gebhart/patrepeval huggingface dataset:
A Framework for Automated Exploration of Trojan Attack Space in FPGA Netlists (2022)

&lt;p&gt;Field Programmable Gate Arrays (FPGAs) provide a flexible compute platform for quick prototyping or hardware acceleration in diverse application domains. However, similar to the global semiconductor life-cycle in the modern supply chain, FPGA-based product development includes processes and interactions with potentially untrusted parties outside the traditional scrutiny of a completely in-house development cycle. An untrusted party or software can maliciously alter a hardware intellectual property (IP) block mapped to an FPGA device during various stages of the FPGA life-cycle. Such malicious alterations, also known as hardware Trojan attacks, have garnered significant research into their detection and prevention in the context of application-specific integrated circuit (ASIC) design flow. However, Trojan attacks in FPGAs have not enjoyed this same attention. Designers often rely on mapping ASIC-specific solutions and evaluation benchmarks to the FPGA domain, which leaves much of the FPGA-specific Trojan space uncovered. We note that the distinctive business model as well as the architectural configurations of FPGAs present unique opportunities for Trojan attacks to an adversary. To this end, we introduce a framework to automatically explore the hardware Trojan attack space in FPGA netlists. It is capable of inserting different types of FPGA-specific Trojans in a netlist enabling rapid exploration of potential Trojan attacks in an FPGA design: soft-template, monolithic, and distributed dark silicon. Soft template Trojans use behavioral templates with random synthesis constraints to increase Trojan structural diversity. Monolithic and distributed dark silicon Trojans use the under-utilized input space (FPGA dark silicon) in FPGA primitives to realize Trojans with effectively zero area and power footprint. Further optimizations are also presented to remove any potential delay impact. We evaluate our framework by generating over 1300 Trojan-inserted benchmarks using each of the introduced FPGA Trojan classes and comparing the impact on utilization, delay, and power.&lt;/p&gt;
Fluorescence Gel Retardation Assay to Detect Protein–Protein Interactions (2004)

A gel mobility retardation assay can be used to detect a protein-protein interaction. The assay is based on the electrophoretic mobility of a protein-protein complex being less than that of either protein alone. Electrophoretic mobility is detected by the fluorescence of a green fluorescent protein variant that is fused to one of the protein partners. The assay is demonstrated by using the interaction of the S-protein and S-peptide fragments of ribonuclease A as a case study.
Integrating Ligand-Receptor Interactions and In Vitro Evolution for Streamlined Discovery of Artificial Nucleic Acid Ligands (2019)

To discover DNA ligands against a predetermined receptor protein complex, we introduce a comprehensive version of ligand-guided selection (LIGS). LIGS is, itself, a variant of systematic evolution of ligands by exponential enrichment (SELEX). Herein, we have optimized LIGS to identify higher affinity aptamers with high specificity. In addition, we demonstrate the expandability of LIGS by performing specific aptamer elution at 25°C, utilizing multiple monoclonal antibodies (mAbs) against cultured cells and primary cells obtained from human donors expressing the same receptor. Eluted LIGS libraries obtained through Illumina high-throughput (HT) DNA sequencing were analyzed by bioinformatics tools to discover five DNA aptamers with apparent affinities ranging from 3.06 ± 0.485 nM to 325 ± 62.7 nM against the target, T cell receptor-cluster of differentiation epsilon (TCR-CD3ε) expressed on human T cells. The specificity of the aptamers was validated utilizing multiple strategies, including competitive binding analysis and a double-knockout Jurkat cell line generated by CRISPR technology. The cross-competition experiments using labeled and unlabeled aptamers revealed that all five aptamers compete for the same binding site. Collectively, the data in this report introduce a modified LIGS strategy as a universal platform to identify highly specific multiple aptamers toward multi-component receptor proteins in their native state without changing the cell-surface landscape.
Stress will kill you anyway! (2020)

Adrenocortical carcinomas are devastating cancers, expressing high levels of glutathione peroxidase 4 (GPX4). Therefore, it was recently suggested that these tumors might be therapeutically targeted by inducing ferroptosis. In this issue of Cell Death and Disease, Weigand et al. describe the organ-specific production of steroid hormones as a potential culprit for the exquisite sensitivity of these cancers to ferroptosis.
Ferroelectric field-effect memory device using Bi4Ti3O12 film (1975)

A ferroelectric field-effect transistor has been investigated using a thin film of bismuth titanate (Bi4Ti3O12) deposited on a Si substrate by rf sputtering. Achievement of the ferroelectric polycrystalline Bi4Ti3O12 films without any cracks necessitates postdeposition heat treatment in air at temperatures ?550 °C for 30 min. The film, heat treated at 650 °C, has a remanent polarization of 4.0 μC/cm2 and a coercive field of about 250 kV/cm at 1 kHz. A FET having a gate structure of Bi4Ti3O12-SiO2-Si was fabricated, where the SiO2 served to prevent charge injection from Si into the ferroelectric film. (This process would degrade the retention of memorized states.) The FET can be switched by voltages of as low as 15 V applied to the gate. The on and off states are very stable at room temperature.
Passive Devices for FTTH Systems Based on Replicated Polymer Optical Waveguides (2005)

A novel replication technology for fabricating polymer optical waveguides has been developed. By utilizing this technology, optical coupler modules and a WDM module are successfully demonstrated with practical characteristics and high reliability for FTTH systems.
The isothiocyanate sulforaphane induces the phase 2 response by signaling of the Keap1-Nrf2-are pathway: Implications for dietary protection against cancer (2008)

In the course of evolution, all eukaryotes have developed sophisticated defense systems that allow their survival and coevolution with other competing organisms. These include the biosynthesis of a wide array of small molecules (secondary metabolites) with extraordinarily sophisticated chemistry in plants, as well as elaborate enzymatic systems capable of coping with the toxicities of electrophiles and oxidants (phase 2 enzymes) in both plants and animals. Phase 2 enzymes catalyze enormously versatile chemical reactions that collectively lead to detoxification of various electrophiles and oxidants. Together with housekeeping antioxidant enzymes (e.g., catalase, superoxide dismutase) and small molecular mass direct antioxidants (e.g, ascorbic acid, tocopherol, glutathione), phase 2 enzymes constitute an integral part of the cellular defense. Furthermore, the discoveries that (1) phase 2 enzymes can be induced selectively (without concomitant induction of phase 1 enzymes) by a wide variety of stimuli that we now simply call “inducers” and (2) this “induced state” that we now refer to as “the phase 2 response” could explain how so many diverse chemical agents could block carcinogenesis in various animal models led to the birth of the hypothesis that induction of phase 2 enzymes could be a powerful strategy for protection against cancer and other chronic diseases [1-3].
Arene Substitution Design for Controlled Conformational Changes of Dibenzocycloocta-1,5-dienes (2020)

We report that an agile eight-membered cycloalkane can be stabilized by fusing a benzene ring on each side, substituted with proper functional groups. The conformational change of dibenzocycloocta-1,5-diene (DBCOD), a rigid-flexible-rigid organic moiety, from its Boat to Chair conformation requires an activation energy of 42 kJ/mol, which is substantially lower than those of existing submolecular shape-changing units. Experimental data corroborated by theoretical calculations demonstrate that intramolecular hydrogen bonding can stabilize Boat, whereas electron repulsive interaction from opposing ester substituents favors Chair. Intramolecular hydrogen bonding formed by 1,10-diamide substitution stabilizes Boat, spiking the temperature at which Boat and Chair can readily interchange from -60 to 60 °C. Concomitantly this intramolecular attraction raises the energy barrier from 42 kJ/mol for unsubstituted DBCOD to 68 kJ/mol for diamide-substituted DBCOD. Remarkably, this value falls within the range of the activation energy of highly efficient enzyme-catalyzed biological reactions. With shape changes once considered only possible with high energy, our work reveals a potential pathway exemplified by a specific submolecular structure to achieve low-energy-driven shape changes for the first time. The intrinsic cycle stability and high-energy output systems that would incur damage under high-energy stimuli could particularly benefit from this new kind of low-energy-driven shape-changing mechanism. This work has laid the basis to construct systems for low-energy-driven stimuli-responsive applications, hitherto a challenge to overcome.
Artifacts in fetal pulse oximetry (1994)

One of the problems with pulse oximeters is that they can often give a saturation reading regardless of accuracy; some commercially available oximeters will give a value when the sensors are left on the table (“room air saturation”); regular taps on the table will even give a modulated or “pulsatile” signal.
A Study of Cheater Detection in FPS Game by using User Log Analysis (2015)

온라인 게임의 인기 장르인 FPS (First Person Shooting) 게임에서 치팅(cheating)을 근절하기 위해 게임 회사는 다양한 클라이언트 보안 솔루션을 운영하고 있지만 불법 프로그램을 이용한 치팅은 끊이지 않고 있으며 이로 인한 피해도 지속적으로 발생하고 있다. 본 논문에서는 서버 단에서 게임 로그 분석을 통해 FPS 게임의 치팅 사용자를 탐지하는 방법을 제안한다. FPS 게임에서 일반적으로 적재되는 로그를 중심으로 치팅 사용자와 일반 사용자의 특성을 비교 분석하고 인공 신경망 알고리즘을 이용해 치팅 사용자를 탐지하는 모델을 생성하였다. 또한 실제 서비스 중인 FPS 게임 로그를 이용해 치팅 사용자 탐지 모델에 대한 성능 평가를 수행하였다.
A study on growth factors regulating bone formation. Part 1. cDNA cloning of murine bone morphogenetic protein by polymerase chain reaction. (1993)

A cDNA clone of murine bone morphogenetic protein (BMP) was obtained by polymerase chain reaction, using oligonucleotides as primers derived from human BMP2 and BMP4. Messenger RNAs were isolated from neonatal murine tissue and used for the synthesis of cDNA with reverse transcriptase.Specifically amplified cDNAs were cloned into bluescript plasmid and subjected to sequencing. One clone which partially encoded murine BMP2 was obtained. The nucleotide sequence, 554 bp in length, shared 88.6% identity with that of human BMP2 and the deduced amino acids including the mature, biologically active protein exhibited 96.2% homology. Within the C-terminal 114 amino acids of the protein, seven cysteine residues were completely conserved which is characteristic of TGF-β superfamily. Substitution of only three amino acids was found when compared with the corresponding human sequence. Isolation of the full length cDNA is now in progress.
Structure-Property Relationships in Self-Assembled Perylene Bisimide Nanowires (2014)

LMOM
Antibodies from multiple sclerosis patients preferentially recognize hyperglucosylated adhesin of non-typeable Haemophilus influenzae (2016)

In autoimmune diseases, there have been proposals that exogenous “molecular triggers”, i.e., specific ‘non-self antigens’ accompanying infectious agents, might disrupt control of the adaptive immune system resulting in serious pathologies. The etiology of multiple sclerosis (MS) remains unclear. However, epidemiologic data suggest that exposure to infectious agents may be associated with increased MS risk and progression may be linked to exogenous, bacterially-derived, antigenic molecules, mimicking mammalian cell surface glycoconjugates triggering autoimmune responses. Previously, antibodies specific to a gluco-asparagine (N-Glc) glycopeptide, CSF114(N-Glc), were identified in sera of an MS patient subpopulation. Since the human glycoproteome repertoire lacks this uniquely modified amino acid, we turned our attention to bacteria, i.e., Haemophilus influenzae, expressing cell-surface adhesins including N-Glc, to establish a connection between H. influenzae infection and MS. We exploited the biosynthetic machinery from the opportunistic pathogen H. influenzae (and the homologous enzymes from A. pleuropneumoniae) to produce a unique set of defined glucosylated adhesin proteins. Interestingly we revealed that a hyperglucosylated protein domain, based on the cell-surface adhesin HMW1A, is preferentially recognized by antibodies from sera of an MS patient subpopulation. In conclusion the hyperglucosylated adhesin is the first example of an N-glucosylated native antigen that can be considered a relevant candidate for triggering pathogenic antibodies in MS.
Synthesis of MoS2 Layers on GaN Using Ammonium Tetrathiomolybdate for Heterojunction Device Applications (2021)

Abstract 2D materials such as molybdenum sulfide (MoS 2 ) integrated with conventional semiconductors lead to the fabrication of novel heterojunctions with pivotal electrical and optoelectronic properties. Herein, an approach is reported which addresses the growth of MoS 2 crystals on the lattice‐matched Ga–polar gallium nitride (GaN) wafer using ammonium tetrathiomolybdate (ATM) as a precursor in a chemical vapor deposition (CVD) process, instead of using the molybdenum‐oxide‐based precursors. Unidirectional triangular MoS 2 crystals and continuous film are obtained on the free‐standing Ga–polar GaN substrate. Further, the interface quality of the as‐synthesized MoS 2 crystals and GaN wafer is explored by X‐ray photoelectron spectroscopy. It is observed that a good quality interface can be obtained by using the ammonia‐containing ATM precursor, where the surface oxygen at the interface is significantly less. A heterojunction device is fabricated with the synthesized MoS 2 layer on GaN, showing excellent rectifying diode characteristics and a photovoltaic action with light illumination. This study reveals the suitability of the ammonia‐containing ATM precursor for the growth of MoS 2 crystals on GaN in the CVD process to obtain a suitable heterostructure for device applications.
High-Resolution Fluorescence In Situ Hybridization to Detect mRNAs in Neuronal Compartments In Vitro and In Vivo (2011)

The localization of specific mRNAs into dendrites and/or axons is an important mechanism to enrich -proteins at their sites of function and influence neuronal development, plasticity, and repair. The fluorescence in situ hybridization (FISH) methods described here have provided high sensitivity and resolution enabling investigation into the mechanism, regulation, and function of mRNA localization in vitro and in vivo. Two methods are described in detail. The first method employs digoxigenin- or fluorophore-conjugated oligonucleotide probes for the detection of localized mRNAs in dendrites, spines, axons, and growth cones of cultured neurons. The second method employs digoxigenin-labeled RNA probes and fluorescence tyramide amplification for the detection of less abundant mRNAs localized to dendrites in vivo. Both methods enable the visualization and quantification of mRNA granules, and changes in their localization in response to various stimuli. The high-resolution FISH technology described here has broader applications beyond the study of mRNA localization. It enables the quantitative analyses of developmental and cell type-specific patterns of gene expression, and how these are modified by physiological signals or during disease states.
Perinatal adaptive response of the adrenal and carotid blood flow in sheep fetuses subjected to total cord occlusion (2005)

During severe acute intrauterine hypoxia, the fetal lamb is able to maintain the blood flow to the brain and the adrenal gland for 3-5 min. Changes in the AFMBV and the CBF were highly correlated to the changes in MABP. Adrenal FMBV and cortisol levels were higher in lamb neonates exposed to severe intrauterine asphyxia.
Multistage devitrification of Mg-Ni-Mm and g-Ni-Y-Mm metallic glasses (Mm = misch metal) (2003)

Devitrification behaviour of Mg-Ni-Mm and Mg-Ni-Y-Mm metallic glasses (Mm = misch metal) was studied by differential scanning calorimetry, isothermal calorimetry, X-ray diffractometry and transmission electron microscopy. These materials exhibited a multistage devitrification with a primary exothermic peak with an onset temperature of about 450 K. Local atomic order changed during primary devitrification. This change occurs without an incubation period and leads to embrittlement of the samples. The activation energy value for the first exothermic heat effect in the Mg 86 Ni 10 Y 2 Mm 2 alloy is higher than the activation energy for Mg self-diffusion, implying that redistribution of the other alloying elements also takes place. The strongest heat effects are connected with the devitrification of the amorphous phase (changes in the local atomic order, precipitation of hcp Mg and the metastable compounds) while the magnitude of the heat effect of the transformation of metastable crystalline phases to stable phases in the Mg 86 Ni 10 Y 2 Mm 2 alloy, for example, is 17 times weaker than the effect of devitrification of the amorphous phase. A continuous heating transformation diagram is derived from the results.
Enantioselective Hydroformylation (2021)

Hydroformylation is powerful catalytic reaction capable of converting alkenes directly into aldehydes by addition of a formyl group and hydrogen across the double bond. Installation of the formyl group at an internal carbon establishes a chiral center, and a variety of chiral ligands may be employed to direct the enantioselectivity of the reaction. The alkene substrates are easily accessed, and the resultant aldehydes are common precursors for diverse synthetic manipulations. This chapter covers enantioselective hydroformylation from its inception, presents the most common metal precursors and ligands, and includes all examples that produce aldehydes with yields above 20% and enantioselectivity above 60:40 er. The initial discussion focuses on the mechanism and stereochemistry, and on the regio‐ and enantioselectivity‐determining steps in particular, as these are crucial for overall yield. The “Scope and Limitations” section is divided by substrate type and offers examples of exceptional catalytic systems that have been reported for each. The application of enantioselective hydroformylation to synthetic procedures is discussed by highlighting some reported examples, comparing it to other protocols that also afford chiral aldehydes, and exploring the standard experimental conditions. The intention of this review is to demonstrate the power and scope of enantioselective hydroformylation to researchers, and to provide a suitable starting point for those interested in its application to their own synthetic strategies.
Preparation and Property of Poly (vinyl alcohol) Modified VE-containing Liposome (2007)

Poly(vinyl alcohol)(PVA)modified VE-containing liposome was prepared with emulsion method.The shape and the encapsulation efficiency were investigated.The stability of liposome in 4℃、25℃,and in condition mimic skin were measured.The results showed that liposomes were spherical-shape.The encapsulation efficiency was 86.42%.PVA improved the liposomal stability and the liposomes were stable in storage condition at 4℃ for 90 days,its leakage rate was 4.88%.Complex structural rearrangements,such as aggregation and size reduction occurred,caused the leakage of entrapped VE.Its leakage rate increased with the calcium concentration,storage time and the decrease of pH.And an intense release was induced at pH5.0 or c(Ca2+)6.0mmol/L.
Low-Field MRI of Laser Polarized Noble Gas (1998)

NMR images of laser polarized 3He gas were obtained at 21 G using a simple, homebuilt instrument. At such low fields magnetic resonance imaging (MRI) of thermally polarized samples (e.g., water) is not practical. Low-field noble gas MRI has novel scientific, engineering, and medical applications. Examples include portable systems for diagnosis of lung disease, as well as imaging of voids in porous media and within metallic systems.
Conditioning Perspectives for Primary Immunodeficiency Stem Cell Transplants (2019)

The majority of children undergoing Hematopoietic Stem cell Transplantation (HSCT) require conditioning therapy to make space and prevent rejection of the donor stem cells. The exception is certain children with Severe Combined immune deficiency, who have limited or no ability to reject the donor graft. Transplant conditioning is associated with significant morbidity and mortality from both direct toxic effects of chemotherapy as well as opportunistic infections associated with profound immunosuppression. The ultimate goal of transplant practice is to achieve sufficient engraftment of donor cells to correct the underlying disease with minimal short- and long-term toxicity to the recipient. Traditional combinations, such as busulfan and cyclophosphamide, achieve a high rate of full donor engraftment, but are associated with significant acute transplant-related-mortality and late effects such as infertility. Less "intensive" approaches, such as combinations of treosulfan or melphalan with fludarabine, are less toxic, but may be associated with rejection or low level chimerism requiring the need for re-transplantation. The major benefit of these novel approaches, however, which we hope will be realized in the decades to come, may be the preservation of fertility. Future approaches look to replace chemotherapy with non-toxic antibody conditioning. The lessons learnt in refining conditioning for HSCT are likely to be equally applicable to gene therapy protocols for the same diseases.
Synthesis and Characterization of Novel Polyimides from Alicyclic Dianhydride (1996)

New alicyclic Polyimides (PIs) were prepared from asymmetric alicyclic dianhydride, 5-(2,5-dioxotetrahydrofuryl)-3-methyl-cyclohexane-1,2-dicarboxylic anhydride (DOCDA) and the corresponding aromatic diamines such as p-phenylenediamine, m-phenylenediamine and oxydianiline etc. by the polycondensation in N-methyl-2-pyrrolidone (NMP) followed by chemical imidization as well as one step polyimidization in m-cresol in the presence of isoquinoline as a catalyst. The resulting PIs with glass transition temperatures ranging from 220 to 328 degrees C had the inherent viscosities within the range of 0.25 similar to 1.42 dL/g. These polymers were readily soluble in aprotic polar solvents such as NMP, dimethylacetamide (DMAc), dimethylesulfoxide (DMSO), etc. Furthermore, some of the polymers showed good solubility properties to common organic solvents like tetrahydrofurane and chlorform. Also, all of these polyimide films were tough, almost colourless, and transparent.