gebhart/patrepeval huggingface dataset:
Ionic Liquid-Aided Synthesis of Anatase TiO2 Nanoparticles: Photocatalytic Water Splitting and Electrochemical Applications (2022)

Titanium dioxide nanoparticles play a crucial role in the production of hydrogen gas evolution. Among the four polymorphic phases of TiO2 (anatase, rutile, brookite, and TiO2 (B)), the anatase phase shows good photo activity in catalytic applications. We prepared a single anatasephase of TiO2 nanoparticles usinga facile one-step ionothermal method with the existence of 1-(3,6-dioxa heptane) 3-methyl imidazolium methane sulfonate IL[DOMIMS]. The ionic liquid-based substitution reaction mechanism was utilized for the ionothermal synthesis of TiO2. The anatase phase structure and nanoparticle-like morphology of synthesized TiO2 nanomaterial were confirmed by XRD analysis and TEM studies. The vibrational frequency of the Ti–O–Ti bond at 544 cm−1 was measured usingthe FTIR spectrum, and the UV absorbance of the sample was studied usingthe UV/visible spectra. The prepared TiO2 nanoparticles showed the best results of H2 generation via awater-splitting reaction, liberating 2084 μmol·g−1·h−1 of H2 gas. TiO2 nanoparticles act as a good material for electrochemical applications such as supercapacitors and sensing of dopamine, as well as a better photocatalyst for the degradation of methylene blue.
Single molecule real time (SMRT) full length RNA-sequencing reveals novel and distinct mRNA isoforms in human bone marrow cell subpopulations (2019)

Abstract Hematopoietic cells are continuously replenished from progenitor cells that reside in the bone marrow. To evaluate molecular changes during this process, we analyzed the transcriptomes of freshly harvested human bone marrow progenitor (lineage-negative) and differentiated (lineage-positive) cells by single molecule, real time (SMRT) full length RNA sequencing. This analysis revealed a ∼5-fold higher number of transcript isoforms than previously detected and showed a distinct composition of individual transcript isoforms characteristic for bone marrow subpopulations. A detailed analysis of mRNA isoforms transcribed from the ANXA1 and EEF1A1 loci confirmed their distinct composition. The expression of proteins predicted from the transcriptome analysis was validated by mass spectrometry and validated previously unknown protein isoforms predicted e.g. for EEF1A1 . These protein isoforms distinguished the lineage negative cell population from the lineage positive cell population. Finally, transcript isoforms expressed from paralogous gene loci (e.g. CFD, GATA2, HLA-A, B &amp; C ) also distinguished cell subpopulations but were only detectable by full length RNA sequencing. Thus, qualitatively distinct transcript isoforms from individual genomic loci separate bone marrow cell subpopulations indicating complex transcriptional regulation and protein isoform generation during hematopoiesis.
Origins of Stereoselectivity in the Corey−Chaykovsky Reaction. Insights from Quantum Chemistry (1999)

Reaction pathways of the Corey-Chaykovsky epoxidation reaction have been compared quantum chemically. Of the concerted, torsional rotation and anti addition pathways the latter two were found to be favored both in the gas phase and in CH(2)Cl(2) in a model system. Several theoretically previously uncharacterized stationary points were located, and selective solvent effects were observed. On the anti addition pathway the C-C bond formation transition state A, suitably substituted to allow comparison with published experimental data, was able to predict both the absolute stereochemistry of the main product and, qualitatively, the distribution of its other stereoisomers. The quantum chemical protocol reported here is useful in designing new sulfides for the Corey-Chaykovsky reaction.
Antibodies to Pneumococcal Proteins PhtD, CbpA, and LytC in Filipino Pregnant Women and Their Infants in Relation to Pneumococcal Carriage (2009)

This study focuses on the immunogenicity of the following three pneumococcal vaccine candidate proteins in Filipino infants, all inducing protection in animal models: pneumococcal histidine triad protein D (PhtD), choline binding protein A (CbpA), and the lysozyme LytC. The immunoglobulin G antibody concentrations to PhtD, its putative, protective, and exposed C-terminal fragment (PhtD C), CbpA, and LytC were measured by enzyme immunoassay in 52 serum samples from pregnant women, 39 cord blood samples, and consecutive serum samples (n = 263) from 52 newborns between 6 weeks and 10 months of age scheduled to be taken at six time points. A nasopharyngeal swab to detect pneumococcal carriage was taken parallel to the serum samples. The antibody concentrations in the cord blood samples were similar to those in the samples from the mothers. In infant sera, the geometric mean antibody concentrations (GMCs) for all three proteins decreased until the age of 18 weeks and started to increase after that age, suggesting that the infants' own antibody production started close to the age of 4 to 5 months. The increase in GMCs by age, most clear-cut for CbpA, was associated with pneumococcal carriage. Anti-PhtD concentrations were higher than anti-PhtD C concentrations but correlated well (r of 0.89 at 10.5 months), suggesting that antibodies are directed to the supposedly exposed and protective C-terminal part of PhtD. Our results show that young children are able to develop an antibody response to PhtD, CbpA, and LytC and encourage the development of pneumococcal protein vaccines for this age group.
Dynamics of Subsynaptic Vesicles and Surface Microclusters at the Immunological Synapse (2010)

Imaging studies have identified clusters of kinases and adaptor proteins that serve as centers of signaling at the contact points between T cells and antigen-presenting cells (APCs). Here, we report that the kinase ZAP-70 and the adaptor proteins LAT and SLP-76 accumulated in separate clusters at the interface between T cells and coverslips coated with a stimulatory antibody against CD3, a component of the T cell antigen receptor complex. A fraction of LAT was detected in motile vesicles that repeatedly moved to surface microclusters of SLP-76 and the adaptor protein GADS (growth factor receptor-bound protein-related adaptor downstream of Shc), where they exhibited decreased motility. LAT molecules in which the residues tyrosine 171 and tyrosine 191 (which are required for the binding of LAT to GADS) were mutated to phenylalanine did not dwell at clusters of SLP-76. At immunological synapses, LAT-containing vesicles also colocalized with microclusters of SLP-76, as detected in experiments in which laser tweezers were used to position T cell-APC conjugates vertically for high-resolution imaging. Phosphorylation of LAT was most prominent when vesicular LAT colocalized with SLP-76. Indeed, the abundance of phosphorylated LAT within a microcluster of SLP-76 was greatest in those clusters that had more recent interactions with LAT-containing vesicles. Finally, negative signals by the inhibitory receptor ILT2 disrupted the assembly of SLP-76-containing microclusters. Together, these data show that the movement of LAT-containing vesicles is linked to the organization of protein microclusters and suggest an important role for vesicular LAT in the SLP-76 signalosome.
Low threshold tandem optical limiters with large dynamic range (1993)

A passive optical limiter is a device that has high linear transmittance for low input fluences and low transmittance for high input fluences. We have previously demonstrated the ability of materials possessing nonlinear absorption, refraction, or scattering to perform as passive optical limiters.1-3 A disadvantage of this approach to optical limiting is that the nonlinear materials often suffer optical damage at fluences about an order of magnitude larger than the limiting threshold for nanosecond pulses. We define the limiting threshold as the incident energy at which the transmittance falls to 50% of the linear transmittance. Practical limiting devices require a damage threshold several orders of magnitude larger. The performance of limiters can be parameterized in terms of the (DR), where we define DR = damage energy/limiting threshold. Here we demonstrate a method of dramatically increasing the dynamic range of passive optical limiters by cascading two or more limiting materials in a single limiting device,4 As the schematic of the limiter in Fig. 1 shows, the device has two elements. We place one (the limiter) at or near focus, while the other (the limiter) is placed at a region of lower intensity upstream from the first. The concept behind this design is that the Primary limiter provides a low limiting threshold, while the purpose of the Secondary limiter is to protect the Primary limiter from optical damage.
A Machine Learning Based Automatic Hardware Trojan Attack Space Exploration and Benchmarking Framework (2022)

Due to the current horizontal business model that promotes increasing reliance on untrusted third-party Intellectual Properties (IPs), Computer-Aided-Design (CAD) tools, and design facilities, hidden malicious functionalities, also known as hardware Trojan attacks, have become a serious threat to the semiconductor industry. Development of effective countermeasures against hardware Trojan attacks require: (1) fast and reliable exploration of the viable Trojan attack space for a given design and (2) a suite of high-quality Trojan-inserted benchmarks that meet specific standards. The latter has become essential for the development and evaluation of design/verification solutions to achieve quantifiable assurance against Trojan attacks. While existing static benchmarks provide a baseline for comparing different countermeasures, they only enumerate a limited number of hand-crafted Trojans from the complete Trojan design space. To accomplish these dual objectives, in this paper, we present MIMIC, a novel machine learning guided framework for automatic Trojan insertion, which can create a large and targeted population of valid Trojans for a given design by mimicking the properties of a small set of known Trojans. While there exist tools to automatically insert Trojan instances using fixed Trojan templates, they cannot analyze known Trojan attacks for creating new instances that accurately capture the threat model. MIMIC works in two major steps: (1) it analyzes structural and functional features of existing Trojan populations in a multi-dimensional space to train machine learning models and generate a large number of “virtual Trojans” of the given design, (2) next, it binds them into the design by matching their functional/structural properties with suitable nets of the internal logic structure. We have developed a complete tool flow for MIMIC, evaluated the framework, and quantified its effectiveness to demonstrate highly promising results.
Design-enabled manufacturing enablement using manufacturing design request tracker (MDRT) (2013)

The shrinking dimensions with advanced technologies pose yield challenges which require continuous enhancement of yield methodologies to quickly detect and fix the marginal layout features. In this paper, we present a practical approach to enhance the DFM and DEM capabilities suite provided by GLOBALFOUNDRIES for 28nm technology and beyond. The MDRT system has been implemented in the Product Lifecycle Management (PLM) system within GLOBALFOUNDRIES.
Azetidine Iminosugars from the Cyclization of 3,5-Di-O-triflates of α-Furanosides and of 2,4-Di-O-triflates of β-Pyranosides Derived from Glucose (2012)

Primary amines with either 3,5-di-O-ditriflates of α-furanosides or 2,4-di-O-triflates of β-pyranosides form bicyclic azetidines in high yield.
Mannoheptulose: glycolytic inhibitor and novel caloric restriction mimetic (2009)

Caloric restriction (CR) is the most robust and reproducible strategy for retarding aging. Benefits of CR have been demonstrated in multiple species, but application to human or companion animal aging represents a challenge. In 1998 the concept of CR "mimetic" (CRM) was introduced as a method to obtain "anti‐aging" and health‐promoting benefits of CR without reducing food intake. We hypothesized that an effective CRM would best mimic the effects of CR if it impeded initial stages of energy metabolism. We focused initially on glycolytic inhibition using 2‐deoxyglucose (2DG). Upon entry into cells, this glucose analog is phosphorylated and becomes a strong competitive inhibitor of phosphohexose isomerase. 2DG effectively induces a CR‐like state in rats based on metabolic effects such as reduced plasma glucose, insulin, body temperature, pulse, heart rate and inhibiting tumor growth. Results show 2DG has a narrow window between efficacy and toxicity so recently we shifted our focus to mannoheptulose (MH), a seven‐carbon sugar that reduces glycolysis via hexokinase inhibition. MH appears non‐toxic with negligible effects on food intake and BW, and increased insulin tolerance by 25% in mice. MH extends median and maximal lifespan (~15%) in D. melanogaster and median lifespan (~30%) in C3H/HeJ mice. These findings, coupled with simple extraction from avocados, suggest that MH may be a practical, highly effective CRM.
Assembly of Wiseana Iridovirus: Viruses for Colloidal Photonic Crystals (2006)

Abstract In vitro assembly of Wiseana iridescent virus (WIV) yields iridescent pellets and films with structural color more vivid than in the native insect. WIV is icosahedral in shape, 140 nm in diameter, with 30 nm long fibrils attached to the outer surface, and exhibits a surface charge ca. 1/6th that of a comparable polymer colloid. The low surface charge and tethered chains on the virus surface allow the facile modification of the interparticle distance. Directed sedimentation yields predominantly an amorphous liquid‐like packing of the virus. Such samples exhibit a broad reflection band that is angle independent and for which the broad maximum can be reversibly shifted from blue towards red with increased hydration. Slow sedimentation and flow‐assisted assembly methods produce thin films with a polycrystalline morphology that exhibit narrower, more intense reflectivity peaks, which are hydration and angle dependent. This study points toward the potential of viral particles for photonic crystals where their unique structural features (icosahedral symmetry, extreme monodispersity, precise surface functionalization, and tethered surface chains of low surface‐charge density) may lead to superior control of optical properties of their assembled arrays.
Hepatitis C Virus Is Infrequently Evaluated and Treated in an Urban HIV Clinic Population (2009)

This retrospective cohort study of HIV/hepatitis C virus (HCV) coinfected patients evaluated time trends and rates of HCV evaluation for patients seen between January 1, 1997 and October 30, 2004. Survival analysis and Cox proportional hazards modeling were used to describe the time to evaluation and covariates associated with this outcome. Patients were predominantly white and male. Of 248 eligible patients, 108 (44%) were evaluated for HCV treatment. The median time to evaluation was 2.98 years. Of 108 evaluated, 17 (16%) received at least one dose of interferon and/or ribavirin. The median time to treatment after being evaluated was 1.39 years. Of the 17 (35%) treated 6 patients had a sustained virologic response, but only 2.4% of the original number of patients were cured. Approximately one half of patients in an HIV-specialty clinic were evaluated for HCV therapy and 16% received treatment, but the median time to treatment from the time of HCV diagnosis was over 4 years. Further efforts to identify and to overcome barriers to HCV treatment are warranted.
Crystal growth, optical properties and neutron responses of Ce<sup>3+</sup> doped LiCaAlF<inf>6</inf> single crystal (2008)

Ce2%: <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">6</sup> LiCAF single crystal (nominal composition) with 2 mm in diameter and 50 mm in length was grown by the micro-pulling-down method. Emission from the perturbed Ce <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3+</sup> centers was observed in α-ray excited radioluminescence. Neutron response was compared with Li-glass (GS20, Saint-Gobain) using <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">252</sup> Cf. Scintillation decay time of Ce2%: LiCAF is 38nsec, which is twice faster than that of GS20. Using Hamamatsu photomultiplier H7416 the photoelectron yield of the Ce: <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">6</sup> LiCAF single crystal is measured about half of that of GS20.
REACTIVE SELF COLLISION AVOIDANCE WITH DYNAMIC TASK PRIORITIZATION FOR HUMANOID ROBOTS (2010)

We propose a self collision avoidance system for humanoid robots designed for interacting with the real world. It protects not only the humanoid robots' hardware but also expands its working range while keeping smooth motions. It runs in real-time in order to handle unpredictable reactive tasks such as reaching to moving targets tracked by vision during dynamic motions like e.g. biped walking. The collision avoidance is composed of two important elements. The first element is reactive self collision avoidance which controls critical segments in only one direction — as opposed to other methods which use 3D position control. The virtual force for the collision avoidance is applied to this direction and therefore the system has more redundant degrees of freedom which can be used for other criteria. The other second element is a dynamic task prioritization scheme which blends the priority between target reaching and collision avoidance motions in a simple way. The priority between the two controllers is changed depending on current risk. We test the algorithm on our humanoid robot ASIMO and works while the robot is standing and walking. Reaching motions from the front to the side of the body without the arm colliding with the body are possible. Even if the target is inside the body, the arm stops at the closest point to the target outside the body. The collision avoidance is working as one module of a hierarchical reactive system and realizes reactive motions. The proposed scheme can be used for other applications: We also apply it to realizing a body schema and occlusion avoidance.
Flow velocity is relatively uniform in the coronary sinusal venous tree: structure-function relation (2016)

A hemodynamic model is developed in the entire coronary sinusal venous tree of the swine heart. A key finding is that the coronary sinusal venous system complies with the area preservation rule for efficient venous return while the coronary arterial tree obeys the minimum energy hypothesis. This model can also serve as a physiological reference state to test various therapeutic rationales through the venous route.
Inhibition of Cell Growth by Antisense Oligonucleotides Targeting the Growth-Related Protein Kinase c-raf (2003)

The progress made in understanding the molecular basis of mammalian cell transformation has led to the unifying concept of growth regulation and its disorders in cancer cells. Today it is well recognized that many products of "cancer genes" encode for proteins that regulate normal mitogenesis and apoptosis. Taken together, this indicates that the carcinogenic process may be viewed as a progressive disorder of signal transduction (1-6). In fact, many of the genes that are mutated or lost in cancer cells, including both the oncogenes and tumor suppressors, encode proteins that are crucial regulators for intra- as well as intercellular signal transduction (1-6). This conceptual framework has provided a basis for the development of novel anticancer strategies and therapeutic modalities with the aim to inhibit cancer growth either by blocking mitogenic signal transduction or to specifically induce apoptosis of cancer cells. Although these various approaches have not been validated clinically, these strategies are likely to identify compounds with less side effects compared to standard chemotherapeutic agents.
Chim3 confers survival advantage to CD4+ T cells upon HIV-1 infection by preventing HIV-1 DNA integration and HIV-1–induced G2 cell-cycle delay (2010)

The long-term expression and the ability of a therapeutic gene to confer survival advantage to transduced cells are mandatory requirements for successful anti-HIV gene therapy. In this context, we developed lentiviral vectors (LVs) expressing the F12-viral infectivity factor (Vif) derivative Chim3. We recently showed that Chim3 inhibits HIV-1 replication in primary cells by both blocking the accumulation of retrotranscripts, independently of either human APOBEC3G (hA3G) or Vif, and by preserving the antiviral function of hA3G. These results were predictive of long-lasting survival of Chim3(+) cells after HIV-1 infection. Furthermore, Vif, like Vpr, deregulates cell-cycle progression by inducing a delay in G(2) phase. Thus, the aim of this study was to investigate the role of Chim3 on both cell survival and cell-cycle regulation after HIV-1 infection. Here, we provide evidence that infected Chim3(+) T cells prevail over either mock- or empty-LV engineered cells, show reduced G(2) accumulation, and, as a consequence, ultimately extend their lifespan. Based on these findings, Chim3 rightly belongs to the most efficacious class of antiviral genes. In conclusion, Chim3 usage in anti-HIV gene therapy based on hematopoietic stem cell (HSC) modification has to be considered as a promising therapeutic intervention to eventually cope with HIV-1 infection.
Total Synthesis and Antibacterial Properties of Carbaplatensimycin (2007)

The chemical synthesis and biological evaluation of carbaplatensimycin, the carbon analogue of the recently reported antibiotic platensimycin has been accomplished. Carbaplatensimycin exhibited similar potency to the natural product as an antibacterial agent against a variety of strains, including methicilin- and vancomycin-resistant bacteria.
RhIII‐ and IrIII‐Catalyzed Asymmetric Transfer Hydrogenation of Ketones in Water (2007)

Asymmetric transfer hydrogenation (ATH) of ketones by formate in neat water is shown to be viable with Rh-TsDPEN and Ir-TsDPEN catalysts, derived in situ from [Cp*MCl2]2 (M=Rh, Ir) and TsDPEN. A variety of ketones were reduced, including nonfunctionalized aryl ketones, heteroaryl ketones, ketoesters, and unsaturated ketones. In comparison with Ir-TsDPEN and the related Ru II catalyst, the Rh III catalyst is most efficient in water, affording enantioselectivities of up to 99 % ee at substrate/catalyst (S/C) ratios of 100-1000 even without working under an inert atmosphere. The aqueous phase reduction is shown to be highly pH-dependent; the optimum pH windows for TOF greater than 50 mol mol(-1) h(-1) for Rh- and Ir-TsDPEN are 5.5-10.0 and 6.5-8.5, respectively. Outside the pH window, the reduction becomes slow or stagnant depending on the pH. However, the enantioselectivities erode only under acidic conditions. At a higher S/C ratio, the aqueous ATH by Rh-TsDPEN is shown to be product- as well as byproduct-inhibited; the product inhibition appears to stem at least partly from the reaction being reversible. The aqueous phase reduction is simple, efficient and environmentally benign, thus presenting a viable alternative for asymmetric reduction.