gebhart/patrepeval huggingface dataset:
The detection, correlation, and comparison of peptide precursor and product ions from data independent LC‐MS with data dependant LC‐MS/MS (2009)

The detection, correlation, and comparison of peptide and product ions from a data independent LC-MS acquisition strategy with data dependent LC-MS/MS is described. The data independent mode of acquisition differs from an LC-MS/MS data acquisition since no ion transmission window is applied with the first mass analyzer prior to collision induced disassociation. Alternating the energy applied to the collision cell, between low and elevated energy, on a scan-to-scan basis, provides accurate mass precursor and associated product ion spectra from every ion above the LOD of the mass spectrometer. The method therefore provides a near 100% duty cycle, with an inherent increase in signal intensity due to the fact that both precursor and product ion data are collected on all isotopes of every charge-state across the entire chromatographic peak width. The correlation of product to precursor ions, after deconvolution, is achieved by using reconstructed retention time apices and chromatographic peak shapes. Presented are the results from the comparison of a simple four protein mixture, in the presence and absence of an enzymatically digested protein extract from Escherichia coli. The samples were run in triplicate by both data dependant analysis (DDA) LC-MS/MS and data-independent, alternate scanning LC-MS. The detection and identification of precursor and product ions from the combined DDA search results of the four protein mixture were used for comparison to all other data. Each individual set of data-independent LC-MS data provides a more comprehensive set of detected ions than the combined peptide identifications from the DDA LC-MS/MS experiments. In the presence of the complex E. coli background, over 90% of the monoisotopic masses from the combined LC-MS/MS identifications were detected at the appropriate retention time. Moreover, the fragmentation pattern and number of associated elevated energy product ions in each replicate experiment was found to be very similar to the DDA identifications. In the case of the corresponding individual DDA LC-MS/MS experiment, 43% of the possible detectable peptides of interest were identified. The presented data illustrates that the time-aligned data from data-independent alternate scanning LC-MS experiments is highly comparable to the data obtained via DDA. The obtained information can therefore be effectively and correctly deconvolved to correlate product ions with parent precursor ions. The ability to generate precursor-product ion tables from this information and subsequently identify the correct parent precursor peptide will be illustrated in a companion manuscript.
Liquid Metal Battery: An Electrometallurgical Approach to Large-Scale Energy Storage (2010)

Abstract not Available.
A Priori Model Estimation for FWI from Constrained Kinematic Inverse Problem (2012)

Exploration inverse methods such as Monte Carlo could provide the general solution for the fullwaveform inversion (FWI) inverse problem allowing incorporating complex a priori information and data with arbitrary noise distributions. Such an approach applied directly to the FWI problem is computationally not tractable. The alternative is to solve the highly non-linear part of the problem with a fast forward problem such as traveltime with a constrained random exploration. The obtained a priori models and uncertainties help greatly in solving the FWI. This approach was successfully applied to an offset vertical seismic profile (OVSP) case.
Open Information Extraction on Scientific Text: An Evaluation (2018)

Open Information Extraction (OIE) is the task of the unsupervised creation of structured information from text. OIE is often used as a starting point for a number of downstream tasks including knowledge base construction, relation extraction, and question answering. While OIE methods are targeted at being domain independent, they have been evaluated primarily on newspaper, encyclopedic or general web text. In this article, we evaluate the performance of OIE on scientific texts originating from 10 different disciplines. To do so, we use two state-of-the-art OIE systems applying a crowd-sourcing approach. We find that OIE systems perform significantly worse on scientific text than encyclopedic text. We also provide an error analysis and suggest areas of work to reduce errors. Our corpus of sentences and judgments are made available.
Observing Short-wave Infrared Atmospheric Fluorescence Near Radioactive Sources: A Feasibility Study (2014)

Abstract : We attempted to image atmospheric fluorescence in the short-wave infrared (SWIR) from several radioactive sources. Our detection system was an InGaAs camera, fitted with a 25 mm lens to image the scene. No definitive fluorescence was detected. We also used our system to observe the SWIR emission from a proton beam source and established certain criteria for use as fluorescence diagnostics. For example, we clearly observed an enhancement at 1050 nm relative to 1600 nm, consistent with known emission features of molecular nitrogen and with previously published results. However, even for a high activity cobalt-60 source, our recorded signal was not consistent with these diagnostics. Rather, we hypothesize that the small signal which was recorded may have been due to direct incidence of gamma rays on our detector. Compared with the ultraviolet (UV), the infrared emission is expected to be only 20% as bright. We suggest that to increase the signal to noise in the SWIR may require either a telescope to collect a greater fraction of the emission or to image a more localized source than the gamma emission. Further research should include coincident UV and SWIR observations.
A Review of an Old Dilemma: Demosaicking First, or Denoising First? (2020)

Image denoising and demosaicking are the first two crucial steps in digital camera pipelines. In most of the literature, denoising and demosaicking are treated as two independent problems, without considering their interaction, or asking which should be applied first. Several recent works have started addressing them jointly in works that involve heavy weight neural networks, thus incompatible with low power portable imaging devices. Hence, the question of how to combine denoising and demosaicking to reconstruct full color images remains very relevant: Is denoising to be applied first, or should that be demosaicking first? In this paper, we review the main variants of these strategies and carry-out an extensive evaluation to find the best way to reconstruct full color images from a noisy mosaic. We conclude that demosaicking should applied first, followed by denoising. Yet we prove that this requires an adaptation of classic denoising algorithms to demosaicked noise, which we justify and specify.
Segugio: Efficient Behavior-Based Tracking of Malware-Control Domains in Large ISP Networks (2015)

In this paper, we propose Segugio, a novel defense system that allows for efficiently tracking the occurrence of new malware-control domain names in very large ISP networks. Segugio passively monitors the DNS traffic to build a machine-domain bipartite graph representing who is querying what. After labelling nodes in this query behavior graph that are known to be either benign or malware-related, we propose a novel approach to accurately detect previously unknown malware-control domains. We implemented a proof-of-concept version of Segugio and deployed it in large ISP networks that serve millions of users. Our experimental results show that Segugio can track the occurrence of new malware-control domains with up to 94% true positives (TPs) at less than 0.1% false positives (FPs). In addition, we provide the following results: (1) we show that Segugio can also detect control domains related to new, previously unseen malware families, with 85% TPs at 0.1% FPs, (2) Segugio's detection models learned on traffic from a given ISP network can be deployed into a different ISP network and still achieve very high detection accuracy, (3) new malware-control domains can be detected days or even weeks before they appear in a large commercial domain name blacklist, and (4) we show that Segugio clearly outperforms Notos, a previously proposed domain name reputation system.
Antihyperglycemic Effect of Aporphines and their Derivatives in Normal and Diabetic Rats (2006)

The antihyperglycemic actions of some aporphines and their derivatives in normal Wistar, streptozotocin (STZ)-induced diabetic (IDDM) and nicotinamide-STZ induced diabetic (NIDDM) rats were investigated in this study. These compounds included thaliporphine, glaucine, boldine, N-methyllaurotetanine, and predicentrine and the derivatives, N-[2-(2-methoxyphenoxy)ethyl]norglaucine and diacetyl- N-allylsecoboldine. Bolus intravenous injection of these compounds decreased the plasma glucose levels in a dose-dependent manner in both normal and diabetic rats. Among them, thaliporphine was found to have the most potent antihyperglycemic effect in both NIDDM and IDDM diabetic rats. It was found that thaliporphine could stimulate the release of insulin in both normal and diabetic rats, and a dose of 1 mg per kg thaliporphine could significantly attenuate the increase of plasma glucose induced by an intravenous glucose challenge test in normal rats. Similar treatment with thaliporphine significantly increased the skeletal muscle glycogen synthesis in both normal and diabetic rats. Hence, the hypoglycemic effect of thaliporphine in diabetic rats could be attributed to the stimulation of insulin release and the increase of glucose utilization.
Peptide–Graphene Interactions Enhance the Mechanical Properties of Silk Fibroin (2015)

Studies reveal that biomolecules can form intriguing molecular structures with fascinating functionalities upon interaction with graphene. Then, interesting questions arise. How does silk fibroin interact with graphene? Does such interaction lead to an enhancement in its mechanical properties? In this study, using large-scale molecular dynamics simulations, we first examine the interaction of graphene with several typical peptide structures of silk fibroin extracted from different domains of silk fibroin, including pure amorphous (P1), pure crystalline (P2), a segment from N-terminal (P3), and a combined amorphous and crystalline segment (P4), aiming to reveal their structural modifications. Our study shows that graphene can have intriguing influences on the structures formed by the peptides with sequences representing different domains of silk fibroin. In general, for protein domains with stable structure and strong intramolecular interaction (e.g., β-sheets), graphene tends to compete with the intramolecular interactions and thus weaken the interchain interaction and reduce the contents of β-sheets. For the silk domains with random or less ordered secondary structures and weak intramolecular interactions, graphene tends to enhance the stability of peptide structures; in particular, it increases the contents of helical structures. Thereafter, tensile simulations were further performed on the representative peptides to investigate how such structure modifications affect their mechanical properties. It was found that the strength and resilience of the peptides are enhanced through their interaction with graphene. The present work reveals interesting insights into the interactions between silk peptides and graphene, and contributes in the efforts to enhance the mechanical properties of silk fibroin.
Cytokine-Independent Detection of Antigen-Specific Germinal Center T Follicular Helper Cells in Immunized Nonhuman Primates Using a Live Cell Activation-Induced Marker Technique (2016)

A range of current candidate AIDS vaccine regimens are focused on generating protective HIV-neutralizing Ab responses. Many of these efforts rely on the rhesus macaque animal model. Understanding how protective Ab responses develop and how to increase their efficacy are both major knowledge gaps. Germinal centers (GCs) are the engines of Ab affinity maturation. GC T follicular helper (Tfh) CD4 T cells are required for GCs. Studying vaccine-specific GC Tfh cells after protein immunizations has been challenging, as Ag-specific GC Tfh cells are difficult to identify by conventional intracellular cytokine staining. Cytokine production by GC Tfh cells may be intrinsically limited in comparison with other Th effector cells, as the biological role of a GC Tfh cell is to provide help to individual B cells within the GC, rather than secreting large amounts of cytokines bathing a tissue. To test this idea, we developed a cytokine-independent method to identify Ag-specific GC Tfh cells. RNA sequencing was performed using TCR-stimulated GC Tfh cells to identify candidate markers. Validation experiments determined CD25 (IL-2Rα) and OX40 to be highly upregulated activation-induced markers (AIM) on the surface of GC Tfh cells after stimulation. In comparison with intracellular cytokine staining, the AIM assay identified >10-fold more Ag-specific GC Tfh cells in HIV Env protein-immunized macaques (BG505 SOSIP). CD4 T cells in blood were also studied. In summary, AIM demonstrates that Ag-specific GC Tfh cells are intrinsically stingy producers of cytokines, which is likely an essential part of their biological function.
Microbial Treatment of Food-Production Waste with Thermopile Enzyme-Producing Bacterial Flora from a Giant Panda (2003)

パンダから分離した耐熱性酵素群を産生する新規な細菌株をGAMブイヨン培地に接種して55℃および60℃で盲目継代を繰り返して高温で増殖する細菌叢を確立し, その高温適応細菌叢を用いて食品関連廃棄物処理の実証試験を行った。高温適応菌を定着させた菌床3kgを入れた家庭用生ごみ処理機にオカラと魚屑を17週間に総計79.7kg, フスマと魚屑を12週間に67.2kg, フスマ, オカラと魚屑の混合物を17週間に100.2kgをおのおの連続的に投入した。その結果, 投入重量のおのおのの95.12%, 95.24%, 97.01%が消失し, 菌床の温度は最高73.2℃, 72.8℃, 72.4℃に達した。これらの結果から, 高温に適応させたパンダ由来細菌叢を用いて, オカラ, フスマなどの食品関連廃棄物を高温で迅速な処理が可能であることが判明した。
ChemInform Abstract: Diels‐Alder Reactions of 2,3‐Dimethylenepyrrole Analogues: A New Synthesis of Indoles. (1990)

Abstract The pyranopyrroles (III) represent stable cyclic analogues of 2,3‐dimethylenepyrrole.
Robust soliton crystals in a thermally controlled microresonator (2018)

We demonstrate robust soliton crystals generation with a fixed frequency pump laser through a thermoelectric-cooler-based thermal-tuning approach in a butterfly-packaged complementary-metal-oxide-semiconductor-compatible microresonator. Varieties of soliton crystal states, exhibiting "palm-like" optical spectra that result from the strong interactions between the dense soliton ensembles and reflect their temporal distribution directly, are experimentally observed by sweeping one cavity resonance across the pump frequency from the blue-detuned side by reducing the operating temperature of the resonator. Benefitting from the tiny intra-cavity energy change, repeatable interconversion between the chaotic modulation instability and stable soliton crystal states can be successfully achieved via simple tuning of the temperature or pump power, showing the easy accessibility and excellent stability of such soliton crystals. This work could facilitate microresonator-based optical frequency combs towards a portable, adjustable, and low-cost system while avoiding the requirements of delicate frequency-sweeping pump techniques.
Analysis of Toll-Like Receptors in Human Milk: Detection of Membrane-Bound and Soluble Forms (2019)

The bioactive and anti-inflammatory role of human milk components has been recognized; active milk components include soluble forms of Toll-like receptors (TLRs). Preterm babies are more susceptible to infections and may succumb to necrotizing enterocolitis (NEC), a gastrointestinal disease which is exacerbated by an excessive inflammatory response after TLR activation. Here, we investigated the presence of Toll-like receptors TLR1/2/4/6 in colostrum and mature milk of women who delivered before (preterm) or after (term) 37 weeks of gestational age, integrating classical immune-related techniques with proteomic LC-MS/MS analysis. We have detected immunoreactivity for TLRs mostly in preterm samples, even for TLR1 and TLR6, until now not described in human milk. We demonstrated the presence of only TLR2 in the milk fat globule membrane, while the immunoreactivity of TLR1/4/6 was ascribed to crossreaction with some interesting milk proteins sharing leucine-rich repeat domains. These results will provide new insights into the definition of the role of TLRs in intestinal immune regulation of the newborns.
THE INHIBITED AUTOXIDATION OF STYRENE: PART III. THE RELATIVE INHIBITING EFFICIENCIES OF ORTHO-ALKYL PHENOLS (1963)

The relative rates of reaction of a large number of ortho-alkyl phenols with styrylperoxy radicals have been measured at 65 °C. These groups have both an accelerating effect owing to their electron-donating character and a retarding effect which arises from steric factors. With two ortho-alkyl groups both the reaction rate and the overall polar contribution to the transition state decrease as the size of the alkyl groups is increased. A single o-t-butyl group produces a small enhancement of the reaction rate over and above its polar effect but this is not observed with any other alkyl groups.
Creating an Infrastructure for Ubiquitous Awareness. (2001)

Much research has examined the use of awareness tools for enhancing coordination. However, the proposed tools tend to either make people aware of one information source in great detail or a variety of sources with very little detail. We refer to this problem as the detail-variety trade-off. Another problem with awareness tools is that they are not interchangeable. Specifically, users of these tools have only limited ability to route awareness information to different types of awareness tools that might better suit their work styles. We believe these two problems are primarily software engineering problems to which we present a solution called CASS (Cross Application Subscription Services), for obtaining awareness information from diverse sources and routing it to a variety of awareness tools. Keywords: Event and Notification Server Architectures, Awareness, Push Technologies 1
Assessment of epithelial thickness by ultrasonic imaging. (1991)

Moisturizing creams and lotions are an important aspect of preventing pressure ulcers. This study reports the increased thickening of the epithelium on 11 subjects who used a moisturizing cream (treatment) for 20 days. The thickening of the epithelium was measured before use of the moisturizing cream, on day 1, day 8, and day 20 of the treatment, and 12 days after the treatment. The ultrasound measurements were similar before the treatment and 12 days post treatment; the measurements increased for the days of treatment. Current research would lead us to believe that short-term increase in epithelial thickness as produced by a moisturizer is a result of increased water content. Ultrasound imaging may be the new standard for comparing the effects of moisturing products.
Ember: a quasi-one-dimensional, unsteady flame solver (2017)

Ember is a quasi-one-dimensional, unsteady reacting flow solver. It can be used to simulate a number of fundamental flame configurations, including premixed laminar flames, opposed flow strained flames (premixed or diffusion), axisymmetric (tubular) flames with positive or negative curvature, and steady 2D flames in a prescribed velocity field (using the method of lines). Ember integrates the governing equations using a variant on the standard Strang splitting method called <em>rebalanced splitting</em>, which eliminates steady-state errors. Ember’s solver is implemented primarily in C++, which is made accessible to the user as a Python module to enable script-driven input files and provide extensibility through user-supplied functions. Ember is parallelized using the Intel TBB library to take advantage of modern multi-core processors.
Towards a Graceful Degradable Multicore-System by Hierarchical Handling of Hard Errors (2013)

We present a novel concept for handling permanent faults in a statically scheduled heterogeneous multi-core system by means of a software-based self-reconfiguration. Hard faults are handled in a hierarchical cross layer manner, either locally by each core itself, or globally by reconfiguring the full system. Local reconfiguration of a defect core is based on the adaptation of the executed task to the current fault state of the core, such that defect components are never used. This adaptation is achieved by a rescheduling of the program code of the task. If this local reconfiguration fails, then the binding of tasks to cores is modified. Because heterogeneous cores are allowed, this may require a rescheduling of the tasks whose binding is changed. Estimations for the runtime of such a global reconfiguration are presented. Moreover, it is shown that systems that support the global reconfiguration achieve the same fault tolerance level as systems with local repair only, but with reduced hardware overhead.
Biosorption and Transformation of Tetra-Chloroethylene and Trichloroethylene Using Mixed-Species Microbial Mats (1999)

Microbial mats are naturally occurring assemblages of aquatic organisms capable of sorbing and degrading various organic compounds. Kinetic transformation and sorption experiments were conducted in sealed batch vials, using microbial mats dosed with unlabeled tetrachloroethylene (PCE) and trichloroethylene (TCE) and radiolabeled forms of these compounds ([14C]PCE and [14C]TCE). Results indicated that sorption equilibrium was attained for both chemicals within a few hours. The sorption isotherm was linear, demonstrating that the sorption mechanism was partitioning. PCE was completely degraded in periods as short as 50 days under favorable growth conditions. Samples were also tested for degradation products, with analyses indicating that PCE and TCE are transformed through both aerobic and anaerobic pathways. The ability of the microbial mats to sorb and degrade PCE and TCE suggests a potential for their application to the bioremediation of media contaminated by these compounds.
Novel anionic photoacid generator (PAGs) and photoresist for sub-50-nm patterning by EUVL and EBL (2007)

A new series of anionic photoacid generators (PAGs), and corresponding polymers were prepared. The thermostability of PAG bound polymers was superior to PAG blend polymers. PAG incorporated into the polymer main chain showed improved resolution when compared with the PAG blend polymers. This was demonstrated by Extreme Ultraviolet lithography (EUVL) results: the fluorine PAG bound polymer resist gave 45 nm (1:1), 35 nm (1:2), 30 nm (1:3) and 20 nm (1:4) Line/Space as well as the 50 nm (1:1),30 nm (1:2) elbow patterns.