gebhart/patrepeval huggingface dataset:
Synthesis of anthelmintically active N‐methylated amidoxime analogues of the cyclic octadepsipeptide PF1022A (2002)

The N-methylated amidoxime analogues of the cyclic octadepsipeptide PF1022A represent novel derivatives with activity against Trichinella spiralis Owen and Nippostrongylus brasiliensis Lane in vitro and against parasitic nematodes in mice and sheep. Some of them show better activity against Hymenolepis nana Siebold, Heterakis spumosa Schneider and Heligmosomoides polygyrus Dujardin in mice than the natural product PF1022A. In particular an improved efficacy against Haemonchus contortus Rudolphi and Trichostrongylus colubriformis Giles in sheep compared to the potent cyclic octadepsipeptide PF1022A and its mono-thionated derivative has been observed. Here we report on a specific modification at the N-methyl amide linkage by using the mono-thionated PF1022A, resulting in novel anthelmintically active backbone analogues of PF 1022A.
NePTuNe: Neural Powered Tucker Networkfor Knowledge Graph Completion (2021)

Knowledge graphs link entities through relations to provide a structured representation of real world facts. However, they are often incomplete, because they are based on only a small fraction of all plausible facts. The task of knowledge graph completion via link prediction aims to overcome this challenge by inferring missing facts represented as links between entities. Current approaches to link prediction leverage tensor factorization and/or deep learning. Factorization methods train and deploy rapidly thanks to their small number of parameters but have limited expressiveness due to their underlying linear methodology. Deep learning methods are more expressive but also computationally expensive and prone to overfitting due to their large number of trainable parameters. We propose Neural Powered Tucker Network (NePTuNe), a new hybrid link prediction model that couples the expressiveness of deep models with the speed and size of linear models. We demonstrate that NePTuNe provides state-of-the-art performance on the FB15K-237 dataset and near state-of-the-art performance on the WN18RR dataset.
The Genetic Basis of Zinc Tolerance in the Metallophyte Arabidopsis halleri ssp. halleri (Brassicaceae): An Analysis of Quantitative Trait Loci (2007)

The species Arabidopsis halleri, an emerging model for the study of heavy metal tolerance and accumulation in plants, has evolved a high level of constitutive zinc tolerance. Mapping of quantitative trait loci (QTL) was used to investigate the genetic architecture of zinc tolerance in this species. A first-generation backcross progeny of A. halleri ssp. halleri from a highly contaminated industrial site and its nontolerant relative A. lyrata ssp. petraea was produced and used for QTL mapping of zinc tolerance. A genetic map covering most of the A. halleri genome was constructed using 85 markers. Among these markers, 65 were anchored in A. thaliana and revealed high synteny with other Arabidopsis genomes. Three QTL of comparable magnitude on three different linkage groups were identified. At all QTL positions zinc tolerance was enhanced by A. halleri alleles, indicating directional selection for higher zinc tolerance in this species. The two-LOD support intervals associated with these QTL cover 24, 4, and 13 cM. The importance of each of these three regions is emphasized by their colocalization with HMA4, MTP1-A, and MTP1-B, respectively, three genes well known to be involved in metal homeostasis and tolerance in plants.
Modularis (2021)

The enormous quantity of data produced every day together with advances in data analytics has led to a proliferation of data management and analysis systems. Typically, these systems are built around highly specialized monolithic operators optimized for the underlying hardware. While effective in the short term, such an approach makes the operators cumbersome to port and adapt, which is increasingly required due to the speed at which algorithms and hardware evolve. To address this limitation, we present Modularis , an execution layer for data analytics based on sub-operators , i.e., composable building blocks resembling traditional database operators but at a finer granularity. To demonstrate the feasibility and advantages of our approach, we use Modularis to build a distributed query processing system supporting relational queries running on an RDMA cluster, a serverless cloud platform, and a smart storage engine. Modularis requires minimal code changes to execute queries across these three diverse hardware platforms, showing that the sub-operator approach reduces the amount and complexity of the code to maintain. In fact, changes in the platform affect only those sub-operators that depend on the underlying hardware (in our use cases, mainly the sub-operators related to network communication). We show the end-to-end performance of Modularis by comparing it with a framework for SQL processing (Presto), a commercial cluster database (SingleStore), as well as Query-as-a-Service systems (Athena, BigQuery). Modularis outperforms all these systems, proving that the design and architectural advantages of a modular design can be achieved without degrading performance. We also compare Modularis with a hand-optimized implementation of a join for RDMA clusters. We show that Modularis has the advantage of being easily extensible to a wider range of join variants and group by queries, all of which are not supported in the hand-tuned join.
PSMA as a Theranostic Target in Hepatocellular Carcinoma: Immunohistochemistry and 68Ga‐PSMA‐11 PET Using Cyclotron‐Produced 68Ga (2021)

Prostate-specific membrane antigen (PSMA) is a validated target for molecular diagnostics and targeted radionuclide therapy. Our purpose was to evaluate PSMA expression in hepatocellular carcinoma (HCC), cholangiocarcinoma (CCA), and hepatic adenoma (HCA); investigate the genetic pathways in HCC associated with PSMA expression; and evaluate HCC detection rate with <sup>68</sup> Ga-PSMA-11 positron emission tomography (PET). In phase 1, PSMA immunohistochemistry (IHC) on HCC (n = 148), CCA (n = 111), and HCA (n = 78) was scored. In a subset (n = 30), messenger RNA (mRNA) data from the Cancer Genome Atlas HCC RNA sequencing were correlated with PSMA expression. In phase 2, <sup>68</sup> Ga-PSMA-11 PET was prospectively performed in patients with treatment-naïve HCC on a digital PET scanner using cyclotron-produced <sup>68</sup> Ga. Uptake was graded qualitatively and semi-quantitatively using standard metrics. On IHC, PSMA expression was significantly higher in HCC compared with CCA and HCA (P < 0.0001); 91% of HCCs (n = 134) expressed PSMA, which principally localized to tumor-associated neovasculature. Higher tumor grade was associated with PSMA expression (P = 0.012) but there was no association with tumor size (P = 0.14), fibrosis (P = 0.35), cirrhosis (P = 0.74), hepatitis B virus (P = 0.31), or hepatitis C virus (P = 0.15). Overall survival tended to be longer in patients without versus with PSMA expression (median overall survival: 4.2 vs. 1.9 years; P = 0.273). FGF14 (fibroblast growth factor 14) mRNA expression correlated positively (rho = 0.70; P = 1.70 × 10<sup>-5</sup> ) and MAD1L1 (Mitotic spindle assembly checkpoint protein MAD1) correlated negatively with PSMA expression (rho = -0.753; P = 1.58 × 10<sup>-6</sup> ). Of the 190 patients who met the eligibility criteria, 31 patients with 39 HCC lesions completed PET; 64% (n = 25) lesions had pronounced <sup>68</sup> Ga-PSMA-11 standardized uptake value: SUV<sub>max</sub> (median [range] 9.2 [4.9-28.4]), SUV<sub>mean</sub> 4.7 (2.4-12.7), and tumor-to-liver background ratio 2 (1.1-11). Conclusion: Ex vivo expression of PSMA in neovasculature of HCC translates to marked tumor avidity on <sup>68</sup> Ga-PSMA-11 PET, which suggests that PSMA has the potential as a theranostic target in patients with HCC.
Hydrolysis of Thyroglobulin by a Mast Cell Enzyme Present in Rat Thyroid Homogenates (1966)

A particulate fraction from rat thyroid homogenates hydrolyzes thyroglobulin at a rapid rate. The pH range of activity is 7.0–10.0, and the maximum reaction rate occurs in 0.5–1.0M of various salts and 0.05M mercaptoethanol. The salt serves to solubilize the enzyme, and the mercaptan functions to reduce thyroglobulin nonenzymatically, thereby producing a better substrate for hydrolysis. The protease is in the cell fraction that sediments between 600 and 24,000 ×g. The products of hydrolysis of thyroglobulin range from free iodoamino acids to peptides of a molecular weight of 100,000. The yield of thyroxine, triiodothyronine and diiodotyrosine is increased by a heat labile supernatant factor, probably a peptidase. Although the enzyme actively hydrolyzes thyroglobulin in homogenates, it probably does not do so in vivo, as it is located in mast cells of the thyroid. (Endocrinology78: 350, 1966)
Microvascular Responses to Ischemic Stroke following Splenectomy (2015)

Splenectomy is known to protect the brain against the tissue injury that results from ischemia and reperfusion (I/R). The mechanisms that underlie this neuroprotective effect of splenectomy remain poorly understood. An early response to brain I/R is the recruitment of inflammatory cells and platelets into the cerebral microvasculature. The objective of this study was to determine if splenectomy alters the recruitment of adherent leukocytes and platelets in cerebral microvessels in the early phase (24 hr) of reperfusion following ischemic stroke. Wild type C57Bl/6 mice underwent splenectomy or sham splenectomy two weeks prior to 45 min middle cerebral artery occlusion (MCAO) followed by 24 h of reperfusion. After 24 h of reperfusion, intravital fluorescence video microscopy was used to monitor and quantify the adhesion of leukocytes (rhodamine‐G6 labeled) and platelets (CFSE‐labeled) in cerebral venules. Infarct volume and peripheral blood counts were also measured. Splenectomy attenuates the recruitment of adherent platelets and leukocytes in the cerebral microvasculature and reduces infarct volume. The increased blood platelet count observed following MCAO was reduced to control levels in splenectomized animals. Peripheral leukocyte count did not differ between the splenectomized and sham splenectomized mice. These results implicate the spleen in I/R‐induced brain inflammation, thrombogenesis, and tissue necrosis as early as 24 h after reperfusion (Supported by a Malcolm Feist Postdoctoral Fellowship)
Outer Membrane Protein Subtypes and Biotypes of Haemophilus influenzae Type b: Relation Between Strains Isolated in 1934-1954 and 1977-1980 (1983)

Journal Article Outer Membrane Protein Subtypes and Biotypes of Haemophilus influenzae Type b: Relation Between Strains Isolated in 1934–1954 and 1977–1980 Get access Stephen J. Barenkamp, Stephen J. Barenkamp Search for other works by this author on: Oxford Academic PubMed Google Scholar Dan M. Granoff, Dan M. Granoff Search for other works by this author on: Oxford Academic PubMed Google Scholar Margaret Pittman Margaret Pittman Search for other works by this author on: Oxford Academic PubMed Google Scholar The Journal of Infectious Diseases, Volume 148, Issue 6, December 1983, Page 1127, https://doi.org/10.1093/infdis/148.6.1127 Published: 01 December 1983
Molecular Ordering of Organic Molten Salts Triggered by Single-Walled Carbon Nanotubes (2003)

When mixed with imidazolium ion-based room-temperature ionic liquid, pristine single-walled carbon nanotubes formed gels after being ground. The heavily entangled nanotube bundles were found to untangle within the gel to form much finer bundles. Phase transition and rheological properties suggest that the gels are formed by physical cross-linking of the nanotube bundles, mediated by local molecular ordering of the ionic liquids rather than by entanglement of the nanotubes. The gels were thermally stable and did not shrivel, even under reduced pressure resulting from the nonvolatility of the ionic liquids, but they would readily undergo a gel-to-solid transition on absorbent materials. The use of a polymerizable ionic liquid as the gelling medium allows for the fabrication of a highly electroconductive polymer/nanotube composite material, which showed a substantial enhancement in dynamic hardness.
Adaptive automotive communications solutions of 10 years lifetime enabled by ETSI RRS software reconfiguration technology (2017)

The vehicles typically have a lifetime of several years, possibly even longer than 10 years, over which communication technology will almost certainly evolve dramatically. The challenge of automotive communication platform is to ensure that a radio communication component remains relevant over the entire lifetime of a vehicle. A highly efficient software reconfiguration solution is introduced in this paper. ETSI Reconfiguration Radio System technology provides a suitable framework for automotive communication platform which allows to either add or replace entire Radio Access Technologies or to upgrade specific components across any of the entire layers.
Synthesis and Application of Cellulose-Polyethyleneimine Composites and Nanocomposites: A Concise Review (2021)

Cellulose/polyethyleneimine composites have increasingly attracted the attention of scientific community, devoted to the design and development of new synthetic strategies and materials for different application fields. In this review, after introducing the main characteristics of the two polymeric components, we provide in the second section a critical overview on the main protocols for the synthesis of these composites, considering both the several cellulose sources and forms, and the different cross-linkers and cross-linking procedures developed for this purpose, outlining advantages and limits for the reported approaches. The last section analyses the principal results obtained in different application fields. A wide discussion is dedicated to the principal use of cellulose/polyethyleneimine composites as sorbents for water remediation from heavy metal ions and organic contaminants. Subsequently, we introduce the literature describing the use of these composites, functionalized appropriately, where necessary, as drug delivery systems, sensors, and heterogeneous catalysts for organic reactions. Finally, after a brief description of other random applications, we furnish a personal analysis of actual limits and potentialities for these systems.
Venetoclax for Patients With Chronic Lymphocytic Leukemia With 17p Deletion: Results From the Full Population of a Phase II Pivotal Trial (2018)

Purpose Venetoclax is an orally bioavailable B-cell lymphoma 2 inhibitor. US Food and Drug Administration and European Medicines Agency approval for patients with 17p deleted relapsed/refractory chronic lymphocytic leukemia [del(17p) CLL] was based on results from 107 patients. An additional 51 patients were enrolled in a safety expansion cohort. Extended analysis of all enrolled patients, including the effect of minimal residual disease (MRD) negativity on outcome, is now reported. Patients and Methods Overall, 158 patients with relapsed/refractory or previously untreated (n = 5) del(17p) CLL received venetoclax 400 mg per day after an initial dose ramp up. Responses were based on 2008 International Workshop on Chronic Lymphocytic Leukemia criteria, with monthly physical exams and blood counts. Computed tomography scan was mandatory at week 36, after which assessment made was by clinical evaluation. Marrow biopsy was performed when complete remission was suspected. MRD was assessed by flow cytometry. Results Patients had a median of two prior therapies (range, zero to 10 therapies), 71% had TP53 mutation, and 48% had nodes that were ≥ 5 cm. Median time on venetoclax was 23.1 months (range, 0 to 44.2 months) and median time on study was 26.6 months (range, 0 to 44.2 months). For all patients, investigator-assessed objective response rate was 77% (122 of 158 patients; 20% complete remission) and estimated progression-free survival at 24 months was 54% (95% CI, 45% to 62%). For 16 patients who received prior kinase inhibitors, objective response rate was 63% (10 of 16 patients) and 24-month progression-free survival estimate was 50% (95% CI, 25% to 71%). By intent-to-treat analysis, 48 (30%) of 158 patients achieved MRD below the cutoff of 10<sup>-4</sup> in blood. Common grade 3 and 4 adverse events were hematologic and managed with supportive care and/or dose adjustments. Conclusion Venetoclax achieves durable responses and was well tolerated in patients with del(17p) CLL. A high rate of blood MRD < 10<sup>-4</sup> was achieved in this high-risk population.
The intrinsic photoferroelectric effect in the smectic C* phase of a chiral azobenzene (2006)

The ferroelectric properties in the liquid-crystalline smectic C* phase of the chiral mesogenic azobenzene (S)-4-(4-decyloxy-phenylazo)benzoic acid 4-(1-methylhexyloxy)-3-nitro-phenyl ester (‘W470’) were studied and found to be strongly dependent on the intensity of incident light. The light-induced trans to cis isomerization of the azobenzene chromophore which is an intrinsic constituent of this SmC* mesogen leads to a pronounced photoferroelectric effect since the ferroelectric SmC* ordering is considerably disturbed by the presence of bent-shaped cis-isomer molecules: At increasing light intensity a strong decrease of both SmC* order parameters, spontaneous electric polarization Ps and director tilt angle θ, is observed. It is further seen that even the nature of the ferroelectric transition is affected by the photoisomerization which leads to a crossover from the nearly tricritrical transition observed in the absence of light to a typical second-order transition. This result is interpreted theoretically taking into account a coupling between the director tilt and the biaxial order parameter which is strongly affected by the light-induced generation of the bent-shaped cis-isomers. The dynamics of the intrinsic photoferroelectric effect in W470 was studied by time-resolved measurements of spontaneous polarisation and director tilt.
Light emission from silicon-rich nitride nanostructures (2006)

Light-emitting Si-rich silicon nitride (SRN) films were fabricated by plasma enhanced chemical vapor deposition followed by low temperature (500–900°C) annealing. The optical properties of SRN films were studied by micro-Raman and photoluminescence spectroscopy and indicate the presence of small Si clusters characterized by broad near-infrared emission, large absorption/emission Stokes shift, and nanosecond recombination. Our results are supported by first-principles simulations indicating that N atoms bonded to the surface of nanometer Si clusters play a crucial role in the emission mechanism of SRN films. Light emission from SRN systems can provide alternative routes towards the fabrication of optically active Si devices.
Potential for cell therapy in Parkinson's disease using genetically programmed human embryonic stem cell–derived neural progenitor cells (2014)

Neural transplantation is a promising strategy for restoring dopaminergic dysfunction and modifying disease progression in Parkinson's disease (PD). Human embryonic stem cells (hESCs) are a potential resource in this regard because of their ability to provide a virtually limitless supply of homogenous dopaminergic progenitors and neurons of appropriate lineage. The recent advances in developing robust cell culture protocols for directed differentiation of hESCs to near pure populations of ventral mesencephalic (A9-type) dopaminergic neurons has heightened the prospects for PD cell therapy. Here, we focus our review on current state-of-the-art techniques for harnessing hESC-based strategies toward development of a stem cell therapeutic for PD. Importantly, we also briefly describe a novel genetic-programming approach that may address many of the key challenges that remain in the field and that may hasten clinical translation.
Supplementary Methods and Figure Legends 1-2 from A New Class of Quinoline-Based DNA Hypomethylating Agents Reactivates Tumor Suppressor Genes by Blocking DNA Methyltransferase 1 Activity and Inducing Its Degradation (2023)

Supplementary Methods and Figure Legends 1-2 from A New Class of Quinoline-Based DNA Hypomethylating Agents Reactivates Tumor Suppressor Genes by Blocking DNA Methyltransferase 1 Activity and Inducing Its Degradation
Immersive boundary conditions: Theory, implementation, and examples (2017)

Many applications in computational geophysics involve the modeling of seismic wave propagation on a set of closely related subsurface models. In such scenarios, it is of interest to recompute the seismic wavefields locally (only in the regions of change), instead of in the full subsurface model. We have developed a method for local acoustic wavefield recomputation that makes it possible to fully immerse a local modeling domain within a larger domain of arbitrary extent and complexity, such that the wave propagation in the full domain is completely accounted for. The method enables wavefield modeling on much smaller local domains, while relying on the up-front generation of a large number of Green’s functions and a wavefield extrapolation step at each time step of the simulation. A Kirchhoff-Helmholtz extrapolation integral is used to predict the interaction of the wavefield leaving the local domain with the exterior domain. The outward propagating wavefield and the wavefield reentering the local domain are applied as a boundary condition along the edges. Thanks to these dynamically calculated boundary conditions, all higher order long-range interactions between the two domains are fully accounted for. We have implemented the method in a conventional finite-difference time-domain scheme and determined that the locally calculated wavefields are equal to wavefields generated on the full domain to within numerical precision. The efficiency of the local modeling algorithm will greatly depend on the nature and size of the problem.
Mitigation of Faraday-induced polarization noise in retracing fibre-optic links (2017)

When an optical fibre crosses a magnetic field, a Faraday effect is generated, which perturbs the optical propagation, causing a modulation of the state of polarization (SOP) of the optical signal along the fibre [1]. This well known effect is often used to develop optical fibre current sensors. Yet, in optical communications systems relying on polarization sensitive elements (e.g. coherent detectors, modulators and integrated-optic components) the SOP Faraday-induced perturbation represents a source of noise. Strong unwanted Faraday effects have been detected in aerial optical cables in presence of lightning events [2]. Moreover, Faraday effects could impair system performances in access and datacom networks with electrical cables and optical fibres in close proximity. Recently, it has been reported that the combination of a quarter-wave plate (QWP) followed by a mirror, named mirrored quarter-wave plate (MQW), can compensate for polarization effects induced by any non-reciprocal circular birefringence, as in the case of Faraday-induced polarization rotation [3, 4]. This property has also been experimentally proved in a free-space optical retracing circuit with a MQW at the reflective end, cancelling the effect of a variable Faraday rotator inserted in the circuit [3].
Fibre-optic delay-line devices for r.f. signal processing (1977)

A bandpass filter and a discriminator for r.f. signals have been constructed by using fibre-optic delay lines, and their frequency-response characteristics have been investigated. Both devices had a fundamental frequency of 193 MHz, and the filter had a 3 dB passband of 10 MHz.