gebhart/patrepeval huggingface dataset:
Aromatic Functionality of Target Proteins Influences Monomer Selection for Creating Artificial Antibodies on Plasmonic Biosensors (2016)

Natural antibodies used as biorecognition elements suffer from numerous shortcomings, such as limited chemical and environmental stability and cost. Artificial antibodies based on molecular imprinting are an attractive alternative to natural antibodies. We investigated the role of aromatic interactions in target recognition capabilities of artificial antibodies. Three proteins with different aromatic amino acid content were employed as model targets. Artificial antibodies were formed on nanostructures using combinations of silane monomers of varying aromatic functionality. We employed refractive index sensitivity of plasmonic nanostructures as a transduction platform for monitoring various steps in the imprinting process and to quantify the target recognition capabilities of the artificial antibodies. The sensitivity of the artificial antibodies with aromatic interactions exhibited a protein-dependent enhancement. Selectivity and sensitivity enhancement due to the presence of aromatic groups in imprinted polymer matrix was found to be higher for target proteins with higher aromatic amino acid content. Our results indicate that tailoring the monomer composition based on the amino acid content of the target protein can improve the sensitivity of plasmonic biosensors based on artificial antibodies without affecting the selectivity.
Hardware/Software Co-Assurance for the Rust Programming Language Applied to Zero Trust Architecture Development (2023)

Zero Trust Architecture requirements are of increasing importance in critical systems development. Zero trust tenets hold that no implicit trust be granted to assets based on their physical or network location. Zero Trust development focuses on authentication, authorization, and shrinking implicit trust zones to the most granular level possible, while maintaining availability and minimizing authentication latency. Performant, high-assurance cryptographic primitives are thus central to successfully realizing a Zero Trust Architecture. The Rust programming language has garnered significant interest and use as a modern, type-safe, memory-safe, and potentially formally analyzable programming language. Our interest in Rust particularly stems from its potential as a hardware/software co-assurance language for developing Zero Trust Architectures. We describe a novel environment enabling Rust to be used as a High-Level Synthesis (HLS) language, suitable for secure and performant Zero Trust application development. Many incumbent HLS languages are a subset of C, and inherit many of the well-known security shortcomings of that language. A Rust-based HLS brings a single modern, type-safe, memory-safe, high-assurance development language for both hardware and software. To study the benefits of this approach, we crafted a Rust HLS subset, and developed a frontend to the hardware/software co-assurance toolchain due to Russinoff and colleagues at Arm, used primarily for floating-point hardware formal verification. This allows us to leverage a number of existing hardware/software co-assurance tools with a minimum investment of time and effort. In this paper, we describe our Rust subset, detail our prototype toolchain, and describe the implementation, performance analysis, formal verification and validation of representative Zero Trust algorithms and data structures written in Rust, emphasizing cryptographic primitives and common data structures.
Continuous Authentication for Voice Assistants (2017)

Voice has become an increasingly popular User Interaction (UI) channel, mainly contributing to the ongoing trend of wearables, smart vehicles, and home automation systems. Voice assistants such as Siri, Google Now and Cortana, have become our everyday fixtures, especially in scenarios where touch interfaces are inconvenient or even dangerous to use, such as driving or exercising. Nevertheless, the open nature of the voice channel makes voice assistants difficult to secure and exposed to various attacks as demonstrated by security researchers. In this paper, we present VAuth, the first system that provides continuous and usable authentication for voice assistants. We design VAuth to fit in various widely-adopted wearable devices, such as eyeglasses, earphones/buds and necklaces, where it collects the body-surface vibrations of the user and matches it with the speech signal received by the voice assistant's microphone. VAuth guarantees that the voice assistant executes only the commands that originate from the voice of the owner. We have evaluated VAuth with 18 users and 30 voice commands and find it to achieve an almost perfect matching accuracy with less than 0.1% false positive rate, regardless of VAuth's position on the body and the user's language, accent or mobility. VAuth successfully thwarts different practical attacks, such as replayed attacks, mangled voice attacks, or impersonation attacks. It also has low energy and latency overheads and is compatible with most existing voice assistants.
Dry‐Released Nanotubes and Nanoengines by Particle‐Assisted Rolling (2013)

Surface tension of self-assembled metal nanodroplets can be applied to overcome the deformation barriers of strain-engineered nanomembranes and produce extremely nanoscale tubes. Aggregated nanoparticles stress nanomembranes and subsequently integrate on the walls of rolled-up nanotubes, which can speed up the tubular engines owing to the enhanced electrocatalytic activity.
Investigation on Combining Partially Premixed Compression Ignition and Diffusion Combustion for Gasoline Compression Ignition—Part 1: Fuel Reactivity and Injection Strategy Effects (2021)

&lt;div&gt;This study investigates the fuel reactivity and the fuel injection strategy effects on gasoline compression ignition (GCI) using the third generation (Gen3) of the gasoline direct injection compression ignition (GDCI) engine with a 14.3 compression ratio (CR). By varying the fuel injection strategy, three GCI combustion modes were studied, including early partially premixed compression ignition (PPCI), late PPCI, and PPCI-diffusion. A double injection strategy was used in all three combustion modes. For early and late PPCI, the first injection took place in the intake stroke, while the onset of the second injection event was varied in the compression stroke. In contrast, in the PPCI-diffusion mode, both injections occurred in the compression stroke with the second injection event taking place near the compression top dead center (TDC).&lt;/div&gt; &lt;div&gt;The investigation was focused at 1500 rpm/6 bar IMEPg. First, the fuel reactivity effects were evaluated on two gasolines with research octane numbers (RON) of 80 and 92. Then, using the RON92 gasoline, the fuel injection strategy effects were investigated. Compared to the RON80 gasoline, the RON92 gasoline was found to require a higher boost to achieve proper PPCI combustion and generate markedly higher combustion losses, thereby causing deteriorated fuel efficiency. In terms of the fuel injection strategy effects, early PPCI produced high fuel efficiency with low nitrogen oxides (NOx) and soot emissions, but it was at the cost of high hydrocarbon (HC) and carbon monoxide (CO) emissions. In contrast, PPCI-diffusion generated drastically reduced combustion losses than both early and late PPCI. Closed-cycle three-dimensional (3-D) combustion computational fluid dynamics (CFD) analysis revealed that PPCI-diffusion had the strongest in-cylinder fuel stratification among the three combustion modes with the main combustion event proceeding through a diffusion-driven process.&lt;/div&gt;
Imitation Attacks and Defenses for Black-box Machine Translation Systems (2020)

Adversaries may look to steal or attack black-box NLP systems, either for financial gain or to exploit model errors. One setting of particular interest is machine translation (MT), where models have high commercial value and errors can be costly. We investigate possible exploits of black-box MT systems and explore a preliminary defense against such threats. We first show that MT systems can be stolen by querying them with monolingual sentences and training models to imitate their outputs. Using simulated experiments, we demonstrate that MT model stealing is possible even when imitation models have different input data or architectures than their target models. Applying these ideas, we train imitation models that reach within 0.6 BLEU of three production MT systems on both high-resource and low-resource language pairs. We then leverage the similarity of our imitation models to transfer adversarial examples to the production systems. We use gradient-based attacks that expose inputs which lead to semantically-incorrect translations, dropped content, and vulgar model outputs. To mitigate these vulnerabilities, we propose a defense that modifies translation outputs in order to misdirect the optimization of imitation models. This defense degrades the adversary's BLEU score and attack success rate at some cost in the defender's BLEU and inference speed.
Development of a microarray chip for gene expression in rabbit ocular research. (2007)

The results of this rabbit microarray study are consistent with those from other wound healing studies, indicating that this array can provide valid information on broad patterns of gene expression. This is the first microarray available for rabbit studies and is a valuable tool that can be used to study molecular events in the eye.
Characterization of a bioactive fiber scaffold with entrapped HUVECs in coaxial electrospun core-shell fiber (2014)

Human umbilical vein endothelial cells (HUVECs) were successfully entrapped in polyethylene oxide (PEO) core /polycaprolactone (PCL) shell electrospun fibers thus creating a "bioactive fiber." The viability and release of biomolecules from the entrapped cells in the bioactive fibers were characterized. A key modification to the core solution was the inclusion of 50% fetal bovine serum (FBS), which improved cell viability substantially. The fluorescein diacetate (FDA) staining revealed that the entrapped cells were intact and viable immediately after the electrospinning process. A long-term cell viability assay using AlamarBlue® showed that cells were viable for over two weeks. Secreted Interleukin-8 (IL-8) was monitored as a candidate released protein, which can also act as an indicator of HUVEC stress. These results demonstrated that HUVECs could be entrapped within the electrospun scaffold with the potential of controllable cell deposition and the creation of a bioactive fibrous scaffold with extended functionality.
Improving the quality of automatic DNA sequence assembly using fluorescent trace-data classifications. (1996)

Virtually all large-scale sequencing projects use automatic sequence-assembly programs to aid in the determination of DNA sequences. The computer-generated assemblies required substantial hand-editing to transform them into submissions for GenBank. As the size of sequencing projects increases, it becomes essential to improve the quality of the automated assemblies so that this time consuming hand-editing may be reduced. Current ABI sequencing technology uses base calls made from fluorescently-labeled DNA fragments run on gels. We present a new representation for the fluorescent trace data associated with individual base calls. This representation can be used before, during, and after fragment assembly to improve the quality of assemblies. We demonstrate one such use-end-trimming of sub-optimal data-that results in a significant improvement in the quality of subsequent assemblies.
Figure S5 from Pharmacologic Properties and Preclinical Activity of Sasanlimab, A High-affinity Engineered Anti-Human PD-1 Antibody (2023)

&lt;p&gt;Supplementary Figure 5 shows the analysis of sasanlimab by SE-HPLC with UV detection at 280 nm&lt;/p&gt;
Androgen withdrawal inhibits tumor growth and is associated with decrease in angiogenesis and VEGF expression in androgen-independent CWR22Rv1 human prostate cancer model. (2004)

Recent evidence suggests that androgens stimulate growth of human prostate cancer partly by regulating expression of growth factors such as vascular endothelial growth factor (VEGF) in vitro and in vivo. In this study, we used CWR22Rv1, a novel androgen-responsive but androgen-independent human prostate cancer model, to evaluate the effect of androgen withdrawal on tumor growth, expression of VEGF and the cell proliferation marker Ki-67, and angiogenesis. A time-release testosterone pellet was implanted three days before inoculation of CWR22Rv1 cells in the mice. The tumor volumes were measured every three days. Serum PSA was measured on days 1, 12, 20, 27 and 34 post inoculation. Castration was performed on the 20th day post inoculation. Immunohistochemical assays were used to evaluate cell proliferation and microvessel density. Enzyme-linked immunosorbent assay (ELISA) was used to quantify VEGF expression. The average tumor volumes in the castration group on the 27th and 34th days were 122 and 168 mm3, respectively, compared to 156 and 210 mm3 in the non-castration group (p<0.01). Serum PSA level in the castration group decreased to about 41% of the level of the non-castration group (p<0.01). The VEGF protein levels in the tumors of castrated and non-castrated mice on day 34 were 0.62 pg and 1.36 pg/100 microg total protein, respectively (p<0.001). The mean percentage of Ki-67-positive tumor cells in the castrated and non-castrated groups were 1.8% and 2.8%, respectively (p=0.015). The mean microvessel densities in the castrated and non-castrated groups were 15 and 22 vessels/field, respectively (p<0.01) We conclude androgen withdrawal reduced both VEGF and microvessel density, and this was associated with decreased cellular proliferation in androgen-independent CWR22Rv1 human prostate cancer tumor in vivo.
Knightian Robustness from Regret Minimization (2014)

We consider auctions in which the players have very limited knowledge about their own valuations. Specifically, the only information that a Knightian player $i$ has about the profile of true valuations, $θ^*$, consists of a set of distributions, from one of which $θ_i^*$ has been drawn. We analyze the social-welfare performance of the VCG mechanism, for unrestricted combinatorial auctions, when Knightian players that either (a) choose a regret-minimizing strategy, or (b) resort to regret minimization only to refine further their own sets of undominated strategies, if needed. We prove that this performance is very good.
Chiral-at-ansa-Bridged Group 4 Metallocene Complexes {(R1R2C)-(3,6-tBu2Flu)(3-R3-5-Me-C5H2)}MCl2: Synthesis, Structure, Stereochemistry, and Use in Highly Isoselective Propylene Polymerization (2010)

New chiral racemic, sterically crowded fluorenyl-cyclopentadienyl compounds having monoaryl-substituted methylene bridges (R1R2C)-((3,6-tBu2Flu)H)(3-R3-5-Me-C5H3) (R1 = H, R2 = Ph, R3 = tBu: 2a; R1 = H, R2 = 2,4,6-Me3C6H2 (Mes); R3 = CMe2Ph (cumyl): 2b; R1 = H, R2 = 3,5-(CF3)2C6H3, R3 = tBu: 2c) or a disubstituted (R1 = CF3, R2 = Ph, R3 = tBu: 2d) as well as an unsubstituted (nonstereogenic) methylene bridge (R1 = R2 = H, R3 = tBu: 2e) were synthesized via nucleophilic additions to substituted fulvenes. The zirconium and hafnium dichloro complexes derived from proligands 2a, 2b, and 2e, namely, {Ph(H)C-(3,6-tBu2Flu)(3-tBu-5-Me-C5H2)}ZrCl2 (3a), {Ph(H)C-(3,6-tBu2Flu)(3-tBu-5-Me-C5H2)}HfCl2 (4a), {Mes(H)C-(3,6-tBu2Flu)(3-cumyl-5-Me-C5H2)}ZrCl2 (3b), and {H2C-(3,6-tBu2-Flu)(3-tBu-5-Me-C5H2)}ZrCl2 (3e), were prepared (63−88% yields). Attempted metalations at the fluorinated proligands 2c and 2d were not successful. Due to the presence of the stereogenic center of the ansa-bridge, 3a, 4a, and 3b exist as mixtures of two diastereomers in which the most bulky substituent in the methylene bridge is either anti (major product in the case of 3a and 4a) or syn (only one observed for 3b) to the 5-methyl substituent in the Cp ring. Diastereomerically pure anti-3a, anti-4a and syn-4a, and syn-3b were isolated and characterized by elemental analysis, NMR spectroscopy, and X-ray crystallography. When activated with MAO, metallocene complex anti-3a showed very high activity in the polymerization of propylene (14 000 kg(PP)·mol(Zr)−1·h−1, toluene, 60 °C) to yield highly isotactic polypropylene (iPP) with [m]4 = 95.8% and Tm = 153 °C. Both diastereomers of hafnium analogues exhibited lower activities (260−270 kg(PP) mol(Hf)−1·h−1) but distinct catalytic behavior: anti-4a yielded low molecular weight and moderately isotactic PP ([m]4 = 88.8%), while highly isotactic PP ([m]4 = 94.0%) with a bimodal distribution was produced with syn-4a. Precursor syn-3b was inactive under standard polymerization conditions, presumably due to deactivation of the cationic metal center by the cumyl Cp substituent. Methylene-bridged 3e produced highly isotactic PP ([m]4 = 96.9%; Tm = 154 °C) with moderate activity (2 320 kg(PP)·mol(Zr)−1·h−1).
Rhodotorula Keratitis: A Rarely Encountered Ocular Pathogen (2014)

Prior cases of Rhodotorula keratitis most often required surgical intervention and were associated with poor outcomes. This case shows that Rhodotorula keratitis can be successfully treated with topical antifungal agents if diagnosed early and appropriate treatment is initiated promptly. We report the first case of Rhodotorula keratitis confirmed by in vivo confocal microscopy. This is also the first description of pseudomycelium formation that has not been previously described in vivo, a morphological structure that this organism rarely demonstrates. Finally, this case shows that confocal microscopy may aid in the early diagnosis and management of fungal keratitis involving this rare but potentially damaging organism.
A self-regulated gradient interphase for dendrite-free solid-state Li batteries (2022)

A functional gradient lithium anode (FGLA), where a LiF-rich layer faces garnet side and gradually changes to a LiAl-rich layer facing Li side, effectively prevents solid-state electrolytes from dendrite penetration at high current densities.
Welding Distortion Analysis of Hull Blocks using Equivalent Load Method Based on Inherent Strain (2012)

Welding deformation reduces the dimensional accuracy of ship hull blocks and decreases productivity due to the correction work. Prediction and minimizing of welding distortion at the design stage will lead to higher quality as well as higher productivity. Therefore, the development of an effective method to predict accurately the weld distortion of hull blocks considering the fabrication sequences is required. In the case of hull block welding work in shipyards, the welding process of curved stiffened plates has large amounts of workload. This paper suggests an efficient method for predicting the welding deformation of stiffened curved plates based on the inherent strain theory combined with the finite element method. The equivalent load was determined by integrating inherent strain components which are calculated in the vicinity of heat affected zone using the highest temperature and the degree of restraint. The welding distortion of curved stiffened panels under equivalent load are calculated by elastic analysis and compared with that by intensive elasto-plastic finite element analysis. It is verified that the proposed method has a high efficiency and accuracy.
Human Heart Anoxia and Reperfusion Tissue (HEART) Model for the Rapid Study of Exosome Bound miRNA Expression As Biomarkers for Myocardial Infarction (2022)

Current biomarkers for myocardial infarction (MI) diagnosis are typically late markers released upon cell death, incapable of distinguishing between ischemic and reperfusion injury and can be symptoms of other pathologies. Circulating microRNAs (miRNAs) have recently been proposed as alternative biomarkers for MI diagnosis; however, detecting the changes in the human cardiac miRNA profile during MI is extremely difficult. Here, to study the changes in miRNA levels during acute MI, a heart-on-chip model with a cardiac channel, containing human induced pluripotent stem cell (hiPSC)-derived cardiomyocytes in human heart decellularized matrix and collagen, and a vascular channel, containing hiPSC-derived endothelial cells, is developed. This model is exposed to anoxia followed by normoxia to mimic ischemia and reperfusion, respectively. Using a highly sensitive miRNA biosensor that the authors developed, the exact same increase in miR-1, miR-208b, and miR-499 levels in the MI-on-chip and the time-matched human blood plasma samples collected before and after ischemia and reperfusion, is shown. That the surface marker profile of exosomes in the engineered model changes in response to ischemic and reperfusion injury, which can be used as biomarkers to detect MI, is also shown. Hence, the MI-on-chip model developed here can be used in biomarker discovery.
Synthesis of Bridged Oligothiophenes:  Toward a New Class of Thiophene-Based Electroactive Surfactants (2003)

[structure: see text] A series of bridged oligothiophenes have been synthesized. Their novel molecular architecture, comprising two oligothiophenes linked together by a bridge at one alpha-extremity and one binding group at the other alpha-extremity, is expected to improve their utility as electroactive surfactants for semiconducting nanoparticles or organic electronics.
The tarantula toxin β/δ-TRTX-Pre1a highlights the importance of the S1-S2 voltage-sensor region for sodium channel subtype selectivity (2017)

Voltage-gated sodium (Na<sub>V</sub>) channels are essential for the transmission of pain signals in humans making them prime targets for the development of new analgesics. Spider venoms are a rich source of peptide modulators useful to study ion channel structure and function. Here we describe β/δ-TRTX-Pre1a, a 35-residue tarantula peptide that selectively interacts with neuronal Na<sub>V</sub> channels inhibiting peak current of hNa<sub>V</sub>1.1, rNa<sub>V</sub>1.2, hNa<sub>V</sub>1.6, and hNa<sub>V</sub>1.7 while concurrently inhibiting fast inactivation of hNa<sub>V</sub>1.1 and rNa<sub>V</sub>1.3. The DII and DIV S3-S4 loops of Na<sub>V</sub> channel voltage sensors are important for the interaction of Pre1a with Na<sub>V</sub> channels but cannot account for its unique subtype selectivity. Through analysis of the binding regions we ascertained that the variability of the S1-S2 loops between Na<sub>V</sub> channels contributes substantially to the selectivity profile observed for Pre1a, particularly with regards to fast inactivation. A serine residue on the DIV S2 helix was found to be sufficient to explain Pre1a's potent and selective inhibitory effect on the fast inactivation process of Na<sub>V</sub>1.1 and 1.3. This work highlights that interactions with both S1-S2 and S3-S4 of Na<sub>V</sub> channels may be necessary for functional modulation, and that targeting the diverse S1-S2 region within voltage-sensing domains provides an avenue to develop subtype selective tools.
NOTCH1 mutations in CLL associated with trisomy 12 (2011)

Two recent studies reported whole-genome sequencing of chronic lymphocytic leukemia (CLL) samples and found repeated mutations in the XPO1 and NOTCH1 genes. XPO1 was found mutated in 2.4% of cases, while NOTCH1 was found mutated in 12.2% or 15.1% of CLL samples. Here we report the results of sequencing of XPO1 and NOTCH1 in 186 CLL cases. Our results confirmed frequency of XPO1 mutations. However, we found only 5 NOTCH1 mutations in 127 IGVH unmutated/ZAP70(+) CLL samples (4%), and one mutation was found in IGVH mutated/ZAP70(-) CLL for a total percentage of 1.5%. Because 4 of 6 mutated samples also showed trisomy 12, we sequenced NOTCH1 in an additional 77 cases with trisomy 12 CLLs, including 47 IGVH unmutated/ZAP70(+) cases. Importantly, we found 41.9% NOTCH1 mutation frequency in aggressive trisomy 12 CLL cases. Our data suggest that activation of NOTCH1 plays a critical role in IGVH unmutated/ZAP70(+) trisomy 12 CLL.