first sheet-helix pair in the barrel domain. These regions are ordered in the product complex with Mg(2+)*OSB. As expected, the Mg(2+)*OSB pair is bound at the C-terminal end of the barrel domain. The electron density for the phenyl succinate component of the product is well-defined; however, the 1-carboxylate appears to adopt multiple conformations. The metal is octahedrally coordinated by Asp(161), Glu(190), and Asp(213), two water molecules, and one oxygen of the benzoate carboxylate group of OSB. The loop between the first two beta-strands in the alpha/beta motif interacts with the aromatic ring of OSB. Lys(133) and Lys(235) are positioned to function as acid/base catalysts in the dehydration reaction. Few hydrogen bonding or electrostatic interactions are involved in the binding of OSB to the active site; instead, most of the interactions between OSB and the protein are either indirect via water molecules or via hydrophobic interactions. As a result, evolution of both the shape and the volume of the active site should be subject to few structural constraints. This would provide a structural strategy for the evolution of new catalytic activities in homologues of OSBS and a likely explanation for how the OSBS from Amycolaptosis also can catalyze the racemization of N-acylamino acids [Palmer, D. R., Garrett, J. B., Sharma, V., Meganathan, R., Babbitt, P. C., and Gerlt, J. A. (1999) Biochemistry 38, 4252-4258].
The Colors of C60 Solutions (1995)

Differences in the absorption intensity in the spectral range between 400 and 500 nm, which the human eye perceives as changes in color, are the reason why solutions of C 60 show different colors. The results of the experiments described rule out the formation of charge transfer complexes or of C 60 aggregates.
Analytical Methods for Detection of Gluten in Food—Method Developments in Support of Food Labeling Legislation (2011)

The current essential therapy of celiac disease is a strict adherence to a gluten-free diet. Besides food products that are naturally gluten-free, "very low gluten" and "gluten-free" bakery products have become available. The availability of immunochemical and other analytical methods to determine gluten markers in foods is of utmost importance to ensure the well being of gluten-sensitive individuals. The aim of this review was to evaluate if currently available methodologies are suitable to meet the requirements of food labeling standards for individual gluten source declaration, in order to achieve policy objectives. Codex Alimentarius and European Union (EU) legislation and gluten detection methodologies applicable at present have been summarized and compared. In 2009, the European Commission issued Regulation No. 41/2009 concerning the composition and labeling of foodstuffs suitable for people intolerant to gluten. This review constitutes a basis to investigate the possibility to develop a proteomic-based method for the specific detection of gluten-containing cereals in food products, especially at or around the limits specified in EU legislation.