gebhart/patrepeval huggingface dataset:
Knowledge-Based, Central Nervous System (CNS) Lead Selection and Lead Optimization for CNS Drug Discovery (2011)

The central nervous system (CNS) is the major area that is affected by aging. Alzheimer's disease (AD), Parkinson's disease (PD), brain cancer, and stroke are the CNS diseases that will cost trillions of dollars for their treatment. Achievement of appropriate blood-brain barrier (BBB) penetration is often considered a significant hurdle in the CNS drug discovery process. On the other hand, BBB penetration may be a liability for many of the non-CNS drug targets, and a clear understanding of the physicochemical and structural differences between CNS and non-CNS drugs may assist both research areas. Because of the numerous and challenging issues in CNS drug discovery and the low success rates, pharmaceutical companies are beginning to deprioritize their drug discovery efforts in the CNS arena. Prompted by these challenges and to aid in the design of high-quality, efficacious CNS compounds, we analyzed the physicochemical property and the chemical structural profiles of 317 CNS and 626 non-CNS oral drugs. The conclusions derived provide an ideal property profile for lead selection and the property modification strategy during the lead optimization process. A list of substructural units that may be useful for CNS drug design was also provided here. A classification tree was also developed to differentiate between CNS drugs and non-CNS oral drugs. The combined analysis provided the following guidelines for designing high-quality CNS drugs: (i) topological molecular polar surface area of <76 Å(2) (25-60 Å(2)), (ii) at least one (one or two, including one aliphatic amine) nitrogen, (iii) fewer than seven (two to four) linear chains outside of rings, (iv) fewer than three (zero or one) polar hydrogen atoms, (v) volume of 740-970 Å(3), (vi) solvent accessible surface area of 460-580 Å(2), and (vii) positive QikProp parameter CNS. The ranges within parentheses may be used during lead optimization. One violation to this proposed profile may be acceptable. The chemoinformatics approaches for graphically analyzing multiple properties efficiently are presented.
Modification of Thermal Emission via Metallic Photonic Crystals (2012)

Photonic crystals are materials that are periodically structured on an optical length scale. It was previously demonstrated that the glow, or thermal emission, of tungsten photonic crystals that have a specific structure - known as the 'woodpile structure' - could be modified to reduce the amount of infrared radiation from the material. This ability has implications for improving the efficiency of thermal emission sources and for thermophotovoltaic devices. The study of this effect had been limited because the fabrication of metallic woodpile structures had previously required a complex fabrication process. In this project we pursued several approaches to simplify the fabrication of metallic photonic crystals that are useful for modification of thermal emission. First, we used the self-assembly of micrometer-scale spheres into colloidal crystals known as synthetic opals. These opals can then be infiltrated with a metal and the spheres removed to obtain a structure, known as an inverse opal, in which a three-dimensional array of bubbles is embedded in a film. Second, we used direct laser writing, in which the focus of an infrared laser is moved through a thin film of photoresist to form lines by multiphoton polymerization. Proper layering of such lines can lead to a scaffold with the woodpile structure, which can be coated with a refractory metal. Third, we explored a completely new approach to modified thermal emission - thin metal foils that contain a simple periodic surface pattern, as shown in Fig. 1. When such a foil is heated, surface plasmons are excited that propagate along the metal interface. If these waves strike the pattern, they can be converted into thermal emission with specific properties.
Linear logic (1992)

Linear logic was introduced by Girard in 1987 Since then many results have supported Girard' s statement, "Linear logic is a resource conscious logic," and related slogans . Increasingly, compute r scientists have come to recognize linear logic as an expressive and powerful logic with connection s to a variety of topics in computer science .
On a "Theorem" of Peterson (1984)

This three-page note gives an example that appears to contradict a theorem in a TOPLAS article by Gary Peterson. Whether or not it does depends on the interpretation of the statement of the theorem, which is given only informally in English. I draw the moral that greater rigor is needed. When I sent this paper to Peterson, he strongly objected to it. I no longer have his message and don’t remember exactly what he wrote, but I think he said that he knew what the correct interpretation was and that I was unfairly suggesting that his theorem might be incorrect. So, I never published this note.
A CreER mouse to study melanin concentrating hormone signaling in the developing brain (2018)

The neuropeptide, melanin concentrating hormone (MCH), and its G protein-coupled receptor, melanin concentrating hormone receptor 1 (Mchr1), are expressed centrally in adult rodents. MCH signaling has been implicated in diverse behaviors such as feeding, sleep, anxiety, as well as addiction and reward. While a model utilizing the Mchr1 promoter to drive constitutive expression of Cre recombinase (Mchr1-Cre) exists, there is a need for an inducible Mchr1-Cre to determine the roles for this signaling pathway in neural development and adult neuronal function. Here, we generated a BAC transgenic mouse where the Mchr1 promotor drives expression of tamoxifen inducible CreER recombinase. Many aspects of the Mchr1-Cre expression pattern are recapitulated by the Mchr1-CreER model, though there are also notable differences. Most strikingly, compared to the constitutive model, the new Mchr1-CreER model shows strong expression in adult animals in hypothalamic brain regions involved in feeding behavior but diminished expression in regions involved in reward, such as the nucleus accumbens. The inducible Mchr1-CreER allele will help reveal the potential for Mchr1 signaling to impact neural development and subsequent behavioral phenotypes, as well as contribute to the understanding of the MCH signaling pathway in terminally differentiated adult neurons and the diverse behaviors that it influences.
Selective Binding of Imidazolium Cations in Building Multi‐Component Layers (2010)

Addition of 1-alkyl-3-methylimidazolium (C(n)-mim) cations 3-5 to a mixture of bis-phosphonium cation 2 and sodium p-sulfonatocalix[4]arene (1) in the presence of lanthanide ions results in the selective binding of an imidazolium cation into the cavity of the calixarene. The result is a multi-layered solid material with an inherently flexible interplay of the components. Incorporating ethyl-, n-butyl- or n-hexyl-mim cations into the multi-layers results in significant perturbation of the structure, the most striking effect is the tilting of the plane of the bowl-shaped calixarene relative to the plane of the multi-layer, with tilt angles of 7.2, 28.9 and 65.5 degrees , respectively. The lanthanide ions facilitate complexation, but are not incorporated into the structures and, in all cases, the calixarene takes on a 5- charge, with one of the lower-rim phenolic groups deprotonated. ROESY NMR experiments and other (1)H NMR spectroscopy studies establish the formation of 1:1 supermolecules of C(n)-mim and calixarene, regardless of the ratio of the two components, and indicate that the supermolecules undergo rapid exchange on the NMR spectroscopy timescale.
X-ray diffraction as a promising tool to characterize bone nanocomposites (2011)

To understand the characteristics of bone at the tissue level, the structure, organization and mechanical properties of the underlying levels down to the nanoscale as well as their mutual interactions need to be investigated. Such information would help understand changes in the bone properties including stiffness, strength and toughness and provide ways to assess the aged and diseased bones and the development of next generation of bio-inspired materials. X-ray diffraction techniques have gained increased interest in recent years as useful non-destructive tools for investigating the nanostructure of bone. This review provides an overview on the recent progress in this field and briefly introduces the related experimental approach. The application of x-ray diffraction to elucidating the structural and mechanical properties of mineral crystals in bone is reviewed in terms of characterization of <i>in situ</i> strain, residual stress-strain and crystal orientation.
Offset-value coding in database query processing (2022)

Recent work shows how offset-value coding speeds up database query execution, not only sorting but also duplicate removal and grouping (aggregation) in sorted streams, order-preserving exchange (shuffle), merge join, and more. It already saves thousands of CPUs in Google's Napa and F1 Query systems, e.g., in grouping algorithms and in log-structured merge-forests. In order to realize the full benefit of interesting orderings, however, query execution algorithms must not only consume and exploit offset-value codes but also produce offset-value codes for the next operator in the pipeline. Our research has sought ways to produce offset-value codes without comparing successive output rows one-by-one, column-by-column. This short paper introduces a new theorem and, based on its proof and a simple corollary, describes in detail how order-preserving algorithms (from filter to merge join and even shuffle) can compute offset-value codes for their outputs. These computations are surprisingly simple and very efficient.
THE BIOLOGY OF SAA: IDENTIFICATION OF THE INDUCER, IN VITRO SYNTHESIS, AND HETEROGENEITY DEMONSTRATED WITH MONOCLONAL ANTIBODIES* (1982)

Continued studies of the macrophage-derived mediator of SAA synthesis (SAA Stimulating Factor) confirm our previous observations that SAASF copurified with leukocytic pyrogen (LP) and lymphocyte activating factor (LAF). Moreover, new data demonstrate three separate isoelectric points for human LP-LAF-SAASF each of which possess the three biological activities. During the purification of 15,000 MW LP from crude stimulated mononuclear cell supernatants, only those fractions with pyrogenic activity in rabbits caused augmented stimulation of lymphocytes (LAF) and induced SAA synthesis in mice. Purified human LP stimulated isolated mouse hepatocytes in vitro to synthesize SAA in a dose-responsive manner. Colchicine treatment of hepatocytes led to decreased secretion of SAA into the medium and to an intracellular accumulation of SAA. Messenger RNA was isolated from the livers of endotoxin-stimulated mice and translated in a wheat-germ cell-free system. A major product was identified at 13-14,000 MW. Immunoprecipitation with anti-mouse AA identified several bands on autoradiography of polyacrylamide gels. These larger SAA precursors may account for the previously noted heterogeneity of human SAA, comprising at least 6 SAA isomers, of similar molecular weight but different solubility and electrophoretic charge characteristics. Two monoclonal antibodies (IgM-K and IgG1-K) have been prepared using standard cell hybridization techniques. They are directed at the variable COOH terminal region of SAA since they detect differences between the 6 human SAAs but do not react with human, monkey, dog or mouse AA proteins, human AP, C-reactive protein, IgG nor albumin. These antibodies will be useful in examining the origin, structure and function of SAA.
Generation of Highly Ozonized Water Using a Microporous Hollow Fiber Module (2002)

The generation of an environmentally friendly and highly ozonized water has been investigated. This was achieved by contacting highly concentrated ozone gas and water through a microporous hollow fibers module. According to the experimental results, it was observed that the ozone mass transfer in this system was controlled by the liquid phase. The maximum gradient approach was then used to model the ozone transfer within the module in both wetted and non-wetted modes. The corresponding validity was checked through the agreement between our experimental results and the calculated results under the gas-filled pore assumption. Furthermore, this model was used for a parameter study, and revealed that the connection of modules in series was more effective than that in parallel for the production of highly ozonized water.
Studies on the Total Synthesis of Tallysomycin. Synthesis of the Threonylbithiazole Moiety Containing a Structurally Unique Glycosylcarbinolamide (2001)

[structure: see text]. Tallysomycins are glycopeptide antibiotics that were first isolated from fermentation broths of Streptoalloteichus hindustanus. They are structurally related to the bleomycins but contain an additional talose sugar attached via a unique glycosylcarbinolamide linkage. Herein we report the synthesis of a key tallysomycin intermediate that incorporates the glycosylcarbinolamide moiety unique to the tallysomycins.
Recent focal plane arrays for astronomy and remote sensing applications at RVS (2010)

Raytheon Vision Systems (RVS) arrays are being deployed world-wide in ground based and space based platforms. RVS has a family of high performance visible through far infrared detector arrays for astronomy and civil space applications. Unique and off-the-shelf product lines are readily available to the community. Large sensor chip assemblies using various detector materials like Si PIN, HgCdTe, InSb, and Si:As IBC, covering a detection range from visible (400nm) to mid-wave infrared (28μm, MWIR) have been demonstrated with excellent quantum efficiency, dark current, and uniformity. These focal plane arrays have been designed using state-of-the-art low noise, low power, and radiation hardened readout integrated circuits. Complete with optical filters, opto-mechanical packaging, active thermal cooling with matching thermal straps, and optional electronics, RVS provides complete solutions for a multitude of sensor types and mission objectives. This paper describes the recent developments of focal plane assemblies for upcoming missions and telescope platforms.
Data from Identification and Validation of T-cell Receptors Targeting <i>RAS</i> Hotspot Mutations in Human Cancers for Use in Cell-based Immunotherapy (2023)

&lt;div&gt;AbstractPurpose:&lt;p&gt;Immunotherapies mediate the regression of human tumors through recognition of tumor antigens by immune cells that trigger an immune response. Mutations in the &lt;i&gt;RAS&lt;/i&gt; oncogenes occur in about 30% of all patients with cancer. These mutations play an important role in both tumor establishment and survival and are commonly found in hotspots. Discovering T-cell receptors (TCR) that recognize shared mutated RAS antigens presented on MHC class I and class II molecules are thus promising reagents for “off-the-shelf” adoptive cell therapies (ACT) following insertion of the TCRs into lymphocytes.&lt;/p&gt;Experimental Design:&lt;p&gt;In this ongoing work, we screened for RAS antigen recognition in tumor-infiltrating lymphocytes (TIL) or by &lt;i&gt;in vitro&lt;/i&gt; stimulation of peripheral blood lymphocytes (PBL). TCRs recognizing mutated RAS were identified from the reactive T cells. The TCRs were then reconstructed and virally transduced into PBLs and tested.&lt;/p&gt;Results:&lt;p&gt;Here, we detect and report multiple novel TCR sequences that recognize nonsynonymous mutant RAS hotspot mutations with high avidity and specificity and identify the specific class-I and -II MHC restriction elements involved in the recognition of mutant RAS.&lt;/p&gt;Conclusions:&lt;p&gt;The TCR library directed against RAS hotspot mutations described here recognize RAS mutations found in about 45% of the Caucasian population and about 60% of the Asian population and represent promising reagents for “off-the-shelf” ACTs.&lt;/p&gt;&lt;/div&gt;
The Sense-City project (2015)

A large scale equipment project, the Sense-City Equipex has received support from the French government in the framework of the 'Programme d’Investissement d’Avenir'. This project is led by the French Institute of Science and Technology for Transport, Development and Networks (IFSTTAR) with ESIEE-Paris, the Laboratory of Physics of Interfaces and Thin Films (LPICM) and the Scientific and Technical Centre for Building (CSTB) as consortium partners. Starting in 2012, Sense-City will offer a suite of high-quality facilities for the design, prototyping and performance assessment of innovative, micro- and nanotechnology based sensors devoted to urban instrumentation. Acknowledging the shortcomings of evaluating sensors performances in laboratory conditions only or in the ever-changing environment of our cities, Sense-City will provide a realistic urban test space in climatic conditions, far more complex than clean rooms and far less complex than actual cities. Sense-city revolves around the 'mini-city' concept, a large, fully customizable climatic hall able to host full- and reduced-scale models of essential urban components. The design of the models will allow for the simulation in climatic conditions of numerous scenarios of sustainable cities. The scenarios to be implemented will correspond to different research topics related to urban sustainability: energy performances in buildings, quality of air, water and soils, quality of fluid distribution networks (gas, sewage, drink water), control of waste disposal areas, durability and safety of infrastructures.
Crystal structures of dichloromethane solvate and ethanol solvate of 1 -chloromethyl-1,4,7-trimethyl-triazonan-1 -ium chloride, (C10H23N3Cl)Cl · CH2Cl2, (C10H23N3Cl)Cl · C2H5OH (2005)

Article Crystal structures of dichloromethane solvate and ethanol solvate of 1 -chloromethyl-1,4,7-trimethyl-triazonan-1 -ium chloride, (C10H23N3Cl)Cl · CH2Cl2, (C10H23N3Cl)Cl · C2H5OH was published on April 1, 2005 in the journal Zeitschrift für Kristallographie - New Crystal Structures (volume 220, issue 1-4).
A Wideband Sliding Correlation Channel Sounder in 65 nm CMOS: Evaluation Board Performance (2021)

Emerging applications such as wireless sensing, position location, robotics, and many more are driven by the ultra-wide bandwidths available at millimeter-wave (mmWave) and Terahertz (THz) frequencies. The characterization and efficient utilization of wireless channels at these extremely high frequencies require detailed knowledge of the radio propagation characteristics of the channels. Such knowledge is developed through empirical observations of operating conditions using wireless transceivers that measure the impulse response through channel sounding. Today, cutting-edge channel sounders rely on several bulky RF hardware components with complicated interconnections, large parasitics, and sub-GHz RF bandwidth. This brief presents a compact sliding correlation-based channel sounder baseband built on a monolithic integrated circuit (IC) using 65 nm CMOS, implemented as an evaluation board achieving a 2 GHz RF bandwidth. The IC is the world's first gigabit-per-second channel sounder baseband implemented in low-cost CMOS. The presented single-board system can be employed at both the transmit and receive baseband to study multipath characteristics and path loss. Thus, the single-board implementation provides an inexpensive and compact solution for sliding correlation-based channel sounding with 1 ns multipath delay resolution.
Data from Selectin Ligand Sialyl-Lewis x Antigen Drives Metastasis of Hormone-Dependent Breast Cancers (2023)

&lt;div&gt;Abstract&lt;p&gt;The glycome acts as an essential interface between cells and the surrounding microenvironment. However, changes in glycosylation occur in nearly all breast cancers, which can alter this interaction. Here, we report that profiles of glycosylation vary between ER-positive and ER-negative breast cancers. We found that genes involved in the synthesis of sialyl-Lewis x (sLe&lt;sup&gt;x&lt;/sup&gt;; &lt;i&gt;FUT3, FUT4&lt;/i&gt;, and &lt;i&gt;ST3GAL6&lt;/i&gt;) are significantly increased in estrogen receptor alpha-negative (ER-negative) tumors compared with ER-positive ones. SLe&lt;sup&gt;x&lt;/sup&gt; expression had no influence on the survival of patients whether they had ER-negative or ER-positive tumors. However, high expression of sLe&lt;sup&gt;x&lt;/sup&gt; in ER-positive tumors was correlated with metastasis to the bone where sLe&lt;sup&gt;x&lt;/sup&gt; receptor E-selectin is constitutively expressed. The ER-positive ZR-75-1 and the ER-negative BT20 cell lines both express sLe&lt;sup&gt;x&lt;/sup&gt; but only ZR-75-1 cells could adhere to activated endothelial cells under dynamic flow conditions in a sLe&lt;sup&gt;x&lt;/sup&gt; and E-selectin–dependent manner. Moreover, L/P-selectins bound strongly to ER-negative MDA-MB-231 and BT-20 cell lines in a heparan sulfate (HS)–dependent manner that was independent of sLe&lt;sup&gt;x&lt;/sup&gt; expression. Expression of glycosylation genes involved in heparan biosynthesis (&lt;i&gt;EXT1&lt;/i&gt; and &lt;i&gt;HS3ST1&lt;/i&gt;) was increased in ER-negative tumors. Taken together, our results suggest that the context of sLe&lt;sup&gt;x&lt;/sup&gt; expression is important in determining its functional significance and that selectins may promote metastasis in breast cancer through protein-associated sLe&lt;sup&gt;x&lt;/sup&gt; and HS glycosaminoglycans. &lt;i&gt;Cancer Res; 71(24); 7683–93. ©2011 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Space Filling Curves: Its Design and Fabrication for Extrusion Based SFF Systems (2005)

Scaffolds with designed interior pore architecture, predefined porosity and a well interconnected predetermined network has been the most favored design approach for tissue engineering applications. Solid freeform fabrication technologies have provided the capability of fabricating tissue scaffolds with desired characteristics due to its integration with CAD enabled tools. However, currently the interior macro pore design of scaffolds have been limited to simple regular shapes of either squares or circles due to limited CAD capability. In this paper we seek to enhance the design of the scaffold architecture by using space filling curves within its interior space. The process involves: definition and characterization of space filling curves such as the Hilbert Curve and Sierpinski Curves, applying the principle of layered manufacturing to determine the scaffold individual layered process planes and layered contours; Feasibility studies applying the curve generators to sample models and the generation of fabrication planning instructions for extrusion based SFF systems is presented.