gebhart/patrepeval huggingface dataset:
Supplementary Data from High-Throughput Screening Identifies Cardiac Glycosides as Potent Inhibitors of Human Tissue Kallikrein Expression: Implications for Cancer Therapies (2023)

Supplementary Data from High-Throughput Screening Identifies Cardiac Glycosides as Potent Inhibitors of Human Tissue Kallikrein Expression: Implications for Cancer Therapies
Effectiveness of biosurfactant for the removal of trihalomethanes by biotrickling filter (2019)

In this study, the biodegradation of a mixture of two trihalomethane (THM) compounds, chloroform (CF) and dichlorobromomethane (DCBM), was evaluated using two laboratory-scale biotrickling filters (BTFs). The two BTFs, hereby designated as "BTF-A" and "BTF-B," were run parallel and used ethanol as co-metabolite at different loading rates (LRs), and a lipopeptide-type biosurfactant that was generated by the gram-positive bacteria, Surfactin, respectively. The results using BTF-A showed that adding ethanol at a higher rate of 4.59 g/(m<sup>3</sup> h) resulted in removal efficiencies of 85% and 87% for CF and DCBM, respectively. Conversely, for the same LR, the use of Surfactin without ethanol (BTF-B) showed comparable removal efficiencies of 85% and 80% for CF and DCBM, respectively. The maximum rate constant for CF and DCBM for the BTF-A was 0.00203 s<sup>-1</sup> and 0.0022 s<sup>-1</sup>, respectively. For the same THMs LR, similar reaction rate constants resulted for the BTF-B. Further studies were conducted to investigate and understand the microbial diversity within both BTFs. The result indicated that for BTF with co-metabolite, <i>Fusarium sp</i>. was the most dominant fungi over 98% followed by <i>F. Solani</i> with less than 2%. <i>F. oxysporum</i> and <i>Fusarium sp</i>. were instead the <i>dominant fungi for the BTF with Surfactin. Before introducing the Surfactin into the BTF, the batch experiment was conducted to evaluate the effectiveness of synthetic surfactant as compared to a biosurfactant (Surfactin). In this regard, vials with Surfactin showed better performance than vials with Tomadol 25-7 (synthetic surfactant)</i>.
The Concept of Green Marketing and Green Product Development on Consumer Buying Approach (2014)

As the ecological issues are getting worse, the consumers’ concerns about the environmental protection have led to the diversification in consumer buying approach towards a green lifestyle. Therefore, firms are taking action to develop potential ecological approaches in the green market industry. Green marketing and green product development are useful techniques that are used by firms to increase competitive advantages and stand a chance of gaining the satisfaction of consumers in order to achieve the firm’s mission and vision. Green marketing and green product development have various benefits to firms in terms of increasing the sustainable environmental benefits and to increase the awareness of brand image of the firm. This study focuses on the concept of green marketing and green product development, the different consumer consumption in regards to green marketing and green product development, and lastly examines the problems that firms have faced when they have failed to implement green marketing and green product development.
Cryptographic Key Derivation from Biometric Inferences for Remote Authentication (2021)

Biometric authentication is getting increasingly popular because of its appealing usability and improvements in biometric sensors. At the same time, it raises serious privacy concerns since the common deployment involves storing bio-templates in remote servers. Current solutions propose to keep these templates on the client's device, outside the server's reach. This binds the client to the initial device. A more attractive solution is to have the server authenticate the client, thereby decoupling them from the device. Unfortunately, existing biometric template protection schemes either suffer from the practicality or accuracy. The state-of-the-art deep learning (DL) solutions solve the accuracy problem in face- and voice-based verification. However, existing privacy-preserving methods do not accommodate the DL methods, as they are tailored to hand-crafted feature space of specific modalities in general. In this work, we propose a novel pipeline, Justitia, that makes DL-inferences of face and voice biometrics compatible with the standard privacy-preserving primitives, like fuzzy extractors (FE). For this, we first form a bridge between Euclidean (or cosine) space of DL and Hamming space of FE, while maintaining the accuracy and privacy of underlying schemes. We also introduce efficient noise handling methods to keep the FE scheme practically applicable. We implement an end-to-end prototype to evaluate our design, then show how to improve the security for sensitive authentications and usability for non-sensitive, day-to-day, authentications. Justitia achieves the same, 0.33% false rejection at zero false acceptance, errors as the plaintext baseline does on the YouTube Faces benchmark. Moreover, combining face and voice achieves 1.32% false rejection at zero false acceptance. According to our systematical security assessments conducted through prior approaches and our novel black-box method, Justitia achieves ~25 bits and ~33 bits of security guarantees for face- and face&voice-based pipelines, respectively.
Easy Method for the Transformation of Levulinic Acid into Gamma-Valerolactone Using a Nickel Catalyst Derived from Nanocasted Nickel Oxide (2019)

Different nickel catalysts have been tested for the transformation of levulinic acid into γ-valerolactone using an easy hydrothermal method, taking advantage of the properties of the high temperature water. A metallic nickel catalyst derived from NiO synthesized by a nanocasting procedure can achieve a productivity to γ-valerolactone, which is two orders of magnitude higher than that obtained by a commercial nickel catalyst. This nanocasted metallic nickel catalyst has shown bifunctionality as it is capable of activating water as the source for hydrogen and undertaking the further hydrogenation step. In contrast with metallic nickel, nickel oxide has shown to be incapable of transforming levulinic acid into γ-valerolactone.
A new gate pattern measurement for evaluating the BTI degradation in circuit conditions (2014)

In this paper, we develop a new “recovery free” measurement technique able to apply arbitrary NBTI stress patterns of `1' & `0' on the gate of the transistor. This technique is very useful to evaluate the BTI degradation seen by the device in circuit conditions. With this method, it is shown that the NBTI shift does not depend on the bit arrangement within a sequence for bit length <;1μs but only on the overall circuit activity. Such a result validates the standard approach based on regular AC stress to address NBTI concern at circuit level. Furthermore, all the revisited results obtained with our new measurement technique are successfully modeled using a dedicated numerical RC model. It gives new insights on the physical mechanisms responsible for NBTI in advanced nodes.
Nutrient Regulation of Signaling & Transcription by O‐GlcNAcylation (2015)

O‐GlcNAcylation of nuclear and cytoplasmic proteins is a major sensor of cellular nutrient status, and has extensive crosstalk with phosphorylation and other post‐translational modifications. This extensive crosstalk regulates transcription, signaling and cellular metabolism in response to nutrient status. O‐GlcNAcylation plays a fundamental role in gene transcription at many levels, including regulation of the basal machinery, as well as modifying the interactions and localizations of transcription factors. O‐GlcNAc is also part of the histone code. Prolonged excess O‐GlcNAcylation, as occurs in diabetes, underlies fundamental mechanisms of glucose toxicity. Abnormal O‐GlcNAcylation is associated with neurodegenerative disease, and is elevated in most types of cancer. Over one‐half of all kinases are both modified and many are regulated by O‐GlcNAcylation. O‐GlcNAcylation either inhibits or activates, depending upon the kinase, and can alter substrate specificity. Hyper‐O‐GlcNAcylation of mitochondrial proteins in diabetic tissues contributes directly to mitochondrial dysfunction. Mitochondrial O‐GlcNAc transferase (OGT) is strikingly elevated and mis‐localized in cardiac mitochondria from diabetic rats. O‐GlcNAcylation is very abundant at nerve terminals, where it is highly enriched on synaptic vesicle proteins, and appears to play a direct role in learning and memory. Focused, inducible knock out of OGT in adult brain neurons produces a satiety defect and a morbidly obese mouse within only three weeks. Supported by NIH R01CA42486, R01DK61671; N01‐HV‐00240; P01HL107153 and the Patrick C. Walsh Prostate Cancer Research Fund. Dr. Hart receives a share of royalty received by the universityon sales of the CTD 110.6 antibody, which are managed by JHU
Biodiversity assessment of the northern Somali coast east of Berbera (1999)

A coastal biodiversity survey was undertaken on the northern Somali coast to establish&#13;\nthe status of the marine resources in the region, threats to the biodiversity and&#13;\nappropriate measures for the sustainable use and conservation of the resources. It&#13;\nformed part of the IUCN Somali Natural Resources Management Programme, funded by&#13;\nthe EC, which aims to improve the socio-economic well-being of the Somali people by&#13;\nenhancing the ecological sustainability of their natural resource use. Fieldwork was&#13;\ncarried out in collaboration with Cooperazione Internationale (COOPI)....
Lazy updates for distributed search structure (1993)

Very large database systems require distributed storage, which means that they need distributed search structures for fast and efficient access to the data. In this paper, we present an approach to maintaining distributed data structures that uses lazy updates, which take advantage of the semantics of the search structure operations to allow for scalable and low-overhead replication. Lazy updates can be used to design distributed search structures that support very high levels of concurrency. The alternatives to lazy update algorithms (eager updates) use synchronization to ensure consistency, while lazy update algorithms avoid blocking. Since lazy updates avoid the use of synchronization, they are much easier to implement than eager update algorithms. We demonstrate the application of lazy updates to the dB-tree, which is a distributed B+ tree that replicates its interior nodes for highly parallel access. We develop a correctness theory for lazy updates so that our algorithms can be applied to other distributed search structures.
Focusing inside negative index materials (2004)

Two key theoretical predictions for flat negative index lenses are that thicker lenses should have both internal and external foci, and that these foci should move linearly with small deviations in frequency. Two-dimensional electric field profiles of microwave transmission through rectangular slabs of composite wire and split-ring resonator material are presented. By scanning inside and outside the material, both internal and external foci are revealed. The power concentration around the internal focus is shown to have a negative curvature, consistent with the theoretical predictions.
Synthetic, Structural, Chemical, and Electrochemical Studies of the Metallatricarbadecaboranyl Analogues of Ferrocene, Ruthenocene, and Osmocene and the Observation of a Reversibleη6−η4Tricarbadecaboranyl Coordination that Is Analogous to theη5−η3Cyclopentadienyl Ring-Slippage Process (2002)

The tricarbadecaboranyl anions, 6-R-nido-5,6,9-C3B7H9- (R = CH3 or C6H5), have been employed to produce a series of metallatricarbadecaboranyl analogues of the group VIII metallocenes, (η5-C5H5)2M, M = Fe, Ru, and Os, including 1-(η5-C5Me5)-2-Me-closo-1,2,3,4-RuC3B7H9 (3), commo-Ru-(2-Me-closo-1,2,3,4-RuC3B7H9)2 (4), commo-Os-(4‘-Me-closo-1‘,2‘,3‘,4‘-OsC3B7H9)(2-Me-closo-1,2,3,4-OsC3B7H9) (5), commo-Os-(2-Me-closo-1,2,3,4-OsC3B7H9)2 (6), 1-(η5-C5H5)-2-Ph-closo-1,2,3,4-FeC3B7H9 (7), and 1-(η5-C5Me5)-2-Ph-closo-1,2,3,4-RuC3B7H9 (8). In the mixed ligand complexes 3, 7, and 8, formal Fe2+ and Ru2+ ions are sandwiched between the tricarbadecaboranyl and cyclopentadienyl monoanionic ligands, while in complexes 4, 5, and 6 the Ru2+ and Os2+ ions are sandwiched between two tricarbadecaboranyl ligands. In all complexes, the metals are η6-coordinated to the puckered six-membered face of the tricarbadecaboranyl cage. Reaction of 7 with Cr(CO)6 resulted in the formation of the arene-substituted complex 1-(η5-C5H5)-2-[(η6-C6H5)Cr(CO)3]-closo-1,2,3,4-FeC3B7H9 (9). Complexes 3 and 7 were also found to undergo reversible cage-slippages between the η6−η4 coordination modes during the association−dissociation reactions of these complexes with tert-butylisocyanide to produce 8-(η5-C5Me5)-8-(CNBut)-9-Me-nido-8,7,9,10-RuC3B7H9 (10) and 8-(η5-C5H5)-8-(CNBut)-9-Ph-nido-8,7,9,10-FeC3B7H9 (11), respectively. This reversible η6−η4 coordination is analogous to the η5−η3 ring-slippage process that is proposed to occur in related reactions of cyclopentadienyl-metal complexes. Electrochemical studies revealed that the tricarbadecaboranyl compounds undergo reversible one-electron oxidations and two successive one-electron reductions. Comparison of oxidation E1/2 values for Cp and RC3B7H9 analogues indicates a comparative electronic effect of +0.44 V for the tricarbadecaboranyl group. Reduction E1/2 values indicate a stabilization energy of 1.2−1.7 V in excess of the comparative electronic effect. It is likely that the overall ligand-induced stabilization of low metal oxidation states arises in part from redox-induced hapticity changes of the tricarbadecaboranyl ligand. Formal M0 dianions are detected that have no precedence in the metallocenes.
Retroviral IFN-α Gene Transfer Combined with Gemcitabine Acts Synergistically via Cell Cycle Alteration in Human Pancreatic Carcinoma Cells Implanted Orthotopically in Nude Mice (2004)

Standard chemotherapy for pancreatic carcinoma is based on the use of gemcitabine. The clinical benefit of interferon-alpha (IFN-alpha) in advanced pancreatic cancer has been shown. However, it has been demonstrated that to be effective, there is a need for a constant amount of IFN-alpha at the site of the tumor. Therefore, we examined transfection of the human pancreatic cancer cell line DAN-G with a retrovirus encoding for IFN-alpha and the effect of IFN-alpha gene expression alone or in combination with gemcitabine on growth inhibition of DAN-G pancreatic cancer cells in vitro and in vivo in orthotopically implanted DAN-G cells in nude mice. DAN-G cells could be efficiently transfected retrovirally by the human IFN-alpha gene and significantly enhanced the levels of IFN-alpha mRNA. In vitro gemcitabine led to an alteration of G1/S phase progression in transduced as well as untransduced cells, whereas IFN-alpha led to a significant decrease in cell viability in the transduced cells via delay in the progression of the S phase but no alteration of G1/S phase progression. In vivo, tumor volume in mice was reduced significantly with gemcitabine combined with IFN-alpha (76% +/- 8.3%) compared with gemcitabine alone (62.9% +/- 7.3%) or IFN-alpha alone (24.4% +/- 5.2%) compared with untreated animals. We conclude that gemcitabine and IFN-alpha concomitantly inhibited tumor cell proliferation significantly.
A Novel and Intuitive Method of Displaying and Interacting with Mass Difference Information: Application to Oligonucleotide Drug Impurities (2015)

A new method is presented for determining relationships between components in complex analytical systems. The method uses the mass differences between peaks in high resolution electrospray ionization (ESI) mass spectra. It relates peaks that share common mass differences. The method is based on the fundamental assumption that peaks in the spectra having the same exact mass difference are related by the same chemical moiety/substructure. Moreover, the presence (or absence/loss) of the same chemical moiety from a series of molecules may reflect similarities in the mechanisms of formation of each molecule. The determined mass differences in the spectra are used to automatically differentiate the types of components in the samples. Contour plots and summary plots of the summed total ion signal as a function of the mass difference are generated, which form powerful tools for the rapid and automated determination of the components in the samples and for comparisons with other samples. For the first time, in this work a unique profile contour plot has been developed that permits the interactive interrogation of the mass range by mass difference data matrix to obtain valuable information about components that share a common mechanism of formation, and all possible mechanisms of formation linked to a selected precursor molecule. The method can be used as an additional and complementary method to the existing analytical methods to determine relationships between components in complex chemical systems.
Broad-Band and Narrow-Band Measurements (1973)

EMC specifications consider two kinds of signals (broad band and narrow band). Special care is to be taken to determine the nature of the signal if meaningful measurements are desired. Tests specified in MIL-STD-462 and in other EMC specifications to decide if there are narrow-band or broad-band emissions are not conclusive, and many times it is difficult to make a decision about the nature of the signal. The decision is less difficult to make when bandwidth effects are understood. This paper tries to show the implications of performing EMC measurements using different receiver bandwidths. It appears that broad-band measurements are valid only in the special case in which the signal has a continuous flat frequency spectrum; in the other cases their meaning is rather questionable. In the conclusion some remarks are made in order to clarify this difficult situation.
hERG Classification Model Based on a Combination of Support Vector Machine Method and GRIND Descriptors (2008)

The human Ether-a-go-go Related Gene (hERG) potassium channel is one of the major critical factors associated with QT interval prolongation and development of arrhythmia called Torsades de Pointes (TdP). It has become a growing concern of both regulatory agencies and pharmaceutical industries who invest substantial effort in the assessment of cardiac toxicity of drugs. The development of in silico tools to filter out potential hERG channel inhibitors in early stages of the drug discovery process is of considerable interest. Here, we describe binary classification models based on a large and diverse library of 495 compounds. The models combine pharmacophore-based GRIND descriptors with a support vector machine (SVM) classifier in order to discriminate between hERG blockers and nonblockers. Our models were applied at different thresholds from 1 to 40 microm and achieved an overall accuracy up to 94% with a Matthews coefficient correlation (MCC) of 0.86 ( F-measure of 0.90 for blockers and 0.95 for nonblockers). The model at a 40 microm threshold showed the best performance and was validated internally (MCC of 0.40 and F-measure of 0.57 for blockers and 0.81 for nonblockers, using a leave-one-out cross-validation). On an external set of 66 compounds, 72% of the set was correctly predicted ( F-measure of 0.86 and 0.34 for blockers and nonblockers, respectively). Finally, the model was also tested on a large set of hERG bioassay data recently made publicly available on PubChem ( http://pubchem.ncbi.nlm.nih.gov/assay/assay.cgi?aid=376) to achieve about 73% accuracy ( F-measure of 0.30 and 0.83 for blockers and nonblockers, respectively). Even if there is still some limitation in the assessment of hERG blockers, the performance of our model shows an improvement between 10% and 20% in the prediction of blockers compared to other methods, which can be useful in the filtering of potential hERG channel inhibitors.
Predicting nucleosome positions on the DNA: combining intrinsic sequence preferences and remodeler activities (2009)

Nucleosome positions on the DNA are determined by the intrinsic affinities of histone proteins to a given DNA sequence and by the ATP-dependent activities of chromatin remodeling complexes that can translocate nucleosomes with respect to the DNA. Here, we report a theoretical approach that takes into account both contributions. In the theoretical analysis two types of experiments have been considered: in vitro experiments with a single reconstituted nucleosome and in vivo genome-scale mapping of nucleosome positions. The effect of chromatin remodelers was described by iteratively redistributing the nucleosomes according to certain rules until a new steady state was reached. Three major classes of remodeler activities were identified: (i) the establishment of a regular nucleosome spacing in the vicinity of a strong positioning signal acting as a boundary, (ii) the enrichment/depletion of nucleosomes through amplification of intrinsic DNA-sequence-encoded signals and (iii) the removal of nucleosomes from high-affinity binding sites. From an analysis of data for nucleosome positions in resting and activated human CD4(+) T cells [Schones et al., Cell 132, p. 887] it was concluded that the redistribution of a nucleosome map to a new state is greatly facilitated if the remodeler complex translocates the nucleosome with a preferred directionality.
Calibration of a Novel Low‐Cost Soil Water Content Sensor Based on a Ring Oscillator (2013)

Wireless sensor networks are becoming more popular to monitor spatial and temporal variability of soil water content. The aim of this paper is to calibrate and test the newly developed SPADE sensor for wireless sensor network applications. During calibration, the measured sensor output is related to dielectric permittivity using an empirical calibration in liquids with well‐defined permittivities. Using these calibration measurements, we have evaluated sensor‐to‐sensor variability and compared the accuracy of a universal calibration between sensor output and permittivity with a sensor‐specific calibration. Our results showed that the sensor‐to‐sensor variability of the SPADE sensor is larger than sensor noise and that a sensor‐specific calibration can improve the accuracy of soil water content estimation as compared to a single universal calibration. To quantify the effect of temperature on the sensor output, we have derived a temperature correction function in a temperature range from 5 to 40°C. The results showed an underestimation for low temperatures (5 to 25°C) and an overestimation for high temperatures (25 to 40°C). A second‐order polynomial function was fitted to the measurements with good agreement ( R 2 = 0.9831, RMSE = 0.1489). The transferability of the temperature correction function from reference liquids to soils was verified using saturated coarse sand and a silty loam soil sample. The temperature‐corrected SPADE sensor measurements in soil showed good agreement with TDR measurements and corresponded well with theoretical predictions from a dielectric mixing model.
Cell-Free Assays for HIV-1 Uncoating (2009)

Uncoating is an essential step in the retrovirus life cycle about which little is known. Uncoating is defined as the specific dissociation of the capsid shell from the viral core in the host cell cytoplasm. In this chapter, biochemical assays for studying HIV-1 uncoating in vitro are described. These techniques have proven useful for characterizing HIV-1 mutants that exhibit defects in the uncoating step of infection.