gebhart/patrepeval huggingface dataset:
A Novel Rearranged Cholestane Glycoside with a d-Lactone Ring System from Ornithogalum saundersiae Bulbs (2002)

The bulbs of Ornithogalum saundersiae have been revealed to contain a variety of cholestane glycosides.Further chemical investigation of the MeOH extract of O. saundersiae bulbs have resulted in the isolation of a novel 24(23→22)abeo-cholestane glycoside with a δ-lactone system (1).The structure of 1 was elucidated on the basis of extensive spectroscopic analysis and the result of acid hydrolysis.
An Intrusion-Tolerant Mechanism for Intrusion Detection Systems (2008)

In accordance with the increasing importance of intrusion detection systems (IDS), users justifiably demand the trustworthiness of the IDS. However, sophisticated attackers attempt to disable the IDS before they launch a thorough attack. Therefore, to accomplish its function, an IDS should have some mechanism to guarantee uninterrupted detection service even in the face of IDS component failures due to attacks. In this paper, we propose an intrusion-tolerant mechanism for network intrusion detection systems (NIDS) that employ multiple independent components. The mechanism monitors the detection units and the hosts on which the units reside and enables the IDS to survive component failure due to intrusions. As soon as a failed IDS component is discovered, a copy of the component is installed to replace it and the detection service continues. We implement the intrusion-tolerant mechanism based on the CSI-KNN-based NIDS and evaluate the prototype in the face of component failures. The results demonstrate that the mechanism can effectively tolerate intrusions.
Un procedimiento para la conversión de citronelal usando un tamiz molecular como catalizador (2007)

Referencia OEPM: P200302477.-- Fecha de solicitud: 14/10/2003.-- Titulares: Universidad Politécnica de Valencia (UPV), Consejo Superior de Investigaciones Científicas (CSIC).
One-Bit Compressed Sensing: Provable Support and Vector Recovery (2013)

In this paper, we study the problem of onebit compressed sensing (1-bit CS), where the goal is to design a measurement matrix A and a recovery algorithm such that a k-sparse unit vector x ∗ can be efficiently recovered from the sign of its linear measurements, i.e., b = sign(Ax ∗). This is an important problem for signal acquisition and has several learning applications as well, e.g., multi-label classification (Hsu et al., 2009). We study this problem in two settings: a) support recovery: recover the support of x ∗ , b) approximate vector recovery: recover a unit vector ˆx such that ‖ˆx − x∗‖2 ≤ ɛ. For support recovery, we propose two novel and efficient solutions based on two combinatorial structures: union free families of sets and expanders. In contrast to existing methods for support recovery, our methods are universal i.e. a single measurement matrix A can recover all the signals. For approximate recovery, we propose the first method to recover a sparse vector using a near optimal number of measurements. We also empirically validate our algorithms and demonstrate that our algorithms recover the true signal using fewer measurements than the existing methods. Proceedings of the 30 th
The Chloramphenicol-Inducible catB Gene in Agrobacterium tumefaciens Is Regulated by Translation Attenuation (2002)

Agrobacterium tumefaciens strains C58, A136, and BG53 are chloramphenicol resistant, and each contains the catB gene originally identified by Tennigkeit and Matzuran (Gene 99:113-116, 1991). The chloramphenicol acetyltransferase activity in all of the strains is chloramphenicol inducible. Examination of the catB gene in strain BG53 indicates that it is regulated by an attenuation mechanism similar to translation attenuation that regulates inducible catA genes resident in gram-positive bacteria and the inducible cmlA gene that confers chloramphenicol resistance in Pseudomonas spp.
Process of Protein Transport by the Type III Secretion System (2004)

The type III secretion system (TTSS) of gram-negative bacteria is responsible for delivering bacterial proteins, termed effectors, from the bacterial cytosol directly into the interior of host cells. The TTSS is expressed predominantly by pathogenic bacteria and is usually used to introduce deleterious effectors into host cells. While biochemical activities of effectors vary widely, the TTSS apparatus used to deliver these effectors is conserved and shows functional complementarity for secretion and translocation. This review focuses on proteins that constitute the TTSS apparatus and on mechanisms that guide effectors to the TTSS apparatus for transport. The TTSS apparatus includes predicted integral inner membrane proteins that are conserved widely across TTSSs and in the basal body of the bacterial flagellum. It also includes proteins that are specific to the TTSS and contribute to ring-like structures in the inner membrane and includes secretin family members that form ring-like structures in the outer membrane. Most prominently situated on these coaxial, membrane-embedded rings is a needle-like or pilus-like structure that is implicated as a conduit for effector translocation into host cells. A short region of mRNA sequence or protein sequence in effectors acts as a signal sequence, directing proteins for transport through the TTSS. Additionally, a number of effectors require the action of specific TTSS chaperones for efficient and physiologically meaningful translocation into host cells. Numerous models explaining how effectors are transported into host cells have been proposed, but understanding of this process is incomplete and this topic remains an active area of inquiry.
Properties and performance of a center/surround retinex (1997)

The last version of Land's (1986) retinex model for human vision's lightness and color constancy has been implemented and tested in image processing experiments. Previous research has established the mathematical foundations of Land's retinex but has not subjected his lightness theory to extensive image processing experiments. We have sought to define a practical implementation of the retinex without particular concern for its validity as a model for human lightness and color perception. We describe the trade-off between rendition and dynamic range compression that is governed by the surround space constant. Further, unlike previous results, we find that the placement of the logarithmic function is important and produces best results when placed after the surround formation. Also unlike previous results, we find the best rendition for a "canonical" gain/offset applied after the retinex operation. Various functional forms for the retinex surround are evaluated, and a Gaussian form is found to perform better than the inverse square suggested by Land. Images that violate the gray world assumptions (implicit to this retinex) are investigated to provide insight into cases where this retinex fails to produce a good rendition.
Vector Gratings Fabricated by Polarizer Rotation Exposure to Hydrogen-Bonded Liquid Crystalline Polymers (2011)

We present a simple yet efficient, competitive, and practical fabrication method, called "polarizer rotation exposure", for preparing vector gratings with a large area and a high diffraction efficiency. The polarization states of ultraviolet light were modulated by rotating the polarizer, and the resultant ultraviolet light was line-focused onto hydrogen-bonded liquid crystalline polymer films set on a linear stage. Mesogenic molecules in the polymer films were reoriented according to the light electric vectors, and vector gratings in which the optical anisotropy is periodically modulated were fabricated by the polarizer rotation exposure method.
Fairy Ring Disease of Cranberry: Assessment of Crop Losses and Impact on Cultivar Genotype (2008)

Fairy ring is a disease of cultivated cranberry common in the eastern growing regions of the United States, especially New Jersey and Massachusetts. Rings may persist for many years, and current control recommendations are costly and largely ineffective. The goal of this study was to accurately assess the impact of this disease on cranberry, a long-lived, high-value, perennial crop. The rate of fairy ring expansion, rate of formation of new rings, and distribution of rings across three cultivars were determined using a geographical information system (GIS) database that incorporated aerial and satellite imagery. Ring growth rates, estimated from imagery collected over a 10-year period in cv. Ben Lear, averaged 0.455 m in radius per year. Rings were observed in 'Ben Lear' three times more frequently than in either 'Early Black' or 'Stevens' cultivars. Direct sampling showed that estimates for yield within rings were 22 to 68% less than unaffected areas of the field for cv. Ben Lear. These estimates included the effects of fruit rot, which was elevated within rings to 18 to 29% of the total harvest. The impact on yield of 'Stevens' and 'Early Black' was lower than in 'Ben Lear'. Most cranberry cultivars are clonal and variation in fruit morphology within rings, particularly in 'Ben Lear', prompted an analysis of vine genotype. Areas affected by fairy ring in 'Ben Lear' showed an increase in genetic diversity at least 0.4 to 4 times that of unaffected areas. Therefore, it appears that fairy ring not only directly reduces yield but also can increase the host genetic diversity. This likely is due to increased seedling establishment resulting from seed drop when fruit decompose. Because seedlings typically yield less than the parental cultivar, the increase in genetic diversity also may contribute to long-term reduction of productivity in a cranberry field.
Abstract 2129: Proteogenomic analysis points to relationship between LINE-1 retrotransposon expression and copy number variation (2020)

Abstract Changes in the DNA copy number of genes (copy number variation/CNV) are widespread in many cancers and affect the expression of tumor suppressors and oncogenes. Many of these CNVs arise from chromosomal aberrations that are the result of improperly repaired DNA damage. LINE-1 retrotransposons - genomic elements that cut DNA and then reverse transcribe themselves into the gap - are expressed in many cancers and likely contribute to DNA damage and CNV in cancer cells. Using multi-omic data from CPTAC, we developed cloud-based tools on the NCI funded Cancer Genomics Cloud to measure LINE-1 RNA, protein, phosphoprotein and insertion in five cancer types - breast, ovarian, endometrial, kidney and colon - and identified mutation, expression and phosphorylation correlates of LINE-1 expression. We found significant LINE-1 expression in all, but kidney cancer. LINE-1 expression was significantly correlated with global copy number variation in breast, endometrial and ovarian cancer, a trend that was reflected in the fact that we observed the highest LINE-1 expression in ovarian cancer, which is characterized by very high CNV, and the lowest LINE-1 expression in kidney cancer, which has less overall CNV. This correlation is mirrored in our finding that, in breast, ovarian and endometrial cancer, p53 mutants express more LINE-1, indicating that high LINE-1 expression occurs in a background that is tolerant of DNA damage and CNV. We also observed an association between LINE-1 expression and phosphorylation of 53BP1 in breast, colon and endometrial cancers. ATM phosphorylated 53BP1 localizes to double strand breaks and promotes repair by non-homologous end-joining (NHEJ). Taken together, this analysis supports the hypothesis that in many cancers LINE-1 contributes to DNA damage and copy number variation, perhaps involving mismatched repair by NHEJ. Funded by NCI Contract No. HHSN261200800001E Citation Format: Wilson H. McKerrow, Xuya Wang, Mark Grivainis, David Fenyö. Proteogenomic analysis points to relationship between LINE-1 retrotransposon expression and copy number variation [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2129.
Binding Affinity via Docking: Fact and Fiction (2018)

In 1982, Kuntz et al. published an article with the title "A Geometric Approach to Macromolecule-Ligand Interactions", where they described a method "to explore geometrically feasible alignment of ligands and receptors of known structure". Since then, small molecule docking has been employed as a fast way to estimate the binding pose of a given compound within a specific target protein and also to predict binding affinity. Remarkably, the first docking method suggested by Kuntz and colleagues aimed to predict binding poses but very little was specified about binding affinity. This raises the question as to whether docking is the right tool to estimate binding affinity. The short answer is no, and this has been concluded in several comprehensive analyses. However, in this opinion paper we discuss several critical aspects that need to be reconsidered before a reliable binding affinity prediction through docking is realistic. These are not the only issues that need to be considered, but they are perhaps the most critical ones. We also consider that in spite of the huge efforts to enhance scoring functions, the accuracy of binding affinity predictions is perhaps only as good as it was 10⁻20 years ago. There are several underlying reasons for this poor performance and these are analyzed. In particular, we focus on the role of the solvent (water), the poor description of H-bonding and the lack of the systems' true dynamics. We hope to provide readers with potential insights and tools to overcome the challenging issues related to binding affinity prediction via docking.
1-Antitrypsin deficiency {middle dot} 6: New and emerging treatments for 1-antitrypsin deficiency (2004)

Alpha-1-antitrypsin (AAT) deficiency is a genetic condition that increases the risk of developing lung and liver disease, as well as other associated conditions. Most treatment of affected individuals is not specifically directed at AAT deficiency but focuses on the resultant disease state. The only currently available specific therapeutic agent-namely, intravenous augmentation with plasma derived AAT protein-is marketed in a limited number of countries. Treatments aimed at correcting the underlying genetic abnormality, supplementing or modifying the gene product, and halting or reversing organ injury are now beginning to emerge. These innovative approaches may prove effective at modifying or eliminating diseases association with AAT deficiency.
Classification and authentication of spices and aromatic herbs by means of HPLC-UV and chemometrics (2023)

Recent increase in the adulteration of spices and aromatic herbs in food industry constitutes a problem that requires exhaustive quality control. As every spice has a different composition with characteristic biomarkers, chromatographic profiles are especially valuable to authenticate these products. Thus, in this work a new high performance liquid chromatography (HPLC) method with UV–vis detection was developed for the characterization, identification and authentication of cinnamon, oregano, thyme, sesame, bay leaf, clove, cumin, and vanilla. Chromatographic separation was optimized based on the separation of six characteristic biomarkers (sesamol, eugenol, thymol, carvacrol, salicylaldehyde and vainillin) and was performed using a C18 reversed-phase column under a 35 min gradient elution based on 0.1% (v/v) formic aqueous solution and methanol by means of UV–Vis detection at 280 nm. 87 samples, purchased in local supermarkets, were analyzed and the obtained profiles were processed by chemometric techniques. First, data treatment was evaluated by principal component analysis (PCA); next soft independent modelling by class analogy (SIMCA) and partial least squares discriminant analysis (PLS-DA) were carried out in order to verify if classification according to their biomarkers was possible. The study concluded that PLS-DA (0.14–0.75% global error) classifies better the types of spice or aromatic herb than SIMCA (0.82–3.67% global error).
Gender, Racial, and Ethnic Inequities in Receipt of Multiple National Institutes of Health Research Project Grants (2023)

In this cross-sectional study of a national cohort of NIH-funded investigators, the gender, ethnic, and racial gaps in receipt of multiple research project grants among NIH investigators was clearly apparent and warrants further investigation and interventions.
A multicenter phase II study of bevacizumab (B) and temsirolimus (T) in women with recurrent epithelial ovarian cancer (OC): A study of the Mayo, Chicago, California, New York, Southeast, and Princess Margaret Phase II Consortia. (2013)

5517 Background: Anti-angiogenic therapy is active in OC; the combination of VEGF and mTOR inhibitors is hypothesized to further improve activity. This report is the OC cohort of a multi-histology phase II study assessing the activity and toxicity of B/T. Methods: Patients (Pts) with recurrent epithelial OC who had received ≤ 2 chemotherapy regimens and no prior treatment with a VEGF or mTOR inhibitor were eligible. A two-stage design was used with second stage accrual if &gt;6 pts had objective responses (OR) or &gt;10 pts of the first 25 remained progression-free (PF) at six months (mo). Pre-defined end-points for a recommendation for further clinical trial evaluation included at least 15/50 with OR or 26/50 PF at six mo. Treatment included T 25 mg IV wkly and B 10 mg/kg IV q14 days on 28 day cycles. Results: 58 pts were enrolled (the first 50 pts are used to determine a final recommendation). Median age=62 (range 35-82). A median of 4 (range 1-23) cycles were administered. 24 were platinum-sensitive, 34 resistant. Off-study reasons included 13 adverse events and disease progression in 38. 3 refused further therapy due to toxicity. 14 of the first 50 pts had partial response (PR) (9 platinum-resistant); 25/50 remained PF (8 PR, 15 SD, 2 non-progressing) at 6 mo. Grade (gr) 3/4 toxicities occurring &gt;2 events include: fatigue (4), stomatitis (7), hypertension (5), neutropenia (4), thrombocytopenia (4), hypokalemia (3). One rectal and one vaginal fistula, and two colonic perforations (one gr 2 and one gr 3 during cycles 3 and 1 respectively) were observed. Episodes of gr 1/2 oral, nasal, pulmonary, vaginal and gastrointestinal hemorrhage were also observed. Conclusions: Although the OR and PFS did not reach pre-defined standards, the numbers of OR and 6 mo PFS suggest potential enhanced activity with a combination of mTOR inhibitor with anti-angiogenic therapy. Other combinations of these targeted agents may result in more satisfactory activity with less toxicity. N01-CM-62203 (PMH) N01-CM-62208 (Southeast Phase 2) N01 CM-62209 (CCCP) N01-CM-62204 (NYCC) N01-CM-2011-0071C (Chicago) N01-CM62205 (Mayo) Clinical trial information: NCT01010126.
Light-Induced Conformational Alterations in Heliorhodopsin Triggered by the Retinal Excited State (2021)

Heliorhodopsins are a recently discovered diverse retinal protein family with an inverted topology of the opsin where the retinal protonated Schiff base proton is facing the cell cytoplasmic side in contrast to type 1 rhodopsins. To explore whether light-induced retinal double-bond isomerization is a prerequisite for triggering protein conformational alterations, we utilized the retinal oxime formation reaction and thermal denaturation of a native heliorhodopsin of <i>Thermoplasmatales archaeon</i> SG8-52-1 (TaHeR) as well as a <i>trans</i>-locked retinal analogue (TaHeR<sub>L</sub>) in which the critical C<sub>13</sub>═C<sub>14</sub> double-bond isomerization is prevented. We found that both reactions are light-accelerated not only in the native but also in the "locked" pigment despite lacking any isomerization. It is suggested that light-induced charge redistribution in the retinal excited state polarizes the protein and triggers protein conformational perturbations that thermally decay in microseconds. The extracted activation energy and the frequency factor for both the reactions reveal that the light enhancement of TaHeR differs distinctly from the earlier studied type 1 microbial rhodopsins.
An Amino Acid Residue (S201) in the Retinal Binding Pocket Regulates the Photoreaction Pathway of Phoborhodopsin (2011)

Phoborhodopsin from Halobacterium salinarum (salinarum phoborhodopsin, spR also called HsSR II) is a photoreceptor for the negative phototaxis of the bacterium. A unique feature of spR is the formation of a shorter wavelength photoproduct, P480, observed at liquid nitrogen temperature beside the K intermediate. Formation of similar photoproduct has not been reported in the other microbial rhodopsins. This photoproduct showed its maximum absorbance wavelength (λ(max)) at 482 nm and can thermally revert back to spR above -160 °C. It was revealed that P480 is a photoproduct of K intermediate by combination of an irradiation and warming experiment. Fourier transform infrared (FTIR) difference spectrum of P480 from spR in C-C stretching vibration region showed similar features with that of K intermediate, suggesting that P480 has a 13-cis-retinal chromophore. The appearance of a broad positive band at 1214 cm(-1) in the P480-spR spectrum suggested that configuration around C9═C10 likely be different between P480 and K intermediate. Vibrational bands in HOOP region (1035 to 900 cm(-1)) suggested that the chromophore distortion in K intermediate was largely relaxed in P480. The amount of P480 formed by the irradiation was greatly decreased by amino acid replacement of S201 with T, suggesting S201 was involved in the formation of P480. According to the crystal structure of pharaonis phoborhodopsin (ppR), a homologue of spR found in Natronomonas pharaonis, S201 should locate near the C14 of retinal chromophore. Thus, the interaction between S201 and C14 might be the main factor affecting formation of P480.
Low-Temperature Solution-Phase Synthesis of NiAu Alloy Nanoparticles via Butyllithium Reduction: Influences of Synthesis Details and Application As the Precursor to Active Au-NiO/SiO2 Catalysts through Proper Pretreatment (2009)

Bimetallic nanoparticles (NPs) have wide applications in electronics, photonics, and catalysis. However, it is particularly challenging to synthesize size-controllable alloy nanoparticles (e.g., NiAu) with bulk immiscible metals as the components. Here we report the synthesis of isolable NiAu alloy nanoparticles with tunable and relatively uniform sizes via a coreduction method employing butyllithium as the reducing agent and trioctylphosphine as the protecting agent. The influences of synthesis conditions (e.g., protecting agent, aging temperature, and the solvent used to wash the product) were investigated, and the synthesis mechanism was preliminarily surveyed. The NiAu alloy nanoparticles obtained were then used as the precursor to prepare an Au−NiO/SiO2 catalyst highly active in low-temperature CO oxidation, and the effects of pretreatment details and catalyst compositions on catalytic activity were studied. Relevant characterization employing XRD, TEM, UV−vis, TG/DTG, and FT-IR was conducted. In addition, the importance of the current synthesis of NiAu alloy NPs and the contribution of the catalyst design were discussed in the context of the literature.
Towards an Energetic Modeling of Rotorcraft Using Bond-Graphs (2013)

Presented at the AHS 69th Annual Forum, Phoenix, Arizona,May 21 –23, 2013. Copyright © 2013 by the AmericanHelicopter Society International, Inc. All rights reserved.
Ratiometric MRI Sensors Based on Core–Shell Nanoparticles for Quantitative pH Imaging (2014)

Ratiometric MRI sensors consist of paramagnetic cores and pH-sensitive polymer shells. The core-shell nanostructure enables the coexistence of two incompatible NMR relaxation properties in one particle. The sensors show pH sensitivity in transverse relaxivity (r2 ), but not in longitudinal relaxivity (r1 ). Quantitative pH imaging is achieved by measuring the r2 /r1 value with a clinical 3 T MRI scanner.