gebhart/patrepeval huggingface dataset:
Human-yeast genetic interaction for disease network: systematic discovery of multiple drug targets (2017)

A novel approach has been used to identify functional interactions relevant to human disease. Using high-throughput human-yeast genetic interaction screens, a first draft of disease interactome was obtained. This was achieved by first searching for candidate human disease genes that confer toxicity in yeast, and second, identifying modulators of toxicity. This study found potentially disease-relevant interactions by analyzing the network of functional interactions and focusing on genes implicated in amyotrophic lateral sclerosis (ALS), for example. In the subsequent proof-of-concept study focused on ALS, similar functional relationships between a specific kinase and ALS-associated genes were observed in mammalian cells and zebrafish, supporting findings in human-yeast genetic interaction screens. Results of combined analyses highlighted MAP2K5 kinase as a potential therapeutic target in ALS. [BMB Reports 2017; 50(11): 535-536].
Distribution of 1-(2-Deoxy-2-fluoro-β-d-arabinofuranosyl) Uracil in Mice Bearing Colorectal Cancer Xenografts (2004)

These results for FAU incorporation into DNA in vitro and in vivo further support clinical evaluation of FAU as a therapeutic agent in tumors with high concentrations of thymidylate synthase that are less likely to respond to 5-fluorouracil treatment. The high circulating concentrations of thymidine reported in mice may limit their utility in evaluating FAU as a PET probe.
Correction: Non-reversible heat-induced gelation of a biocompatible Fmoc-hexapeptide in water (2020)

Correction for 'Non-reversible heat-induced gelation of a biocompatible Fmoc-hexapeptide in water' by Jonathan P. Wojciechowski et al., Nanoscale, 2020, 12, 8262-8267, DOI: .
CXCL2/CXCR2 axis induces cancer stem cell characteristics in CPT‐11‐resistant LoVo colon cancer cells via Gαi‐2 and Gαq/11 (2018)

Cancer stem cells (CSCs) exist in colon cancer and exhibit characteristics of stem cells which are due to lineages of tissues where they arise. Epithelial to mesenchymal transition (EMT)-undergoing cancer cells display CSC properties and therapeutic resistance. Cancer and stromal cells comprise of a tumor microenvironment. One way the two populations communicate with each other is to secret CXC ligands (CXCLs). CXCLs are capable of causing chemotaxis of specific types of stromal cells and control angiogenesis. Double immunofluorescence, western blot analysis, and colony-formation assay were carried out to compare parental and CPT-11-resistant LoVo cells. CPT-11-R LoVo colon cancer cells showed increased expression of CXCL1, CXCL2, CXCL3, and CXCL8. They displayed significantly increased intracellular protein levels of CXCL2 and CXCR2. CPT-11-R LoVo cells showed significantly elevated expression in aldehyde dehydrogenase 1 (ALDH1), cluster of differentiation 24 (CD24), cluster of differentiation 44 (CD44), and epithelial cell adhesion molecule (EpCAM). CXCL2 knockdown by short hairpin RNA resulted in reduced expression of CSC proteins, cyclins, EMT markers, G proteins, and matrix metalloproteinases (MMPs). Finally, Gαi-2 was found to promote expression of CSC genes and tumorigenesis which were more apparent in the resistant cells. In addition, Gαq/11 showed a similar pattern with exceptions of EpCAM and MMP9. Therefore, CXCL2-CXCR2 axis mediates through Gαi-2 and Gαq/11 to promote tumorigenesis and contributes to CSC properties of CPT-11-R LoVo cells.
Topology-constrained surface reconstruction from cross-sections (2015)

In this work we detail the first algorithm that provides topological control during surface reconstruction from an input set of planar cross-sections. Our work has broad application in a number of fields including surface modeling and biomedical image analysis, where surfaces of known topology must be recovered. Given curves on arbitrarily oriented cross-sections, our method produces a manifold interpolating surface that exactly matches a user-specified genus. The key insight behind our approach is to formulate the topological search as a divide-and-conquer optimization process which scores local sets of topologies and combines them to satisfy the global topology constraint. We further extend our method to allow image data to guide the topological search, achieving even better results than relying on the curves alone. By simultaneously satisfying both geometric and topological constraints, we are able to produce accurate reconstructions with fewer input cross-sections, hence reducing the manual time needed to extract the desired shape.
Barocaloric properties of quaternary Mn3(Zn,In)N for room-temperature refrigeration applications (2021)

The magnetically frustrated manganese nitride antiperovskite family displays significant changes of entropy under hydrostatic pressure that can be useful for the emerging field of barocaloric cooling. Here we show that barocaloric properties of metallic antiperovskite Mn nitrides can be tailored for room-temperature application through quaternary alloying. We find an enhanced entropy change of $|\mathrm{\ensuremath{\Delta}}{S}_{\mathrm{t}}|=37\phantom{\rule{4pt}{0ex}}\mathrm{J}\phantom{\rule{0.16em}{0ex}}{\mathrm{K}}^{\ensuremath{-}1}\phantom{\rule{0.16em}{0ex}}{\mathrm{kg}}^{\ensuremath{-}1}$ at the ${T}_{t}=300\phantom{\rule{4pt}{0ex}}\mathrm{K}$ antiferromagnetic transition of quaternary ${\mathrm{Mn}}_{3}{\mathrm{Zn}}_{0.5}{\mathrm{In}}_{0.5}\mathrm{N}$ relative to the ternary end members. The pressure-driven barocaloric entropy change of ${\mathrm{Mn}}_{3}{\mathrm{Zn}}_{0.5}{\mathrm{In}}_{0.5}\mathrm{N}$ reaches $|\mathrm{\ensuremath{\Delta}}{S}_{\mathrm{BCE}}|=20\phantom{\rule{4pt}{0ex}}\mathrm{J}\phantom{\rule{0.16em}{0ex}}{\mathrm{K}}^{\ensuremath{-}1}\phantom{\rule{0.16em}{0ex}}{\mathrm{kg}}^{\ensuremath{-}1}$ in 2.9 kbar. Our results open up a large phase space where compounds with improved barocaloric properties may be found.
Three-Year Outbreak of Pseudobacteremia With Burkholderia cepacia Traced to a Contaminated Blood Gas Analyzer (1996)

Between November 1990 and June 1993, Burkholderia cepacia was isolated from the blood cultures of 13 neonates born at the Ottawa General Hospital. Eight of the 13 neonates appeared symptomatic, and only 4 were treated with appropriate antimicrobial therapy, but all improved clinically. In August 1993, the blood gas analyzer in the neonatal intensive-care unit was found to be contaminated heavily with B cepacia. Eight available patient isolates were identical to the isolates recovered from the blood gas analyzer by ribotyping analysis. Infection control measures were implemented to prevent future contamination of the analyzer, and no further cases have been identified.
Neurons, viscose fluids, freshwater polyp hydra-and self-organizing information systems (2003)

Principles of self-organisation are presented and are applied to the fields of the Web, which has developed its form from the bottom up; e-science, in which a grid of intelligent components interacted towards a greater understanding of the science concerned; peer-to-peer systems, that lend themselves to information systems that do not work with centralized authority; software and hardware agents; and mobile applications, which often defy centralized control.
Single-Biomolecule Resolution Imaging with an Optical Microscope (2005)

A Fluorescence Apertureless Near-field Scanning Optical Microscope (FANSOM) has been developed with FWHM optical resolution below 10 nm when imaging at ~600 nm wavelengths The apparatus combines an epi fluorescence optical microscope and an atomic force microscope (AFM) to obtain single-molecule sensitivity and optical resolution limited by the sharpness of the AFM probe. The AFM probe is used to stimulate or reduce the detected fluorescence emission rate depending on the AFM tip material and the polarization of the excitation light. The probe-sample interaction is described by near-field dipole-dipole physics, resulting in a stimulated emission rate that varies by r 6 . When tapping the probe over the substrate being imaged, the near-field component is sharply modulated at that tapping frequency, thereby enabling separation from the far-field background during post-processing. Images of fluorescent single-molecules taken in a physiological environment will be presented.
Supplemental figure 21 from Preclinical Characterization of BET Family Bromodomain Inhibitor ABBV-075 Suggests Combination Therapeutic Strategies (2023)

&lt;p&gt;ABBV-075 induces differentiation markers in HL-60 cells&lt;/p&gt;
ChemInform Abstract: Sequential Radical Ring Expansion and Allylation Reactions Using 2‐Bromo‐3‐(phenylthio)propene: Their Application to the Synthesis of Bridged Ring Systems. (1998)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Design of illumination devices for delivery of photodynamic therapy in the oral cavity (2010)

We present three designs for delivery of light in the oral cavity for photodynamic therapy (PDT) under the requirements of average irradiance of 50 mW/cm<sup>2</sup> and spatial non-uniformities well under 10% over a square area of 25 mm<sup>2</sup>. The main goal is to design a device that avoids having to shield the oral cavity prior to irradiation for PDT. Illumination theory is instrumental in identifying an effective geometry for the device. The designs proposed build upon the technology that is already available for PDT and use illumination theory concepts to maximize the efficiency of the light delivery. One design combines a cylindrical diffusing fiber with a reflector derived from the edge-ray theorem while a second consists of a fiber illuminator coupled to a lightpipe device. Both designs are successful in delivering the light reducing the need of shielding and in providing the desired irradiance and uniformity. The two approaches performed comparably and provided a higher irradiance than needed, thus inspiring the design of a third, simpler design based on an off-axis cylinder reflector.
Cost Effective Recovery of Low-TDS Frac Flowback Water for Re-use (2011)

The project goal was to develop a cost-effective water recovery process to reduce the costs and envi-ronmental impact of shale gas production. This effort sought to develop both a flowback water pre-treatment process and a membrane-based partial demineralization process for the treatment of the low-Total Dissolved Solids (TDS) portion of the flowback water produced during hydrofracturing operations. The TDS cutoff for consideration in this project is < 35,000 {approx} 45,000 ppm, which is the typical limit for economic water recovery employing reverse osmosis (RO) type membrane desalination processes. The ultimate objective is the production of clean, reclaimed water suitable for re-use in hydrofracturing operations. The team successfully compiled data on flowback composition and other attributes across multiple shale plays, identified the likely applicability of membrane treatment processes in those shales, and expanded the proposed product portfolio to include four options suitable for various reuse or discharge applications. Pretreatment technologies were evaluated at the lab scale and down-selected based upon their efficacy in removing key contaminants. The chosen technologies were further validated by performing membrane fouling studies with treated flowback water to demonstrate the technical feasibility of flowback treatment with RO membranes. Process flow schemes were constructed for each of the four product options based on experimental performance data from actual flowback water treatment studies. For the products requiring membrane treatment, membrane system model-ing software was used to create designs for enhanced water recovery beyond the typical seawater desalination benchmark. System costs based upon vendor and internal cost information for all process flow schemes were generated and are below target and in line with customer expectations. Finally, to account for temporal and geographic variability in flowback characteristics as well as local disposal costs and regulations, a parametric value assessment tool was created to assess the economic attractiveness of a given flowback recovery process relative to conventional disposal for any combination of anticipated flowback TDS and local disposal cost. It is concluded that membrane systems in combination with appropriate pretreatment technologies can provide cost-effective recovery of low-TDS flow-back water for either beneficial reuse or safe surface discharge.
High-speed camera with real time processing for frequency domain imaging (2011)

We describe a high-speed camera system for frequency domain imaging suitable for applications such as in vivo diffuse optical imaging and fluorescence lifetime imaging. 14-bit images are acquired at 2 gigapixels per second and analyzed with real-time pipeline processing using field programmable gate arrays (FPGAs). Performance of the camera system has been tested both for RF-modulated laser imaging in combination with a gain-modulated image intensifier and a simpler system based upon an LED light source. System amplitude and phase noise are measured and compared against theoretical expressions in the shot noise limit presented for different frequency domain configurations. We show the camera itself is capable of shot noise limited performance for amplitude and phase in as little as 3 ms, and when used in combination with the intensifier the noise levels are nearly shot noise limited. The best phase noise in a single pixel is 0.04 degrees for a 1 s integration time.
Performance Characteristics of a Multicore Interferometric Fiber Optic Gyroscope Using a 7-Core Fiber (2020)

The sensitivity of an interferometric fiber optic gyroscope (IFOG) scales with the length of the sensing optical path. Thus, IFOG development history has seen much work devoted to shrinking ever-increasing lengths of optical fiber into a fixed volume. Indeed, the success of the IFOG as a guidance and navigation technology is founded, to a large extent, on the many advancements in fiber-optics which were required to compact numerous state-of-the-art components - including a multi-kilometer length of optical fiber - to within the size of a teacup. An exciting technology which promises to continue this trend is multicore optical fiber, in which multiple, independent optical waveguides (cores) are placed within the same glass cladding which would ordinarily contain only one core. The dense arrangement of cores in such fibers can be exploited in an IFOG by connecting them in series, and thereby increasing the instrument sensitivity proportionally. As originally proposed by Bergh [1], these features present an opportunity to increase sensitivity while reducing the sensor footprint and simplifying the optical fiber coil - a key driver of cost and complexity in IFOGs. Here we detail performance characteristics of an all-fiber multicore IFOG employing a bend-insensitive, single-mode, 7-core fiber in the sensing coil. Like the recent, first-ever demonstration by Mitani et al. [2], [3], we employ an open-loop testbed architecture with a depolarized sensing loop, in which fiber cores are connected in series via a pair of multicore fan-in/fan-out devices. Here however, the fan-in/fan-out components are tapered fiber devices, packaged in conventional fiber-optic component sleeves, and with the core interconnections made via standard fusion splices [4]. Measurements of noise and long-term stability of the instrument show that its performance is commensurate with the 7X enhanced sensitivity afforded by the optical path length increase. For this 7-core, 154 m long, 10 cm diameter fiber coil, we show long-term gyro bias stability under 0.02 deg/hr and angle random walk of 2.4 mdeg/√(hr). This compares favorably with both noise models and performance measurements in IFOGs of similar scale factor, thus confirming the sensitivity improvement conferred by use of 7-core fiber. The all-fiber configuration of the sensing loop makes this instrument highly practicable as a drop-in replacement for current IFOGs, with no change to existing front-end designs. Moreover, as multicore fiber technology continues to push the frontiers of optical fiber transmission capacity, future designs may benefit from even greater core multiplicity - an exciting prospect for the next generation of compact, low-cost, high-accuracy IFOGs.
Transforming Growth Factor α Production and Epidermal Growth Factor Receptor Expression in Normal and Oncogene Transformed Human Mammary Epithelial Cells (1989)

We have characterized the expression of transforming growth factor alpha (TGF alpha) and its receptor, the epidermal growth factor receptor (EGF-R), in normal and malignantly transformed human mammary epithelial cells. Human mammary epithelial cells were derived from a reduction mammoplasty (184), immortalized by benzo-a-pyrene (184A 1N4), and further transformed by the oncogenes simian virus 40 T (SV40 T), v-Ha-ras, and v-mos alone or in combination using retroviral vectors. 184 and 184A 1N4 cells require EGF for anchorage-dependent clonal growth. In mass culture, they secrete TGF alpha at high concentrations and exhibit an attenuated requirement for exogenous EGF/TGF alpha. SV40 T transformed cells have 4-fold increased EGF-R, have acquired the ability to clone in soft agar with EGF/TGF alpha supplementation, but are not tumorigenic. Cells transformed by v-mos or v-Ha-ras are weakly tumorigenic and capable of both anchorage dependent and independent growth in the absence of EGF/TGF alpha. Cells transformed by both SV40 T and v-Ha-ras are highly tumorigenic, are refractory to EGF/TGF alpha, and clone with high efficiency in soft agar. The expression of v-Ha-ras is associated with a loss of the high (but not low) affinity binding component of the EGF-R. Malignant transformation and loss of TGF alpha/EGF responsiveness did not correlate with an increase in TGF alpha production. Thus, TGF alpha production does not appear to be a tumor specific marker for human mammary epithelial cells. Differential growth responses to EGF/TGF alpha, rather than enhanced production of TGF alpha, may determine the transition from normal to malignant human breast epithelium.
QRS axis based classification of electrode interchange in wearable ECG devices (2015)

Wearable ECG monitoring is becoming a convenient way for patients as well as doctors, in tracking and diagnosing heart diseases among large population in rural areas. Wearable ECG devices along with the smartphones are used to capture and transmit ECG data to hospitals where medical practitioners di
Catecholate/Salicylate Heteropodands:  Demonstration of a Catecholate to Salicylate Coordination Change1 (2000)

While iron release from enterobactin-mediated iron transport occurs primarily via an esterase that destroys the siderophore, other catechol siderophores that are not susceptible to hydrolysis act as bacterial growth factors. Elucidating the structures of protonated ferric enterobactin may reveal the pathway by which synthetic analogues fulfill bacterial iron requirements. In order to more completely model this potential delivery pathway for ferric iron, as well as to understand the pH dependent structural dynamics of ferric enterobactin, two ligands, (2-hydroxybenzoyl-2-aminoethyl)-bis(2,3-dihydroxybenzoyl-2-aminoethyl)amine (TRENCAMSAM) and (2-hydroxy-3-methoxybenzoyl-2-aminoethyl)-bis(2,3-dihydroxybenzoyl-2- aminoethyl)amine (TRENCAM(3M)SAM), have been synthesized as models for monoprotonated enterobactin. The coordination chemistry of these ligands with Fe3+ and Al3+ has been investigated. Fe[TRENCAMSAM]2- crystallizes in the triclinic space group P1: Z = 1, a = 11.3307(6) A, b = 12.5479(7) A, c = 15.5153(8) A, alpha = 94.513(1) degree, beta = 105.867(1) degree, gamma = 94.332(1) degree. The structure is a two-metal two-ligand dimer supported by mu-oxo bridges from two catecholate moieties. Al[TRENCAMSAM]2- crystallizes in the triclinic space group P1: Z = 2, a = 9.1404(2) A, b = 13.3570(1) A, c = 15.5950(1) A, alpha = 95.711(1) degree, beta = 104.760(1) degree, gamma = 92.603(1) degree. The complex is a monomer with a five-coordinate, square-pyramidal aluminum cation. Al[TRENCAM(3M)SAM]2- crystallizes in the monoclinic space group C2/m: Z = 8, a = 34.244(2) A, b = 11.6206(6) A, c = 21.9890(12) A, beta = 101.478(1) degree. The complex is also a monomer, but with a highly distorted five-coordinate, square-pyramidal aluminum cation coordination sphere. At high pH these complexes do not display a salicylate mode of binding; however, at low pH Al[TRENCAMSAM]2- converts to protonated Al[H3TRENCAMSAM]+, which is a six-coordinate, tris-salicylate complex. Al[H3TRENCAMSAM]+ crystallizes in the triclinic space group P1: Z = 2, a = 11.5475(4) A, b = 12.1681(4) A, c = 12.5094(4) A, alpha = 109.142(1) degree, beta = 104.327(1) degree, gamma = 103.636(1) degree. This is the first catecholamide enterobactin analogue that has been structurally characterized in both a catecholate and salicylate mode of coordination.
Study of down-sized silica highly non-linear fiber (2005)

Theoretical limit of reducing cladding diameter for HNLF have been obtained by finite element method (FEM) and mechanical strength of glass. Simulation results are confirmed by trial coin sized HNLF modules using over 200 m of 56 μm HNLF. (2 pages)
Advanced Hydrogels for the Controlled Delivery of Insulin (2021)

Insulin is a peptide hormone that is key to regulating physiological glucose levels. Its molecular size and susceptibility to conformational change under physiological pH make it challenging to orally administer insulin in diabetes. The most effective route for insulin delivery remains daily injection. Unfortunately, this results in poor patient compliance and increasing the risk of micro- and macro-vascular complications and thus rising morbidity and mortality rates in diabetics. The use of 3D hydrogels has been used with much interest for various biomedical applications. Hydrogels can mimic the extracellular matrix (ECM) and retain large quantities of water with tunable properties, which renders them suitable for administering a wide range of sensitive therapeutics. Several studies have demonstrated the fixation of insulin within the structural mesh of hydrogels as a bio-scaffold for the controlled delivery of insulin. This review provides a concise incursion into recent developments for the safe and effective controlled delivery of insulin using advanced hydrogel platforms with a special focus on sustained release injectable formulations. Various hydrogel platforms in terms of their methods of synthesis, properties, and unique features such as stimuli responsiveness for the treatment of Type 1 diabetes mellitus are critically appraised. Key criteria for classifying hydrogels are also outlined together with future trends in the field.
Discovery of Pyrazolocarboxamides as Potent and Selective Receptor Interacting Protein 2 (RIP2) Kinase Inhibitors (2019)

Herein we report the discovery of pyrazolocarboxamides as novel, potent, and kinase selective inhibitors of receptor interacting protein 2 kinase (RIP2). Fragment based screening and design principles led to the identification of the inhibitor series, and X-ray crystallography was used to inform key structural changes. Through key substitutions about the N1 and C5 N positions on the pyrazole ring significant kinase selectivity and potency were achieved. Bridged bicyclic pyrazolocarboxamide <b>11</b> represents a selective and potent inhibitor of RIP2 and will allow for a more detailed investigation of RIP2 inhibition as a therapeutic target for autoinflammatory disorders.