gebhart/patrepeval huggingface dataset:
Machine learning approaches to refining post-translational modification predictions and protein identifications from tandem mass spectrometry (2012)

Tandem mass spectrometry (MS/MS) is the dominant approach for large-scale peptide sequencing in high-throughput proteomic profiling studies. The computational analysis of MS/MS spectra involves the identification of peptides from experimental spectra, especially those with post-translational modifications (PTMs), as well as the inference of protein composition based on the putative identified peptides. In this thesis, we tackled two major challenges associated with an MS/MS analysis: 1) the refinement of PTM predictions from MS/MS spectra and 2) the inference of protein composition based on peptide predictions. We proposed two PTM prediction refinement algorithms, PTM-Clust and its Bayesian nonparametric extension iPTMClust, and a protein identification algorithm, pro-HAP, that is based on a novel two-layer hierarchical clustering approach that leverages prior knowledge about protein function. Individually, we show that our two PTM refinement algorithms outperform the state-of-the-art algorithms and our protein identification algorithm performs at par with the state of the art. Collectively, as a demonstration of our end-to-end MS/MS computational analysis of a human chromatin protein complex study, we show that our analysis pipeline can find high confidence putative novel protein complex members. Moreover, it can provide valuable insights into the formation and regulation of protein complexes by detailing the specificity of different PTMs for the members in each complex.
Protective effect of sulforaphane on indomethacin‐induced cytotoxicity via heme oxygenase‐1 expression in human intestinal Int 407 cells (2009)

Sulforaphane is known to be an indirect antioxidant that acts by inducing NF-E2-related factor 2 (Nrf2)-dependent phase II enzymes. In the present study, we investigated the effect of sulforaphane on the expression of heme oxygenase-1 (HO-1) in human intestinal Int 407 cells. RT-PCR and Western blot data revealed that sulforaphane induced an increase in HO-1 expression at the mRNA and protein levels, respectively. This induction was also marked by an increase in HO-1 activity. Actinomycin D (an RNA synthesis inhibitor) and cycloheximide (a protein synthesis inhibitor) inhibited sulforaphane-responsive HO-1 mRNA expression, indicating that sulforaphane is a requirement for transcription and de novo protein synthesis. Moreover, sulforaphane increased the nuclear levels of Nrf2 and increased the binding activity of nuclear proteins to the antioxidant responsive element consensus sequence. We also found that U0126, an ERK kinase inhibitor, suppressed the sulforaphane-induced HO-1 expression and nuclear translocation of Nrf2. Moreover, the cytoprotective effect of sulforaphane on indomethancin-induced cytotoxicity was partially blocked by ERK and HO-1 inhibitors, further demonstrating that sulforaphane attenuated oxidative stress through a pathway that involved ERK and HO-1. Taken together, this study gives additional support to the possible use of sulforaphane as a dietary preventive agent against oxidative stress-induced intestinal injury.
Positioning for the Internet of Things: A 3GPP Perspective (2017)

Many use cases in the Internet of Things (IoT) will require or benefit from location information, making positioning a vital dimension of the IoT. The 3rd Generation Partnership Project (3GPP) has dedicated a significant effort during its Release 14 to enhance positioning support for its IoT technologies to further improve the 3GPP-based IoT eco-system. In this article, we identify the design challenges of positioning support in Long-Term Evolution Machine Type Communication (LTE-M) and Narrowband IoT (NB-IoT), and overview the 3GPP's work in enhancing the positioning support for LTE-M and NB-IoT. We focus on Observed Time Difference of Arrival (OTDOA), which is a downlink based positioning method. We provide an overview of the OTDOA architecture and protocols, summarize the designs of OTDOA positioning reference signals, and present simulation results to illustrate the positioning performance.
A Photonic Method for Overcoming the Mode Partition Noise Contribution in the AM Noise Spectra of Periodic Electrical Signals (2010)

We measure the AM Noise of periodic electrical signals in the frequency domain. Mode partition noise is found to be detrimental and dependent on the signal’s duration. A photonic technique is presented alleviating this ambiguity.
Derivation of the Hematopoietic Stem Cell Compartment from Human Embryonic Stem Cell Lines (2005)

Since the derivation of human embryonic stem cell (hESC) lines, both experimental and clinical hematology have generated rising interest in differentiating functional hematopoietic progenitors from these pluripotent cell lines. Although the ability to generate primitive hematopoietic cells with in vivo reconstitution function has direct clinical application, success of this approach awaits a more in-depth understanding of factor and mechanisms that govern specification of pluripotent hESCs to hematopoietic lineage specification. Here, we highlight some of our laboratory's recent efforts in this area, in the hopes of providing insights toward this complex yet important area of biomedical research.
All-perfluoropolymer, nonlinear stability-assisted monolithic surface combines topology-specific superwettability with ultradurability (2023)

Developing versatile and robust surfaces that mimic the skins of living beings to regulate air/liquid/solid matter is critical for many bioinspired applications. Despite notable achievements, such as in the case of developing robust superhydrophobic surfaces, it remains elusive to realize simultaneously topology-specific superwettability and multipronged durability owing to their inherent tradeoff and the lack of a scalable fabrication method. Here, we present a largely unexplored strategy of preparing an all-perfluoropolymer (Teflon), nonlinear stability-assisted monolithic surface for efficient regulating matters. The key to achieving topology-specific superwettability and multilevel durability is the geometric-material mechanics design coupling superwettability stability and mechanical strength. The versatility of the surface is evidenced by its manufacturing feasibility, multiple-use modes (coating, membrane, and adhesive tape), long-term air trapping in 9-m-deep water, low-fouling droplet transportation, and self-cleaning of nanodirt. We also demonstrate its multilevel durability, including strong substrate adhesion, mechanical robustness, and chemical stability, all of which are needed for real-world applications.
A high sensitivity two-color interferometer for pulsed power plasmas (1997)

A high sensitivity, high bandwidth, two-color interferometer (1064 and 532 nm) has been tested on the Hawk pulsed power generator at the Naval Research Laboratory. The phase resolution is 10−5 waves with a rise time of 3 ns, a new capability for diagnosing plasmas, and neutrals in pulsed power experiments. The two-color feature is used to distinguish phase shifts from free (plasma) electrons and bound (neutral and ion) electrons. Simultaneous electron and neutral density measurements were demonstrated in a plasma opening switch (POS) experiment. The ability to measure small phase shifts with fast rise time were demonstrated in a plasma filled diode experiment. The high sensitivity and vibration isolation enable neutral gas distribution measurements from supersonic nozzles used in plasma radiation source experiments. Examples of these measurements and future applications are described.
Synthesis of a New Bivalent Hirudin Analog (hirufos), which includes a stable 4′‐phosphono‐L‐phenylalanine mimic of (L‐tyrosine O4‐sulfate)‐63 (1994)

Abstract The synthesis on solid phase of a new derivative of the anticoagulant protein hirudin is described (see Scheme and Fig.1 , I ). The henicosapeptide is a bivalent conjugate of the C‐terminus of hirudin and of the active‐site‐binding tetrapeptide D ‐Phe‐Pro‐Arg‐Pro linked via a tetraglycine spacer. The peptide, for which the name hirufos was coined, incorporates a stable phosphono derivative of L ‐phenylalanine which, combined with the other structural modifications, leads to a potent anticoagulant agent. Synthesis was readily achieved by the (9 H ‐fluoren‐9‐yl)‐methoxycarbonyl (Fmoc) strategy followed by acidolytic cleavage from the resin and deprotection, including the liberation of the crucial phosphonic group on L ‐phenylalanine.
Model of Endothelin-1–Induced Chronic Optic Neuropathy in Rat (2003)

ET-1 led to a mean reduction in optic nerve blood flow of 68%. There were no significant differences in RGC survival among the four ET-1 doses used in this study. Pooled across all ET-1 doses, RGC survival decreased incrementally at 21, 42, and 84 days (P < 0.001; mean +/- SD, 0.77 +/- 0.25, 0.60 +/- 0.27, and 0.50 +/- 0.26, respectively) and was statistically significantly lower at each time point than in the BSS-treated animals. The axon survival data also showed a similar time-dependent loss. Only one of 21 animals showed significantly increased disc cupping, and there was no relationship between RGC survival and change in cupping. CONCLUSIONS. Chronic administration of ET-1 to the rat optic nerve results in a time-dependent loss of RGCs and their axons without apparent change in optic disc topography.
Investigation of Prediction Accuracy, Sensitivity, and Parameter Stability of Large-Scale Propagation Path Loss Models for 5G Wireless Communications (2016)

This paper compares three candidate large-scale propagation path loss models for use over the entire microwave and millimeter-wave (mmWave) radio spectrum: the alpha-beta-gamma (ABG) model, the close-in (CI) free space reference distance model, and the CI model with a frequency-weighted path loss exponent (CIF). Each of these models have been recently studied for use in standards bodies such as 3GPP, and for use in the design of fifth generation (5G) wireless systems in urban macrocell, urban microcell, and indoor office and shopping mall scenarios. Here we compare the accuracy and sensitivity of these models using measured data from 30 propagation measurement datasets from 2 GHz to 73 GHz over distances ranging from 4 m to 1238 m. A series of sensitivity analyses of the three models show that the physically-based two-parameter CI model and three-parameter CIF model offer computational simplicity, have very similar goodness of fit (i.e., the shadow fading standard deviation), exhibit more stable model parameter behavior across frequencies and distances, and yield smaller prediction error in sensitivity testing across distances and frequencies, when compared to the four-parameter ABG model. Results show the CI model with a 1 m close-in reference distance is suitable for outdoor environments, while the CIF model is more appropriate for indoor modeling. The CI and CIF models are easily implemented in existing 3GPP models by making a very subtle modification -- by replacing a floating non-physically based constant with a frequency-dependent constant that represents free space path loss in the first meter of propagation.
Regulation of the junB gene by v-src. (1992)

The proteins encoded by cellular and viral src genes are believed to be involved in the transmission of mitogenic signals, the nuclear recipients of which are largely unknown. In this work, we report that four different v-src-transformed cell lines from three different species possess elevated levels of junB transcripts. Transient expression of junB promoter-chloramphenicol acetyltransferase constructs in NIH 3T3 cells was used to demonstrate that the increase in junB transcripts was specifically associated with v-src expression and could not be recapitulated with a c-src, v-H-ras, or v-raf expression vector. Deletion mutants were used to localize the v-src-responsive region in the junB promoter to a 121-nucleotide region encompassing the CCAAT and TATAA elements. This region is distinct from one in the 5' untranslated region of the junB gene which is required to maintain its high-level basal expression. Point mutagenesis of the junB TATAA box completely abolished v-src responsiveness, suggesting that proteins which bind to this element are modified by src transformation. Several v-src and c-src mutants were used to demonstrate that elevated tyrosine kinase activity of src proteins is required for the observed effects on junB expression. Finally, homology between the TATAA box regions of junB and the unrelated but src-responsive gene 9E3/CEF-4 suggests that modulation of gene activity through proteins which bind to this region may be a recurrent, although not exclusive, theme in src transforming action. Our results suggest that src proteins may modulate some nuclear effectors through pathways not involving cellular ras or raf gene products.
Enantioselective Total Synthesis of Octalactin A Using Asymmetric Aldol Reactions and a Rapid Lactonization to Form a Medium‐Sized Ring. (2006)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Understanding the Role of Interfaces for Water Management in Platinum Group Metal-Free Electrodes in Polymer Electrolyte Fuel Cells (2019)

A systematic analysis, both experimental and model-assisted, has been performed over three main configurations of platinum group metal-free (PGM-free) electrodes in polymer electrolyte fuel cells (PEFCs): catalyst-coated membrane CCM technology is being compared to the gas-diffusion electrode (GDE) method of electrode fabrication and juxtaposed to a hybrid/combined GDE-CCM method of membrane-electrode assembly (MEA) fabrication. The corresponding electrodes were evaluated for their electrochemical performance, modeled, and studied with in situ and operando X-ray computed tomography (X-ray CT). The study establishes that through-thickness inhomogeneities play the most important role in water withdrawal/water management and affect most significantly PGM-free PEFC performance. The catalyst integration technique results in formation of interfacial regions with increased porosity and surface roughness. These regions form critical interfaces de facto responsible for flooding type behavior of the PEFC as shown for a first time by operando X-ray CT. The computational model shows that the PEFC performance critically depends on liquid water formation and transport at cold and wet conditions.
IIPS: Infrastructure IP for Secure SoC Design (2014)

Security is becoming an increasingly important parameter in current system-on-chip (SoC) design due to diverse hardware security attacks that can affect manufacturers, system designers or end users. To effectively address the security issues, design-time considerations, e.g. incorporation of design-for-security (DfS) features, are becoming essential. However, DfS measures for diverse security threats require specific design modifications to achieve target security level, which significantly increases design effort thus time-to-market, and usually incurs considerable design overhead. In addition, the general heterogeneous architecture of current SoCs makes many core-level DfS mechanisms unusable at SoC level. In this paper, we propose a centralized on-chip infrastructure IP for SoC security (IIPS), which alleviates the SoC designers from separately addressing different security issues through design modifications in multiple cores. It also provides ease of integration and functional scalability. We consider a specific implementation of IIPS that provides protection against: (1) scan-based attack for information leakage through low-overhead authentication; (2) counterfeiting attacks through integration of a Physical Unclonable Function (PUF); and (3) hardware Trojan attacks through a test infrastructure fortrust validation. To make the IP amenable for plug-and-play during SoC design, working protocols of the security functions are designed to comply with IEEE 1500 Standard for Embedded Core Test (SECT). Since IIPS resides outside the functional modules, it does not incur functional performance or power overhead. Simulations and experiments on example SoC designs validate the effectiveness of IIPS in providing protections against diverse attacks at a low hardware overhead.
A logic of situated know-how (1991)

Know-how is an important concept in Artificial Intelligence. It has been argued previously that it cannot be successfully reduced to the knowledge of facts. In this paper, I present sound and complete axiomatizations for two non-reductive and intuitively natural formal definitions of the know-how of an agent situated in a complex environment. I also present some theorems giving useful properties of know-how, and discuss and resolve an interesting paradox (which is described within). This is done using a new operator in the spirit of Dynamic Logic that is introduced herein and whose semantics and proof-theory are given. 1 Introduction Knowledge and action are the two staples of AI. Traditionally, research in AI has focused on the conception of knowledge corresponding to know-that or the knowledge of facts. In earlier work, I have argued that an important notion of knowledge from the point of AI is the one corresponding to know-how or the knowledge of skills, and that this cannot be e...
N,N‐Dimethylselenourea (2003)

Abstract N,N‐Dimethylselenourea product: N,N‐Dimethylselenourea reactant: 37 g. (0.5 mole) of dimethylcyanamide
Proposal of Micro-Trichroic Structures for High-Sensitivity Color Image Sensors (2011)

We propose a micro-trichroic structure based on multiplexed Bragg reflectors. Employing such a structure on each image sensor (IS) cell can enhance the ability of color ISs. Numerical calculations confirm the feasibility of the proposed structure. We also emulated a structure with several layers, and reduced the number of layers substantially by decreasing the diffraction angles.
Soft Machines That are Resistant to Puncture and That Self Seal (2013)

A soft machine composed of a composite of elastomer and fibers resists puncture from sharp objects, and continues to operate even if punctured.
High Ammonia Levels in Brain Induce Tubulin in Cerebrum but Not in Cerebellum (1988)

Ingestion of large amounts of ammonium increases markedly the content of tubulin in brain. The effect on tubulin induction of ammonium ingestion for up to 100 days was investigated. Brain tubulin content showed a rapid initial increase (28%) at 2 days and reached 50% after 100 days on the diet. To discern if ammonia, the increase in urea synthesis, or both was responsible for tubulin induction, rats were maintained at several levels of uremia (by administering diets containing 0 to 80% protein) or in hyperammonemia (by urease treatment). Only ammonium administration in the diet and urease injection induced tubulin in brain. Tubulin was quantified in three different brain regions. There was a regional selectivity of tubulin induction by ammonia in rat brain. Whereas the cerebellum remained unaltered, the paleencephalon showed the highest increase, and the cerebral cortex exhibited only a modest increase.
Energy for central steam heating (1979)

The potential for energy conservation and the resulting net savings in costs if a central steam heating plant is replaced by individual gas-fired hot water boilers in the various buildings are discussed. A case study followed in the paper reveals that the savings in fuel will pay for the cost of the new hot water boiler installation in approximately four years. Calculations for annual savings that will likely occur as a result of replacing the central steam plant with individual hot water boilers. (MCW)
Addressing COVID-19 vaccine hesitancy (2022)

Immunization programmes have been globally recognized as one of the most successful medical interventions against infectious diseases. Despite the proven efficacy and safety profiles of coronavirus disease 2019 (COVID-19) vaccines, there are still a substantial number of people who express vaccine hesitancy. Factors that influence vaccine decision-making are heterogenous, complex, and context specific and may be caused or amplified by uncontrolled online information or misinformation. With respect to COVID-19, the recent emergence of novel variants of concern that give rise to milder disease also drives vaccine hesitancy. Healthcare professionals remain one of the most trusted groups to advise and provide information to those ambivalent about COVID-19 vaccination and should be equipped with adequate resources and information as well as practical guidance to empower them to effectively discuss concerns. This article seeks to summarize the currently available information to address the most common concerns regarding COVID-19 vaccination.
Cardiovascular changes in calcium-deficient chick embryos. (1987)

We have developed an experimental system involving calcium-deficient chick embryos to examine the relationship between calcium homeostasis and cardiovascular activities. We have found that the calcium-deficient embryos, when compared with control animals, exhibit tachycardia and are significantly hypertensive. The effects are unlikely to be due to gross cardiac malformations or hypertrophy. The hypertensive condition appears to be a specific result of the systemic calcium deficiency since calcium supplementation to these embryos significantly restores the functions to normality.
Robust speed control suppressing vibration caused by angular transmission error of planetary gear (2003)

This paper proposes a new robust speed control suppressing vibration caused by angular transmission error of planetary gear. For this purpose, first, this paper constructs a new numerical simulation model of angular transmission error of planetary gear, which is confirmed by the experimental data of the tested robot arm. Next, the proposed robust speed control system is designed by the two-degrees-of-freedom control system based on disturbance observer and coprime factorization. The numerical simulation results show that the proposed system regulates the motor velocity and suppresses the vibration.
KHAPE: Asymmetric PAKE from Key-Hiding Key Exchange. (2021)

OPAQUE [Jarecki et al., Eurocrypt 2018] is an asymmetric password authenticated key exchange (aPAKE) protocol that is being developed as an Internet standard and for use within TLS 1.3. OPAQUE combines an Oblivious PRF (OPRF) with an authenticated key exchange to provide strong security properties, including security against pre-computation attacks (called saPAKE security). However, the security of OPAQUE relies crucially on the security of the OPRF. If the latter breaks (by cryptanalysis, quantum attacks or security compromise), the user’s password is exposed to an offline dictionary attack. To address this weakness, we present KHAPE, a variant of OPAQUE that does not require the use of an OPRF to achieve aPAKE security, resulting in improved resilience and near-optimal computational performance. An OPRF can be optionally added to KHAPE, for enhanced saPAKE security, but without opening the password to an offline dictionary attack upon OPRF compromise.
Finding bugs with a constraint solver (2000)

A method for finding bugs in code is presented. For given small numbers j and k, the code of a procedure is translated into a relational formula whose models represent all execution traces that involve at most j heap cells and k loop iterations. This formula is conjoined with the negation of the procedure's specification. The models of the resulting formula, obtained using a constraint solver, are counterexamples: executions of the code that violate the specification.
INTEGRATED DIGITAL MICROFLUIDIC PLATFORM FOR QUALITY CONTROL IN NEXT-GENERATION SEQUENCING LIBRARY PREPARATION. (2011)

Abstract not provided.