gebhart/patrepeval huggingface dataset:
Inhibition of thermolysin by phosphonamidate transition-state analogs: measurement of phosphorus-31-nitrogen-15 bond lengths and chemical shifts in two enzyme-inhibitor complexes by solid-state nuclear magnetic resonance (1990)

31P and 15N chemical shifts and 31P-15N bond lengths have been measured with solid-state NMR techniques in two inhibitors of thermolysin, carbobenzoxy-Glyp-L-Leu-L-Ala (ZGpLA) and carbobenzoxy-L-Phep-L-Leu-L-Ala (ZFpLA), both as free lithium salts and when bound to the enzyme. Binding of both inhibitors to thermolysin results in large changes in the 31P chemical shifts. These changes are more dramatic for the tighter binding inhibitor ZFpLA, where a approximately 20 ppm downfield movement of the 31P isotropic chemical shift (sigma iso) is observed. This shift is due to changes in the shift tensor elements sigma 11 and sigma 22, while sigma 33 remains essentially constant. We observed a similar pattern for ZGpLA, but only a approximately 5 ppm change occurs in sigma iso. The changes in the 15N chemical shifts for both inhibitors are small upon binding, amounting to downfield shifts of 2 and 4 ppm for ZGpLA and ZFpLA, respectively. This indicates that there are no changes in the protonation state of the 15N in either the ZFpLA- or the ZGpLA-thermolysin complex. NMR distance measurements yield a P-N bond length rP-N = 1.68 +/- 0.03 A for the tight binding inhibitor ZFpLA both in its free lithium salt form and in its thermolysin-ZFpLA complex, a distance that is much shorter than the 1.90-A distance reported by X-ray crystallography studies [Holden et al. (1987) Biochemistry 26, 8542-8553].(ABSTRACT TRUNCATED AT 250 WORDS)
Online control policy optimization for minimizing map uncertainty during exploration (2004)

Tremendous progress has been made recently in simultaneous localization and mapping of unknown environments. Using sensor and odometry data from an exploring mobile robot, it has become much easier to build high-quality globally consistent maps of many large, real-world environments. To date, however, relatively little attention has been paid to the controllers used to build these maps. Existing exploration strategies usually attempt to cover the largest amount of unknown space as quickly as possible. Few strategies exist for building the most reliable map possible, but the particular control strategy can have a substantial impact on the quality of the resulting map. In this paper, we devise a control algorithm for exploring unknown space that explicitly tries to build as large a map as possible while maintaining as accurate a map as possible. We make use of a parameterized class of spiral trajectory policies, choosing a new parameter setting at every time step to maximize the expected reward of the policy. We do this in the context of building a visual map of an unknown environment, and show that our strategy leads to a higher accuracy map faster than other candidate controllers, including any single choice in our policy class.
Novel pentamidine analogs in the treatment of experimental Pneumocystis carinii pneumonia (1990)

We have recently demonstrated that substitution of imidazoline moieties for the amidine groups of pentamidine produces a molecule that is effective against rat Pneumocystis carinii pneumonia and that is apparently less toxic than pentamidine. For this reason, 10 novel imidazoline substituted compounds were evaluated for their effect against rat P. carinii pneumonia. While several of the new compounds were observed to have advantages over pentamidine in the treatment of disease in the rat model, only one compound stood out as a potential new clinical agent. Treatment for 2 weeks with intravenous (i.v.) doses of 1,3-di(4-imidazolino-2-methoxyphenoxy)propane (DIMP) at 1 mg/kg per day produced an anti-P. carinii pneumonia effect equivalent to i.v. doses of pentamidine at 10 mg/kg per day. Although pentamidine and one of the test drugs, 1,3-di(4-imidazolinophenoxy)propane, showed no activity against P. carinii pneumonia when administered per os, DIMP exhibited potent anti-P. carinii pneumonia activity when given by daily gavage doses of 40 and 25 mg/kg. DIMP retained significant activity when given every other day by a gavage dose of 25 mg/kg. No toxicity was observed with the drug at any of the dose levels or by either of the routes of administration. However, the low solubility of the drug prevented testing at higher i.v. doses. Our conclusion is that DIMP has the potential of providing a safer and more effective alternative to pentamidine for the treatment of P. carinii pneumonia.
Anticancer Efficacy and Mechanisms of a Dual Targeting of Norepinephrine Transporter and Thyrointegrin αvβ3 Antagonist in Neuroblastoma (2022)

<b>Background:</b> In neuroendocrine tumors, the norepinephrine transporter (NET) is very active and has been exploited for diagnostic imaging purposes and/or therapy with localized radiotherapy. Integrin αvβ3 is generously expressed by and/or activated on cancer cells, but not by nonmalignant cells. <b>Purpose:</b> In the present investigation, the anticancer efficacy of the dual targeting of norepinephrine transporter (NET), benzylguanidine (BG), and thyrointegrin αvβ3 receptors antagonist triazole tetraiodothyroacetic acid (TAT) conjugated via the non-cleavable linker polyethylene glycol (P, PEG400) in the treatment of human neuroblastoma was evaluated. <b>Experimental approach:</b> The synthesized dual targeting compound, a novel new chemical entity named BG-P<sub>400</sub>-TAT, has purity > 98% and was formulated and tested in neuroblastoma models using neuroblastoma cell lines (SK-N-FI, SMS-KCN and SMS-KANR) implanted in SCID and NSG mice models. <b>Key Results:</b> BG-P<sub>400</sub>-TAT demonstrated significant (<i>**P<</i>0.01, <i>***P<</i> 0.001) suppression of neuroblastoma tumor progression, growth, and viability in both mice models implanted with the neuroblastoma. The pharmacokinetic and biodistribution profile of BG-P<sub>400</sub>-TAT showed a significant increase in BG-P<sub>400</sub>-TAT levels in plasma and xenografts of NSG compared to SCID mice. Further our RNAseq genome-wide expression profiling experiments in neuroblastoma cell line SKNAS results showed that BG-P<sub>400</sub>-TAT treatment altered the signal transduction pathways, intracellular multiprotein complexes and Independent GSEA. <b>Conclusion & Implications:</b> BG-P<sub>400</sub>-TAT represents a potential lead candidate for the treatment of neuroblastoma and other neuroendocrine tumors.
Failure Data Analysis for Aircraft Maintenance Planning (2004)

This paper presents an application of Weibull method for forecasting the failure rate of Boeing 737 Auxiliary power unit (APU) oil pumps. The Weibull method is extremely useful for maintenance planning. Using Weibull failure forecasting, a maintenance planner can make quantitative trades between scheduled and unscheduled maintenance or non-destructive inspection and replacement. The method also helps for determining the age at which an operating part in an aircraft system should be replaced with a new part. In this study, the failure rate of APU oil pump of Boeing 737 aircraft is modeled by using the Weibull technique. The results were in close agreement with the real data indicating the validity of the Weibull model in predicting failure rate of failure for APU oil pumps. In addition, the optimum replacement age of the pumps is also calculated for various cost ratios.
Midkine and NANOG Have Similar Immunohistochemical Expression Patterns and Contribute Equally to an Adverse Prognosis of Oral Squamous Cell Carcinoma (2017)

To increase the overall survival rate and obtain a better prognosis for oral squamous cell carcinoma (OSCC) patients, the detection of more effective and reliable tumor prognostic markers is needed. This study is focused on the analysis of correlation between the clinicopathological features of OSCCs and the immunohistochemical (IHC) expression patterns of MIDKINE (MK) and NANOG. Sixty-two primary OSCC patients were selected and their pretreatment biopsy specimens were immunohistochemically analyzed for the MK and NANOG proteins. The IHC expression patterns, clinicopathological features, and overall survival rates were assessed to identify any correlations. MK and NANOG showed significantly similar IHC expression patterns: both demonstrated enhanced expression in histologically high-grade and clinically late-stage OSCCs. Weak or negative expression of MK and NANOG was correlated with negative neck node metastasis. Clinicopathologically, late tumor stage, neck node metastasis, high-grade tumor, and palliative treatment groups showed significantly lower overall survival rates. The enhanced expression of MK and NANOG was associated with lower overall survival rates. In particular, enhanced co-detection of MK and NANOG showed significant correlation with poor prognosis. In conclusion, enhanced IHC expression patterns of MK and NANOG in OSCC patients was significantly associated with lower overall survival rates and unfavorable clinicopathological features. These results demonstrate that analysis of IHC expression patterns of MK and NANOG in pretreatment biopsy specimens during the work-up period can provide a more definitive prognosis prediction for each OSCC patient that can help clinicians to develop a more precise individual treatment modality.
Primaquine Diphosphate, a Known Antimalarial Drug, Blocks Vascular Leakage Acting Through Junction Stabilization (2021)

Endothelial barrier integrity is important for vascular homeostasis, and hyperpermeability participates in the progression of many pathological states, such as diabetic retinopathy, ischemic stroke, chronic bowel disease, and inflammatory disease. Here, using drug repositioning, we discovered that primaquine diphosphate (PD), previously known as an antimalarial drug, was a potential blocker of vascular leakage. PD inhibited the linear pattern of vascular endothelial growth factors (VEGF)-induced disruption at the cell boundaries, blocked the formation of VEGF-induced actin stress fibers, and stabilized the cortactin actin rings in endothelial cells. PD significantly reduced leakage in the Miles assay and mouse model of streptozotocin (STZ)-induced diabetic retinopathy. Targeted prediction programs and deubiquitinating enzyme activity assays identified a potential mechanism of action for PD and demonstrated that this operates via ubiquitin specific protease 1 (USP1). USP1 inhibition demonstrated a conserved barrier function by inhibiting VEGF-induced leakage in endothelial permeability assays. Taken together, these findings suggest that PD could be used as a novel drug for vascular leakage by maintaining endothelial integrity.
Ring Opening Metathesis Polymerization (1992)

Abstract : The central theme of this research is ring opening metathesis polymerization of norbornenes and substituted norbornadienes by well characterized imido alkylidene catalysts of the type M(CHR)(NR')(OR )2 (where R, R', and R are some alkyl or aryl groups), or most recently alkylidyne alkylidene rhenium catalysts of the type Re(CHR)(CR')(OR )2. Initially we focused on developing catalysts that would tolerate functionalities (such as carbonyl groups). The findings concerning the polymerization of 2,3- bistrifluoromethylnorbornadiene suggested that the polymer was virtually all trans and tactic. It is now believed to be syndiotactic. Such materials are highly polarizable above Tg(200 C). A significant fraction of the present effort is being expended toward understanding how this stereoselectivity arises and how it can be controlled by changing the nature of the catalyst.
Cryogenic Evaluation of Nanocrystalline Cores Using Partial Cancellation (2022)

The selection of appropriate magnetic materials is critical for achieving high efficiency in power electronics. Although ferrite is well established in research and industry, new magnetic materials like nanocrystalline boast several benefits as an alternative. These benefits include a high saturation flux density, less fragility, and a wide operating temperature range, making nanocrystalline well suited for applications requiring extreme operating conditions. An example of such an application is the use of superconductors (HTS) as transmitter or receiver coils in an IPT system, since the operating conditions demand stability under a high flux density and extremely low temperatures. For such applications, nanocrystalline core losses and B-H curves are characterised at room temperature and under cryogenic conditions using a partial cancellation method. The core losses and B-H curves are measured up to saturation, both in liquid nitrogen (LN2) and at room temperature.
Combining Bottom‐Up Self‐Assembly with Top‐Down Microfabrication to Create Hierarchical Inverse Opals with High Structural Order (2015)

Colloidal particles can assemble into ordered crystals, creating periodically structured materials at the nanoscale without relying on expensive equipment. The combination of small size and high order leads to strong interaction with visible light, which induces macroscopic, iridescent structural coloration. To increase the complexity and functionality, it is important to control the organization of such materials in hierarchical structures with high degrees of order spanning multiple length scales. Here, a bottom-up assembly of polystyrene particles in the presence of a silica sol-gel precursor material (tetraethylorthosilicate, TEOS), which creates crack-free inverse opal films with high positional order and uniform crystal alignment along the (110) crystal plane, is combined with top-down microfabrication techniques. Micrometer scale hierarchical superstructures having a highly regular internal nanostructure with precisely controlled crystal orientation and wall profiles are produced. The ability to combine structural order at the nano- and microscale enables the fabrication of materials with complex optical properties resulting from light-matter interactions at different length scales. As an example, a hierarchical diffraction grating, which combines Bragg reflection arising from the nanoscale periodicity of the inverse opal crystal with grating diffraction resulting from a micrometer scale periodicity, is demonstrated.
3D plasmonic design approach for efficient transmissive Huygens metasurfaces (2019)

In this paper we present a design concept for 3D plasmonic scatterers as high- efficiency transmissive metasurface (MS) building blocks. A genetic algorithm (GA) routine partitions the faces of the walls inside an open cavity into a M x N grid of voxels which can be either covered with metal or left bare, and optimizes the distribution of metal coverage needed to generate electric and magnetic modes of equal strength with a targeted phase delay (Φt) at the design wavelength. Even though the electric and magnetic modes can be more complicated than typical low order modes, with their spectral overlap and equal strengths, they act as a Huygens source, with the accompanying low reflection magnitude. Square/hexagonal voxels inside square/rectangular cavities are thoroughly analyzed for operation at 8 µm, although the technique can be applied to different cavity geometries for operation across the electromagnetic spectrum. Results from full-wave simulations show the GA routine can repeatedly pinpoint scatterer geometries emitting at any Φt value across 2π phase space with transmittances of at least 60%, making these MS building blocks an attractive plasmonic alternative for practical optical applications. Full-scale metasurface devices are calculated from near-fields of the individual elements to validate the optical functionality.
Activation and Functionalization of C—H Bonds (2004)

An introduction to the field of activation and fimctionalization of C-H bonds by solution-phase transition-metal-based systems is presented, with an emphasis on the activation of aliphatic C-H bonds. The focus of this chapter is on stoichiometric and catalytic reactions that operate via organometallic mechanisms, i.e., those in which a bond is formed between the metal center and the carbon undergoing reaction
Research highlights: manipulating cells inside and out (2015)

We highlight recent work manipulating cells: from whole cells, to intracellular content, and even subcellular gradients in proteins. In the first manuscript, using interdigitated electrode arrays at a controlled tilt angle to a microchannel allows for an array of acoustic nodes that apply force and isolate larger circulating tumor cells from remaining cells in RBC-lysed blood. Moving to the subcellular scale, recent work shows the ability to use rapid bubble generation induced by a pulsed laser to transfect hundreds of thousands of cells in parallel, especially with larger cargo, such as live bacteria. Manipulating at an even finer level, our third highlighted paper applies magnetic nanoparticle-based techniques to the localization of proteins within the cytoplasm in gradient configurations. A recurring theme in the literature is how interfacing at the cellular scale is a key feature enabled by micro & nanotechnology. This feature can be exploited to achieve new capabilities for cell biologists which opens up new fundamental cell biology questions. This matching of scales and the unique advantages are well demonstrated in the articles highlighted.
Targeted therapy in gastrointestinal malignancies (2014)

Increased understanding of cancer pathogenesis has identified several pathways that serve as potential targets for novel targeted agents in development. The selection of targeted cancer therapy based on biomarkers has instigated a new era of personalized medicine and changed the way we practice oncology. Many targeted agents are approved for treatment of gastrointestinal malignancies most targeting tumor angiogenesis, and many more are in different phases of development. Here we briefly summarize nine different targeted agents that are approved currently in the U.S. and several other agents currently being studied in various gastrointestinal cancers.
ChemInform Abstract: Nothospondin, a New AP‐1 Inhibitory Quassinoid from the Cameroonian Plant Nothospondias staudtii. (2011)

Abstract The quassinoid, nothospondin (I), is obtained along with the known compound glaucarubinone.
Interference Mitigation Methods for LTE-Advanced Networks with Macro and HeNB Deployments (2011)

This paper is focused on interference mitigation for LTE-Advanced multi-layer networks with macro and HeNBs. The autonomous HeNB power setting in the downlink is studied for different HeNB access methods. Our studies show that using the so-called escape carrier configuration and autonomous HeNB power setting is a promising strategy for enabling gradual introduction of user-deployed HeNBs in existing macro-layer networks.
OpenCAPI Memory Interface Signal Integrity Study for High-Speed DDR5 Differential DIMM Channel with Standard Loss FR-4 Material and SNIA SFF-TA-1002 Connector (2019)

DDR5 Differential DIMM (DDIMM) is being defined in JEDEC and will be introduced to the market in 2020. DDR5 DDIMM uses OMI (OpenCAPI Memory Interface) as the host interface. On the DDIMM printed circuit board (PCB), the minimum data transfer rate per data differential pair over the OMI bus is 25.6Gbps. This is a significant data rate increase for DRAM modules over conventional single-ended data transferring DIMMs. For example, the DDR5 LRDIMM data transfer rate per pin is 3.2Gbps. Careful attention must be paid to the bill of materials of the DDIMM to control its cost towards general market acceptance of this new DIMM technology. As a result, it is desired to use standard loss FR-4 material to build the DDIMM PCB. Validating the DDIMM PCB wiring for the high-speed differential memory bus requires accurate high-speed link simulations. These simulations require accurate models representing differential wiring in the DDIMM PCB stack-up. The models must be built using not only representative physical dimensions but also accurate frequency dependent material properties obtained through PCB characterization. The Short Pulse Propagation (SPP) method will be used to extract PCB frequency dependent material properties. PCB suppliers usually have different Copper Clad Laminate (CCL) and prepreg material set selections largely due to the supplier relations. The test coupons of this study will be built using CCL and prepreg materials from two suppliers. System level differential memory bus simulation based on SPP characterization will be performed and the simulation results from different material/stack-up designs will be benchmarked. DDR5 DDIMM will be paired with the Storage Networking Industry Association (SNIA) SFF-TA-1002 high speed connector which differs significantly from the JEDEC RDIMM connector for improved electrical signaling characteristics. In this work, the SNIA high-speed connector to PCB interface design will be studied as it is of utmost importance for achieving good signal integrity. In addition to high speed signal integrity, the DDIMM PCB mechanical interaction with the SFF-TA-1002 connector is studied and it will be highlighted in this paper. The PCB mechanical outline design proposal is made to mitigate module/connector mechanical interference. To understand the PCB yield impact, DIMM PCB suppliers' process capabilities for critical feature/dimensions will be studied as well.
Dephosphorylation and activation of Acetyl‐CoA‐carboxylase from lactating rabbit mammary gland (1979)

Acetyl-CoA carboxylase, the rate limiting enzyme in fatty acid synthesis, is completely dependent on citrate for activity and is inhibited by long chain Otty acyl CoA [I].Kim and coworkers [2-51 partially
Prospective Evaluation of Minimally Invasive Plate Osteosynthesis in 36 Nonarticular Tibial Fractures in Dogs and Cats (2011)

Consistent restoration of alignment was accomplished using MIPO techniques. Furthermore, MIPO appeared to yield faster healing times and lower complication rates than those reported with conventional plate osteosynthesis.
Observation ofB¯(s)0→J/ψf1(1285)Decays and Measurement of thef1(1285)Mixing Angle (2014)

Decays of B(s)(0) and B(0) mesons into J/ψ π+π-π+π- final states, produced in pp collisions at the LHC, are investigated using data corresponding to an integrated luminosity of 3 fb-1 collected with the LHCb detector. B(s)(0) → J/ψ f1(1285) decays are seen for the first time, and the branching fractions are measured. Using these rates, the f1(1285) mixing angle between strange and nonstrange components of its wave function in the qq structure model is determined to be ±(24.0-2.6-0.8+3.1+0.6)°. Implications on the possible tetraquark nature of the f1(1285) are discussed.
Constructing genus-3 hyperelliptic Jacobians with CM (2016)

Given a sextic CM field $K$ , we give an explicit method for finding all genus- $3$ hyperelliptic curves defined over $\mathbb{C}$ whose Jacobians are simple and have complex multiplication by the maximal order of this field, via an approximation of their Rosenhain invariants. Building on the work of Weng [ J. Ramanujan Math. Soc. 16 (2001) no. 4, 339–372], we give an algorithm which works in complete generality, for any CM sextic field $K$ , and computes minimal polynomials of the Rosenhain invariants for any period matrix of the Jacobian. This algorithm can be used to generate genus-3 hyperelliptic curves over a finite field $\mathbb{F}_{p}$ with a given zeta function by finding roots of the Rosenhain minimal polynomials modulo $p$ .
Ketone Hydrogenation Technology (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
Tubulin‐β‐III overexpression by uterine serous carcinomas is a marker for poor overall survival after platinum/taxane chemotherapy and sensitivity to epothilones (2013)

Tubulin-β-III overexpression in USCs discriminates poor prognosis, serves as a marker for sensitivity to epothilones, and may contribute to paclitaxel resistance. Immunohistochemistry reliably identifies tumors with overexpression of tubulin-β-III, and a subset of individuals likely to respond to patupilone and ixabepilone. Epothilones warrant clinical investigation for treatment of USCs.