gebhart/patrepeval huggingface dataset:
Association between Predicted Effects of TP53 Missense Variants on Protein Conformation and Their Phenotypic Presentation as Li-Fraumeni Syndrome or Hereditary Breast Cancer (2021)

Rare germline pathogenic <i>TP53</i> missense variants often predispose to a wide spectrum of tumors characterized by Li-Fraumeni syndrome (LFS) but a subset of variants is also seen in families with exclusively hereditary breast cancer (HBC) outcomes. We have developed a logistic regression model with the aim of predicting LFS and HBC outcomes, based on the predicted effects of individual <i>TP53</i> variants on aspects of protein conformation. A total of 48 missense variants either unique for LFS (<i>n</i> = 24) or exclusively reported in HBC (<i>n</i> = 24) were included. LFS-variants were over-represented in residues tending to be buried in the core of the tertiary structure of TP53 (<i>p</i> = 0.0014). The favored logistic regression model describes disease outcome in terms of explanatory variables related to the surface or buried status of residues as well as their propensity to contribute to protein compactness or protein-protein interactions. Reduced, internally validated models discriminated well between LFS and HBC (C-statistic = 0.78-0.84; equivalent to the area under the ROC (receiver operating characteristic) curve), had a low risk for over-fitting and were well calibrated in relation to the known outcome risk. In conclusion, this study presents a phenotypic prediction model of LFS and HBC risk for germline <i>TP53</i> missense variants, in an attempt to provide a complementary tool for future decision making and clinical handling.
ChemInform Abstract: SYNTH. VON (+-)-GRANDISOL (1973)

Die Synthese der Titelverbindung (V) basiert auf der Verwendung von Ni(O)- Komplexen zur katalytischen Darstellung von cis-1,2-Divinyl-cyclobutanen au 1,3-Dienen.
Abstract B22: Dynamics of cancer cell survival dependency on Bcl-2 family members (2009)

Abstract Apoptosis is regulated through the interactions of the Bcl-2 family of proteins. Overexpression of anti-apoptotic Bcl-2 family members plays a key role in promoting survival for cells undergoing various insults that would normally trigger cell death. Consequently, these proteins are believed to serve as contributing factors to the processes of tumor initiation, tumor progression and the development of resistance to therapeutics. ABT-263, an antagonist of Bcl-2, Bcl-xL, and Bcl-w, is currently being tested in clinical trials. Some cancer cells express high amounts of Mcl-1, another Bcl-2 family anti-apoptotic protein that shares pro-survival function with Bcl-2 but is not targeted by ABT-263. Preclinical data indicates Mcl-1 overexpressing cells are not sensitive to ABT-263. To understand this mechanism of Mcl-1 dependence, A2058 melanoma cells were infected with a lentivirus encoding inducible shRNA against Mcl-1. Upon induction of MCL1 knockdown, massive cell death occurred. Interestingly, a small subset of the cell population managed to survive. Subsequent western blot analysis confirmed a sustained depletion of Mcl-1. Further study indicated A2058 cells deficient in Mcl-1 survived by upregulating expression of Bcl-2, a process we term “switching dependency”. In addition, these cells became sensitized to ABT-263 treatment. An A2058 xenograft model indicates that combined knockdown of both Mcl-1 and Bcl-2 significantly inhibited tumor growth when compared to tumors treated with ABT-263 lacking either protein individually. Real-time kinetic studies reveal a rapid sensitization of A2058 cells to ABT-263 upon sh-RNA induction. To understand whether de novo protein synthesis of Bcl-2 plays a mechanistic role in dependency switching, A2058 sh-Mcl-1 cells were treated with the protein synthesis inhibitor cycloheximide. Kinetic analysis indicates that de novo protein synthesis is not required for dependency switching. Real-time quantitative PCR was then employed to determine if a relationship exists between the decrease in Mcl-1 mRNA, and subsequent sensitivity to ABT-263, is a consequence of a change in Bcl-2 mRNA levels. Surprisingly, the results indicate as the loss of Mcl-1 message occurs, there is no concurrent change in Bcl-2 mRNA. Taken together these data indicate that dependency switching, and therefore survival, occurs without de novo Bcl-2 protein synthesis or alterations in protein turnover. Furthermore, dependency switching is a possible mechanism cancer cells employ to develop resistance toward various anti-cancer therapies with novel implications for both the concept of oncogene addiction and development of targeted cancer therapeutics. Therefore there is an immediate need for elucidation of this novel cancer resistance mechanism. Citation Information: Mol Cancer Ther 2009;8(12 Suppl):B22.
Thermal Probe Maskless Lithography for 27.5 nm Half-Pitch Si Technology (2013)

Thermal scanning probe lithography is used for creating lithographic patterns with 27.5 nm half-pitch line density in a 50 nm thick high carbon content organic resist on a Si substrate. The as-written patterns in the poly phthaladehyde thermal resist layer have a depth of 8 nm, and they are transformed into high-aspect ratio binary patterns in the high carbon content resist using a SiO2 hard-mask layer with a thickness of merely 4 nm and a sequence of selective reactive ion etching steps. Using this process, a line-edge roughness after transfer of 2.7 nm (3σ) has been achieved. The patterns have also been transferred into 50 nm deep structures in the Si substrate with excellent conformal accuracy. The demonstrated process capabilities in terms of feature density and line-edge roughness are in accordance with today's requirements for maskless lithography, for example for the fabrication of extreme ultraviolet (EUV) masks.
Feshbach resonances in an optical lattice (2005)

We present a theory for ultracold atomic gases in an optical lattice near a Feshbach resonance. In the single-band approximation the theory describes atoms and molecules that can both tunnel through the lattice. Moreover, an avoided crossing between the two-atom and the molecular states occurs at every site. We determine the microscopic parameters of the generalized Hubbard model that describes this physics, using the experimentally known parameters of the Feshbach resonance in the absence of the optical lattice. As an application we also calculate the zero-temperature phase diagram of an atomic Bose gas in an optical lattice.
Random Coding Exponent for MIMO Channels (2008)

We derive Gallager's random coding error exponent for multiple-input multiple-output (MIMO) channels, assuming no channel-state information (CSI) at the transmitter and perfect CSI at the receiver. This measure gives insight into a fundamental tradeoff between the communication reliability and information rate of MIMO channels, enabling to determine the required codeword length to achieve a prescribed error probability at a given rate below the channel capacity. We quantify the effects of the number of antennas, channel coherence time, and spatial fading correlation on the MIMO exponent. In addition, the general formulae for the ergodic capacity and the cutoff rate in the presence of spatial correlation are deduced from the exponent expressions. These formulae are applicable to arbitrary structures of transmit and receive correlation, encompassing all the previously known results as special cases of our expressions.
The SOL Genomics Network. A Comparative Resource for Solanaceae Biology and Beyond (2005)

The SOL Genomics Network (SGN; http://sgn.cornell.edu) is a rapidly evolving comparative resource for the plants of the Solanaceae family, which includes important crop and model plants such as potato (Solanum tuberosum), eggplant (Solanum melongena), pepper (Capsicum annuum), and tomato (Solanum lycopersicum). The aim of SGN is to relate these species to one another using a comparative genomics approach and to tie them to the other dicots through the fully sequenced genome of Arabidopsis (Arabidopsis thaliana). SGN currently houses map and marker data for Solanaceae species, a large expressed sequence tag collection with computationally derived unigene sets, an extensive database of phenotypic information for a mutagenized tomato population, and associated tools such as real-time quantitative trait loci. Recently, the International Solanaceae Project (SOL) was formed as an umbrella organization for Solanaceae research in over 30 countries to address important questions in plant biology. The first cornerstone of the SOL project is the sequencing of the entire euchromatic portion of the tomato genome. SGN is collaborating with other bioinformatics centers in building the bioinformatics infrastructure for the tomato sequencing project and implementing the bioinformatics strategy of the larger SOL project. The overarching goal of SGN is to make information available in an intuitive comparative format, thereby facilitating a systems approach to investigations into the basis of adaptation and phenotypic diversity in the Solanaceae family, other species in the Asterid clade such as coffee (Coffea arabica), Rubiaciae, and beyond.
Mobile Educational Augmented Reality Games: A Systematic Literature Review and Two Case Studies (2018)

Augmented reality (AR) has evolved from research projects into mainstream applications that cover diverse fields, such as entertainment, health, business, tourism and education. In particular, AR games, such as Pokémon Go, have contributed to introducing the AR technology to the general public. The proliferation of modern smartphones and tablets with large screens, cameras, and high processing power has ushered in mobile AR applications that can provide context-sensitive content to users whilst freeing them to explore the context. To avoid ambiguity, I define mobile AR as a type of AR where a mobile device (smartphone or tablet) is used to display and interact with virtual content that is overlaid on top of a real-time camera feed of the real world. Beyond being mere entertainment, AR and games have been shown to possess significant affordances for learning. Although previous research has done a decent job of reviewing research on educational AR applications, I identified a need for a comprehensive review on research related to educational mobile AR games (EMARGs). This paper explored the research landscape on EMARGs over the period 2012–2017 through a systematic literature review complemented by two case studies in which the author participated. After a comprehensive literature search and filtering, I analyzed 31 EMARGs from the perspectives of technology, pedagogy, and gaming. Moreover, I presented an analysis of 26 AR platforms that can be used to create mobile AR applications. I then discussed the results in depth and synthesized my interpretations into 13 guidelines for future EMARG developers.
Artifacts In Magnetic Resonance Imaging and Computed Tomography Caused By Dental Materials (2012)

Metal based restoration materials had strong influence on CT and less artifacts in MRI images. Rare earth elements such as Ytterbium trifluoride found in composites caused artifacts in both MRI and CT. Recognizing these findings would help dental materials manufacturers and developers to produce materials which can cause less artifacts in MRI and CT images.
Intestinal Permeability, Gastric Intramucosal pH, and Systemic Endotoxemia in Patients Undergoing Cardiopulmonary Bypass (1996)

Cardiopulmonary bypass is associated with increases in gut permeability, which precede gut mucosal ischemia. In cardiac surgical patients, a low pHi is not necessarily indicative of an adverse clinical outcome. Endotoxemia as measured by the Limulus amebocyte lysate assay is common. The increased intestinal absorption of 51Cr-EDTA and gastric mucosal acidosis occur as independent phenomena and are not related in severity or time of onset.
CCDC 168262: Experimental Crystal Structure Determination (2002)

An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
Hybrid designs generating maximum-length sequences (1988)

Two hybrid schemes for the design of maximum-length sequence generators (MLSGs) are presented. Compared to an n-stage maximum-length LFSR (for generating 2/sup n/-1 nonzero distinct states) that uses m exclusive-or (XOR) gates, this hybrid MLSG will use exactly (m+1)/2 XOR gates if its characteristic polynomial meets certain requirements. For applications such as exhaustive testing, this hybrid MLSG is then reconfigured to include the all-zero state. It is shown that the reconfiguration is very simple and the hardware overhead is low.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
ChemInform Abstract: UNEXPECTED FORMATION OF P‐AMINOAZOBENZENE AT A RELATIVELY HIGH TEMPERATURE (1983)

Abstract Die Umsetzung von Dinitrotetrachlorbenzol (I) mit Anilin (II) liefert das Anilinonitrotetrachlorbenzol (III) und Nitrit (IV), das mit Anilin (II) zum Aminoazobenzol (V) weiterreagiert.
ChemInform Abstract: Synthesis of the Thymidine Building Blocks for a Nonhydrolyzable DNA Analogue (1993)

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.
Switching activity estimation using limited depth reconvergent path analysis (1997)

We describe a method of polynomial simulation to calculate switching activities in a general-delay combinational logic circuit. This method is a generalization of the exact signal probability evaluation method due to Parker and McCluskey, which as been extended to handle temporal correlation and arbitrary transport delays.
Water Jet‐Induced Circulation in Channel. III: Comparison with Aeration (1988)

Circulation and mixing of lakes and reservoirs resulting from air plumes brings a simultaneous buildup of dissolved oxygen. The same kind of circulation, but without direct oxygen addition, can be achieved with water jets which can, in addition, be set at any orientation. Measurements of the velocity profiles and circulation for water injection through a linear manifold in a channel are presented here and compared with those for aeration‐induced circulation. In particular, the velocity profiles above the manifold set at the channel bottom, lateral surface flow profiles, the extent of the circulation, and the influence of manifold position are described. The results are similar to those for aeration in most respects. For water‐injection rates to 2.3dm3/m⋅s (11 gpm/ft), the maximum lateral surface velocity was directly proportional to the rate and varied inversely with the square root of manifold depth. Surface current thickness increased linearly with lateral distance out to the end of the circulation cell at four times the depth. A simple equation is presented for the equivalence of flows induced by water jets and aeration.
Software - Implemented Self-healing System (2007)

The term “Self-healing” denotes the capability of a software system in dealing with bugs. Fault tolerance for dependable computing is to provide the specified service through rigorous design whereas self-healing is meant for run-time issues. The paper describes various issues on designing a self-healing software application system that relies on the on-the-fly error detection and repair of web application or service agent code and data. Self-Healing is a very new area of research that deals with fault tolerance for dynamic systems. Self-healing deals with imprecise specification, uncontrolled environment and reconfiguration of system according to its dynamics. Software, which is capable of detecting and reacting to its malfunctions, is called self-healing software. Such software system has the ability to examine its failures and to take appropriate corrections. Self-Healing system must have knowledge about its expected behavior in order to examine whether its actual behavior deviates from its expected behavior in relation of the environment. A fault-model of Self-Healing system is to state what faults or injuries to be self-healed including fault duration, fault source such as, operational errors, defective system requirements or implementation errors etc. Self-healing categories of aspects include fault-model or fault hypothesis, System-response, System-completeness and Design-context. Based on many important literatures, this paper aims also to illustrate critical points of the emergent research topic of Self – Healing Software System.
Self‐splicing group I and group II introns encode homologous (putative) DNA endonucleases of a new family (1994)

A new family of protein domains consisting of 50-80 amino acid residues is described. It is composed of nearly 40 members, including domains encoded by plastid and phage group I introns; mitochondrial, plastid, and bacterial group II introns; eubacterial genomes and plasmids; and phages. The name "EX1HH-HX3H" was coined for both domain and family. It is based on 2 most prominent amino acid sequence motifs, each encompassing a pair of highly conserved histidine residues in a specific arrangement: EX1HH and HX3H. The "His" motifs often alternate with amino- and carboxy-terminal motifs of a new type of Zn-finger-like structure CX2,4CX29-54[CH]X2,3[CH]. The EX1HH-HX3H domain in eubacterial E2-type bacteriocins and in phage RB3 (wild variant of phage T4) product of the nrdB group I intron was reported to be essential for DNA endonuclease activity of these proteins. In other proteins, the EX1HH-HX3H domain is hypothesized to possess DNase activity as well. Presumably, this activity promotes movement (rearrangement) of group I and group II introns encoding the EX1HH-HX3H domain and other gene targets. In the case of Escherichia coli restrictase McrA and possibly several related proteins, it appears to mediate the restriction of alien DNA molecules.
Gigabit optical access using WDM PON based on spectrum slicing and reflective SOA (2005)

We report on the experimental results of a low cost 40 users WDM PON providing 1.25 Gbit/s per user. We focus on the upstream path using spectrum slicing of a SLED at the OLT and remote modulation at the colorless ONU with a reflective SOA. Bidirectionnal transmission over 20 km is demonstrated. (2 pages)
Bridged bis(amidinate) lanthanide aryloxides: syntheses, structures, and catalytic activity for addition of amines to carbodiimides (2013)

Various lanthanide aryloxide complexes supported by bridged bis(amidinate) ligand L, LLnOAr(DME) (L = Me3SiNC(Ph)N(CH2)3NC(Ph)NSiMe3, DME = dimethoxyethane, Ln = Y, Ar = 2,6-(Me)2C6H3 (1), 2,6-((i)Pr)2C6H3 (2), 2,6-((t)Bu)2-4-(Me)C6H2 (3); Ar = 2,6-((t)Bu)2-4-(Me)C6H2, Ln = Nd (4), Sm (5), Yb (6)) were synthesized, and complexes 1, 2 and 4–6 were characterized by single crystal X-ray diffraction. All the complexes are efficient precatalysts for catalytic addition of amines to carbodiimides. The catalytic activity is influenced by lanthanide metals and the aryloxide groups (Nd (4) Sm (5) < Y (3) Yb (6) and -2,6-(Me)2C6H3 < -2,6-((i)Pr)2C6H3 < -2,6-((t)Bu)2-4-(Me)C6H2). The catalytic addition reaction with 3 showed a good scope of substrates. The mechanism investigation revealed the real active intermediate being the monoguanidinate complexes supported by an aryloxide and an amidine-functionalized amidinate group, L′Ln[O2,6-((t)Bu)2-4-(Me)C6H2][RNCNHRN(Ar′)] (L′ = Me3SiNHC(Ph)N(CH2)3NC(Ph)NSiMe3, R = (i)Pr, Ar′ = phenyl, Ln = Yb (8), Y (11); R = Cy, Ar′ = phenyl, Ln = Yb (10), Y (12); R = (i)Pr, Ar′ = 4-ClC6H4, Ln = Yb (9)), which were isolated from the reactions of 6 (or 3) with amine and carbodiimide in a molar ratio of 1:1:1 and structurally characterized. The Ln-active group in the present precatalyst is a Ln–amidinate species, not the Ln–OAr group.
A new method that enables in situ measurement of drug release from complex carrier-mediated systems (2017)

A new method that enables in situ measurement of drug release from complex carrier-mediated systems
Structural Insights into Clostridium perfringens Delta Toxin Pore Formation (2013)

Clostridium perfringens Delta toxin is one of the three hemolysin-like proteins produced by C. perfringens type C and possibly type B strains. One of the others, NetB, has been shown to be the major cause of Avian Nectrotic Enteritis, which following the reduction in use of antibiotics as growth promoters, has become an emerging disease of industrial poultry. Delta toxin itself is cytotoxic to the wide range of human and animal macrophages and platelets that present GM2 ganglioside on their membranes. It has sequence similarity with Staphylococcus aureus β-pore forming toxins and is expected to heptamerize and form pores in the lipid bilayer of host cell membranes. Nevertheless, its exact mode of action remains undetermined. Here we report the 2.4 Å crystal structure of monomeric Delta toxin. The superposition of this structure with the structure of the phospholipid-bound F component of S. aureus leucocidin (LukF) revealed that the glycerol molecules bound to Delta toxin and the phospholipids in LukF are accommodated in the same hydrophobic clefts, corresponding to where the toxin is expected to latch onto the membrane, though the binding sites show significant differences. From structure-based sequence alignment with the known structure of staphylococcal α-hemolysin, a model of the Delta toxin pore form has been built. Using electron microscopy, we have validated our model and characterized the Delta toxin pore on liposomes. These results highlight both similarities and differences in the mechanism of Delta toxin (and by extension NetB) cytotoxicity from that of the staphylococcal pore-forming toxins.
Simultaneous analysis of furosemide and bumetanide in horse plasma using high performance liquid chromatography (1989)

A high performance liquid chromatographic method is described for the simultaneous determination of furosemide and bumetanide in horse plasma. The C8 (3 microns) reversed phase column (4.8 x 150 mm) provided clear separation of furosemide and bumetanide with other components present in the horse plasma. The detection limit for both the drugs was 10 ng/mL. Both drugs were stable in plasma (at natural or acidic pH) for up to 24 h. The method is sufficiently sensitive to detect furosemide levels in plasma obtained from horses receiving a therapeutic dose of furosemide.