gebhart/patrepeval huggingface dataset:
The future of antibiotics begins with discovering new combinations (2021)

Antibiotic resistance is a worldwide and growing clinical problem. With limited drug development in the antibacterial space, combination therapy has emerged as a promising strategy to combat multidrug-resistant bacteria. Antibacterial combinations can improve antibiotic efficacy and suppress antibacterial resistance through independent, synergistic, or even antagonistic activities. Combination therapies are famously used to treat viral and mycobacterial infections and cancer. However, antibacterial combinations are only now emerging as a common treatment strategy for other bacterial infections owing to challenges in their discovery, development, regulatory approval, and commercial/clinical deployment. Here, we focus on discovery-where the sheer scale of combinatorial chemical spaces represents a significant challenge-and discuss how combination therapy can impact the treatment of bacterial infections. Despite these challenges, recent advancements, including new in silico methods, theoretical frameworks, and microfluidic platforms, are poised to identify the new and efficacious antibacterial combinations needed to revitalize the antibacterial drug pipeline.
Origin of transparency in scattering biomimetic collagen materials (2020)

Living tissues, heterogeneous at the microscale, usually scatter light. Strong scattering is responsible for the whiteness of bones, teeth, and brain and is known to limit severely the performances of biomedical optical imaging. Transparency is also found within collagen-based extracellular tissues such as decalcified ivory, fish scales, or cornea. However, its physical origin is still poorly understood. Here, we unveil the presence of a gap of transparency in scattering fibrillar collagen matrices within a narrow range of concentration in the phase diagram. This precholesteric phase presents a three-dimensional (3D) orientational order biomimetic of that in natural tissues. By quantitatively studying the relation between the 3D fibrillar network and the optical and mechanical properties of the macroscopic matrices, we show that transparency results from structural partial order inhibiting light scattering, while preserving mechanical stability, stiffness, and nonlinearity. The striking similarities between synthetic and natural materials provide insights for better understanding the occurring transparency.
An 80 Gbit/s 1:2 demultiplexer in InP-based HEMT technology (2004)

An 80 Gbit/s 1:2 demultiplexer (DEMUX) is presented that was fabricated using 0.1-/spl mu/m-gate-length InP-based HEMT technology. A data input buffer with a common-gate amplifier in front is employed to achieve a low return loss over wide frequency range and to suppress signal distortion, which is mainly caused by multiple reflections between a DEMUX chip and a signal source. A DEMUX core consisting of a D-type flip-flop (FF) and a tri-stage FF assures the edge alignment of two channels of de-serialized signals. The 1:2 DEMUX operated at up to 80 Gbit/s, which was limited by our measurement equipment. At that bit-rate, the input sensitivity and clock phase margin estimated from monitoring eye-openings were about 100 mVp-p and 160 degrees, respectively. The skew of the two output signals was only 2 ps.
System Design for Large OLED Displays (2006)

Large AMOLED displays with performance competitive with LCD displays are possible with current OLED materials and backplane technology. The choice of architecture, design, and driving methods are discussed along with next-generation manufacturing technology. Article not available.
Host Identity Protocol (HIP) Architecture (2006)

This memo describes a snapshot of the reasoning behind a proposed new
namespace, the Host Identity namespace, and a new protocol layer, the
Host Identity Protocol (HIP), between the internetworking and
transport layers. Herein are presented the basics of the current
namespaces, their strengths and weaknesses, and how a new namespace
will add completeness to them. The roles of this new namespace in the
protocols are defined. The memo describes the thinking of the authors
as of Fall 2003. The architecture may have evolved since. This
document represents one stable point in that evolution of
understanding. This memo provides information for the Internet
community.
Radical Additions of Xanthates to Vinyl Epoxides and Related Derivatives: A Powerful Tool for the Modular Creation of Quaternary Centers (2006)

An open relationship: The triethylborane/O2-mediated addition of xanthates to vinyl epoxides and derivatives represents an efficient process to form carbon–carbon bonds. Complex structures can be rapidly assembled in a modular, convergent manner, under mild conditions, using readily available reagents (see scheme, Bn=benzyl). The formation of quaternary centers proved especially facile.
Partial Oxidation of Butane at Microsecond Contact Times (1996)

Using a single layer of woven Pt/Rh gauze as a chemical reactor for the oxidation of n-butane, we find it possible to achieve greater than 90% oxygen conversion with high selectivity to olefins and oxygenated hydrocarbons at contact times on the order of 100 μsec at atmospheric pressure. This reactor configuration operates by rapidly heating the reactants to temperatures greater than 800°C in about 5 μsec followed by rapid quenching to avoid homogeneous chain branching reactions between butane and oxygen. The highly transparent gauze allows most of the reactants to pass between the wires of the gauze without undergoing reaction or being appreciably heated. This gas then mixes with hot products produced on the wire surface or within the boundary layer about the wires to rapidly quench and preserve intermediate products. It is critical to quench the products to temperature around 400°C within less than 1 msec to avoid successive homogeneous decomposition reactions of intermediates such as olefins and aldehydes. This process is capable of directly producing oxygenates and olefins at carbon selectivities of greater than 70%.
Layperson's Esthetic Preference to the Presence or Absence of the Interdental Papillae in the Low Smile Line: A Web‐based Study (2019)

The visual display [presence] of the interdental papillae, that is, pink tissues, is notably preferred to the absence of the interdental papillae when replaced by either a "black triangle" or long contact area in the commonly known low smile line. This emphasizes the need to assess the Interdental Smile Line (ie, visual display of interdental papillae during smiling) in all patients and the importance to preserve and/or re-establishment of the interdental papillae, that is, pink tissues, even in patients with a low smile line.
ChemInform Abstract: Z‐Shaped Pyrrolo[3,2‐b]pyrroles and Their Transformation into π‐Expanded Indolo[3,2‐b]indoles. (2016)

Abstract The unique Z‐shaped pyrrolopyrrole dyes show relatively strong fluorescence in solution.
Presence of Double-Stranded RNAs in Human and Calf Isolates of Cryptosporidium parvum (2000)

Nikolai V. Khramtsov, Peter A. Chung, Christine C. Dykstra, Jeffrey K. Griffiths, Una M. Morgan, Michael J. Arrowood, Steve J. Upton, Presence of Double-Stranded RNAs in Human and Calf Isolates of Cryptosporidium parvum, The Journal of Parasitology, Vol. 86, No. 2 (Apr., 2000), pp. 275-282
Detection of a transformation-related antigen in chemically induced sarcomas and other transformed cells of the mouse. (1979)

Antisera prepared against BALB/c Meth A sarcoma in syngeneic or compatible F1 mice recognize a protein with an apparent molecular weight of 53,000 in extracts of [35S]methionine-labeled transformed BALB/c cells. This component, designated p53, was not detected in normal adult mouse fibroblasts, lymphoid cells, or hematopoietic cells or in mouse embryo cells or 3T3 cells. An extensive variety of antisera, including alloantisera and heterologous antisera directed against structural antigens of murine leukemia viruses, was tested for reactivity with p53; other than Meth A antisera, only comparably prepared antisera against another BALB/c sarcoma, CMS4, had anti-p53 activity. All transformed mouse cells tested were found to express p53; these tests included chemically induced sarcomas, leukemias, spontaneously transformed fibroblasts, and cells transformed by simian virus 40 and murine sarcoma virus. The presence of p53 in tumors of no known viral etiology indicates coding by resident cellular genes; this does not exclude endogenous viruses as the source of coding sequences or the possibility that transforming viruses code directly for p53.
Generation and interaction of parabolic pulses in high gain fiber amplifiers and oscillators (2001)

Parabolic pulses are generated from ultrashort pulse amplification in a high gain normal dispersion fiber amplifier. The pulses are robust against interactions and collisions and can be conveniently generated in a fiber laser configuration.
Microfluidic Isotachophoresis: Theory and Applications (2021)

Isotachophoresis (ITP) is a versatile electrophoretic technique which can be used for sample preconcentration, separation, purification, mixing, and control and acceleration of chemical reactions. Although the basic technique is nearly a century old and widely used, there has been a persistent need for an easily approachable, succinct, and rigorous review of ITP theory and analysis. This is important as interest and adoption of the technique has grown over the last two decades, especially because of its implementation into microfluidics and integration with on-chip chemical and biochemical assays. We here provide a review of ITP theory with a strong emphasis on steady and unsteady transport starting from physicochemical first principles including conservation of species, conservation of current, the approximation of charge neutrality, pH equilibrium of weak electrolytes, and so-called regulating functions governing transport dynamics. We combine these generally applicable (to all types of ITP) theoretical discussions with applications of ITP in the field of microfluidic systems, particularly on-chip biochemical analyses. Our discussion includes principles governing ITP focusing of weak and strong electrolytes, ITP dynamics in peak and plateau modes, review of simulation tools, experimental tools and detection methods, applications of ITP for on-chip separations and trace analyte manipulation, and design considerations and challenges for microfluidic ITP systems. We conclude with remarks on possible future research directions. The intent of this review is to help make ITP analysis and design principles more accessible to the scientific and engineering communities, and to provide a rigorous basis for increased adoption of ITP into microfluidics.
Probing Cu doped Ge0.3Se0.7 based resistance switching memory devices with random telegraph noise (2010)

The ultimate sensitivity of any solid state device is limited by fluctuations. Fluctuations are manifestations of the thermal motion of matter and the discreteness of its structure which are also inherent ingredients during the resistive switching process of resistance random access memory (RRAM) devices. In quest for the role of fluctuations in different memory states and to develop resistive switching based nonvolatile memory devices, here we present our study on random telegraph noise (RTN) resistance fluctuations in Cu doped Ge0.3Se0.7 based RRAM cells. The influence of temperature and electric field on the RTN fluctuations is studied on different resistance states of the memory cells to reveal the dynamics of the underlying fluctuators. Our analysis indicates that the observed fluctuations could arise from thermally activated transpositions of Cu ions inside ionic or redox “double-site traps” triggering fluctuations in the current transport through a filamentary conducting path. Giant RTN fluctuations characterized by relative resistance variations of up to 50% in almost macroscopic samples clearly point to the existence of weak links with small effective cross-sectional areas along the conducting paths. Such large resistance fluctuations can be an important issue for the industrial applications of RRAM devices because they might lead to huge bit-error rates during reading cycles.
Sandwich-Type Germanotungstates:  Structure and Magnetic Properties of the Dimeric Polyoxoanions [M4(H2O)2(GeW9O34)2]12- (M = Mn2+, Cu2+, Zn2+, Cd2+) (2004)

The novel dimeric germanotungstates [M(4)(H(2)O)(2)(GeW(9)O(34))(2)](12)(-) (M = Mn(2+), Cu(2+), Zn(2+), Cd(2+)) have been synthesized and characterized by IR spectroscopy, elemental analysis, magnetic measurements, and (183)W-NMR spectroscopy. X-ray single-crystal analyses were carried out on Na(12)[Mn(4)(H(2)O)(2)(GeW(9)O(34))(2)].38H(2)O (Na(12)()-1), which crystallizes in the monoclinic system, space group P2(1)/n, with a = 13.0419(8) A, b = 17.8422(10) A, c = 21.1626(12) A, beta = 93.3120(10) degrees, and Z = 2; Na(11)Cs(2)[Cu(4)(H(2)O)(2)(GeW(9)O(34))(2)]Cl.31H(2)O (Na(11)()Cs-2) crystallizes in the triclinic system, space group P, with a = 12.2338(17) A, b = 12.3833(17) A, c = 15.449(2) A, alpha = 100.041(2) degrees, beta = 97.034(2) degrees, gamma = 101.153(2) degrees, and Z = 1; Na(12)[Zn(4)(H(2)O)(2)(GeW(9)O(34))(2)].32H(2)O (Na(12)()-3) crystallizes in the triclinic system, space group P, with a = 11.589(3) A, b = 12.811(3) A, c = 17.221(4) A, alpha = 97.828(6) degrees, beta = 106.169(6) degrees, gamma = 112.113(5) degrees, and Z = 1; Na(12)[Cd(4)(H(2)O)(2)(GeW(9)O(34))(2)].32.2H(2)O (Na(12)()-4) crystallizes also in the triclinic system, space group P, with a = 11.6923(17) A, b = 12.8464(18) A, c = 17.616(2) A, alpha = 98.149(3) degrees, beta = 105.677(3) degrees, gamma = 112.233(2) degrees, and Z = 1. The polyanions consist of two lacunary B-alpha-[GeW(9)O(34)](10)(-) Keggin moieties linked via a rhomblike M(4)O(16) (M = Mn, Cu, Zn, Cd) group leading to a sandwich-type structure. (183)W-NMR studies of the diamagnetic Zn and Cd derivatives indicate that the solid-state polyoxoanion structures are preserved in solution. EPR measurements on Na(12)()-1 at frequencies up to 188 GHz and temperatures down to 4 K yield a single, exchange-narrowed peak, at g(iso) = 1.9949, typical of Mn systems, and an upper limit of |D| = 20.0 mT; its magnetization studies still await further theoretical treatment. Detailed EPR studies on Na(11)()Cs-2 over temperatures down to 2 K and variable frequencies yield g( parallel ) = 2.4303 and g( perpendicular ) = 2.0567 and A( parallel ) = 4.4 mT (delocalized over the Cu(4) framework), with |D| = 12.1 mT. Magnetization studies in addition yield the exchange parameters J(1) = -11 and J(2) = -82 cm(-)(1), in agreement with the EPR studies.
Disturbance Rejection Control in Motorcycle that Considers Cooperativeness with the Rider’s Driving Operation (2008)

&lt;div class="htmlview paragraph"&gt;It’ll be expected that tandem riders increase in the future. So, there is a need to improve the motorcycle stability of tandem riding from the perspectives of safety and comfort. In this research, we focus on tandem riding at low speed because the motorcycle especially becomes unstable. In order to improve the stability of a motorcycle after disturbance is input by the passenger’s posture change, we design a front wheel steer control system that assists the rider’s driving operation. And we simulate it. It is necessary to consider cooperation with the rider’s driving operation. In this study, as a means to consider the cooperative control of the man-machine system, the fuzzy logic was applied to this system.&lt;/div&gt;
Sound Generation in a Thermoacoustic Microscope (1986)

Using an exact, three-dimensional, Green's function solution to the thermoelastic equations in semi-infinite solid, we have calculated the relative generation efficiencies of thermal waves, longitudinal acoustic waves and transverse acoustic waves induced by a periodically modulated beam of light or particles. The angular distributions and strengths of energy transfer and momentum transfer contributions are compared. Scattering and mode-conversion effects are discussed. Theory Thermoacoustic microscopes' are devices which generate sound in solids by means of focused beams of light or particles (either electrons or ions). These beams may be either pulsed or periodically modulated and, loosely speaking, generate sound through the response of the solid to the energy and momentum they deposit in it. The detection of that sound is accomplished by means of an acoustic transducer somewhere on the surface of the solid, and the microscopic image is generated by recording the signal from the transducer as the beam is scanned over the region of interest. In this paper we present a detailed, three-dimensional theory for the generation of sound in such a microscope. The starting point for the calculation is the (linearized) set of equations2 which describe the conservation of energy and momentum in the solid,
A Motif Co-Occurrence Approach for Genome-Wide Prediction of Transcription-Factor-Binding Sites inEscherichia coli (2004)

Various computational approaches have been developed for predicting cis-regulatory DNA elements in prokaryotic genomes. We describe a novel method for predicting transcription-factor-binding sites in Escherichia coli. Our method takes advantage of the principle that transcription factors frequently coregulate gene expression, but without requiring prior knowledge of which groups of genes are coregulated. Using position weight matrices for 49 known transcription factors, we examined spacings between pairs of matrix hits. These pairs were assigned probabilities according to the overrepresentation of their separation distance. The functions of many open reading frames (ORFs) downstream from predicted binding sites are unknown, and may correspond to novel regulon members. For five predictions, knockouts with mutated replacements of the predicted binding sites were created in E. coli MG1655. Quantitative real-time PCR (RT-PCR) indicates that for each of the knockouts, at least one gene immediately downstream exhibits a statistically significant change in mRNA expression. This approach may be useful in analyzing binding sites in a variety of organisms.
Automated detection of motion in breast DCE-MRI to assess study quality and prevent unnecessary call-backs (2015)

Poster: ECR 2015 / C-1845 / Automated detection of motion in breast DCE-MRI to assess study quality and prevent unnecessary call-backs by: L. Wang1, A. Gubern Merida2, O. Diaz3, Y. Diez3, R. M. Mann2, S. Diekmann1, F. Zohrer1, H. Laue1, J. Schwaab4; 1Bremen/DE, 2Nijmegen/NL, 3Girona/ES, 4Heidelberg/DE
Segmental Replacement of the Femur in Baboons with Fiber Metal Implants and Autologous Bone Grafts of Different Particle Size (1982)

A study was made of bone ingrowth into fiber metal composite prostheses used to replace large segments of the femur in baboons. Bone grafts of two different types were used to cover the segment: chips of bone with large particle size and ground bone with a smaller particle size. The prosthetic segment was bridged by bone at 3 and 6 months in all cases irrespective of the structure of the transplant. In animals sacrificed at 6 months bone ingrowth occurred, with a marked difference between specimens with the two different grafts. In the ground bone specimens ingrowth occurred over the total surface area, and bone penetrated deep into the composite. With the chip grafts ingrowth was more irregular occurring only in some areas and it was always superficial. The difference is believed to be due to the improved contact between the fiber metal surface and the transplant. The lesser bulk of the ground transplant is advantageous when the soft tissue cover of the bone is thin.
Coupling Multiphase Hydrodynamic and NMR Pore-Scale Modeling for Advanced Characterization of Saturated Rocks (2015)

We use the novel method of the density functional hydrodynamics (DFH) [1 – 4] to model complex multiphase scenarios occurring in natural cores on a pore-scale. Such scenarios may be extremely diverse, ranging from those inherent in RCA and SCAL measurements, and to much more complex processes relevant to chemical EOR. We perform the numerical simulation of several multiphase flow scenarios by means of the direct hydrodynamic (DHD) simulator, which is a numerical code containing implementation of DFH. We have demonstrated some of the capabilities of our numerical tool, DHD, for simulation of multiphase flow previously [4 – 6]. Now we focus on a combination of two different methods for characterization of a multiphase system in pores. The first method comes from hydrodynamic and thermodynamic description obtained through DHD simulation. The second method emerges from numerical modeling of NMR response corresponding to T2 relaxation and pulsed gradient spin-echo (PGSE) experiments [7 – 10], which are routinely conducted not only in laboratory, but also downhole using NMR logging tools. We model the NMR response by solving numerically the generalized Bloch-Torrey equations [11] containing relaxation, diffusion and magnetization transport terms. The equations are subject to boundary conditions describing surface relaxation. The NMR description we use enables performing modeling of T2 relaxation and PGSE experiments, and their combination. The numerical NMR solver is also implemented within the DHD simulator. This facilitates application of NMR modeling (i.e., makes it automatic) to digitized cores with multiphase saturation, whose state has previously been described and simulated in the frame of the DFH. Such close coupling of two characterization methods different by nature is extremely important and brings an opportunity for improvement of NMR response interpretation techniques, which suffer from the inverse and ill-posed nature of the fluids characterization problem.
Abstract IA17: Functional genomics, small RNAs and cancer (2012)

Abstract Efforts to sequence cancer genomes have begun to uncover comprehensive lists of genes altered in cancer. Unfortunately, the complexity and sheer volume of data that emerges from these efforts has made dissecting the underlying biology of cancer difficult. In addition, the number and types of candidate targets that require functional validation in vivo represent a significant barrier to using this information as a starting point for drug development programs, since many do not represent targets amenable to traditional small molecule or antibody-based therapeutic approaches. To address this problem, we have combined comprehensive analyses of cancer genomes with novel materials science to develop a platform that enables the ready in vivo validation of cancer targets. Specifically, we have developed a screening platform to perform loss of function screens at genome scale and have applied this in a massively parallel manner to screen several hundred full characterized cancer cell lines. We have combined the outputs of these screens with data emerging from the study of cancer genomes to identify candidate oncogenes. To credential these targets in vivo, we have helped develop novel nanocomplexes formed from siRNA bound to tandem peptides containing tumor-penetrating, endosomal escape and siRNA-binding domains that permit deep penetration in tumor. We use these nanoparticles to target a hitherto undiscovered ovarian cancer oncogene, ID4, an undruggable transcriptional regulator, and show that these tumor-penetrating nanocomplexes induced complete suppression of tumor growth and significant improvement of survival. Taken together, these studies provide a platform for the discovery and initial validation of candidate cancer targets. Citation Format: William C. Hahn. Functional genomics, small RNAs and cancer [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer; 2012 Jan 8-11; Miami Beach, FL. Philadelphia (PA): AACR; Cancer Res 2012;72(2 Suppl):Abstract nr IA17.