gebhart/patrepeval huggingface dataset:
Rapid Visual Authentication Based on DNA Strand Displacement (2021)

Novel ways to track and verify items of a high value or security is an ever-present need. Taggants made from deoxyribonucleic acid (DNA) have several advantageous properties, such as high information density and robust synthesis; however, existing methods require laboratory techniques to verify, limiting applications. Here, we leverage DNA nanotechnology to create DNA taggants that can be validated in the field in seconds to minutes with a simple equipment. The system is driven by toehold-mediated strand-displacement reactions where matching oligonucleotide sequences drive the generation of a fluorescent signal through the potential energy of base pairing. By pooling different "input" oligonucleotide sequences in a taggant and spatially separating "reporter" oligonucleotide sequences on a paper ticket, unique, sequence-driven patterns emerge for different taggant formulations. Algorithmically generated oligonucleotide sequences show no crosstalk and ink-embedded taggants maintain activity for at least 99 days at 60 °C (equivalent to nearly 2 years at room temperature). The resulting fluorescent signals can be analyzed by the eye or a smartphone when paired with a UV flashlight and filtered glasses.
Abstract B78: Referral delay after community diagnosis of non-small cell lung cancer impairs survival. (2012)

Abstract Context: “Rush to surgery” among patients with worse symptoms, delays related to morbidity, and inclusion of patients with advanced disease have produced a mixed picture of importance of time to treatment to survival of non-small cell lung cancer (NSCLC). Objective: To assess the contribution of diagnosis to first surgery interval to survival among patients diagnosed in the community with early stage NSCLC. Methods: Patients (N=174) diagnosed between 2003 and 2009 and treated at the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins were followed for vital status through 2011. Diagnosis to first surgery interval was examined overall; as two segments: referral interval and treatment interval; as short and longer intervals (&amp;lt;22, &amp;lt;31, and &amp;lt;43 days); and as a continuous variable. Our primary end point was survival since first surgery. Results: Cox method hazard analysis revealed older age at diagnosis (OR=1.02 per year 95% confidence intervals:1.00-1.05), stage IIB (OR=2.17, 95% confidence intervals:1.12-4.21), large, &amp;gt;4 cm (OR=3.68, 95% confidence intervals: 1.05-12.93) or unknown tumor size (OR+4.45, 95% confidence intervals: 1.21-16.38), and longer length of diagnosis to first surgery interval predicted worse survival (OR= 1.04 per week delay, 95% confidence intervals: 1.00-1.09). Factors of race, place of residence, marital status, morbidity and insurance coverage were not predictive of survival or interval length. No threshold effect of time to surgery was observed. Conclusions: Surgery is not only the best treatment for early stage NSCLC but it is urgent once a diagnosis is made. Patients benefit from universal consideration of lung cancer as a time sensitive condition that merits rapid response to reduce tumor burden, especially among patients with small tumors. We will need to know more about referral delays encountered by patients, because particularly small tumors found upon low dose computed tomography scan will increase. Referral delay experienced in the community is unduly long (61 days). In addition to patient choices, an unconscious physician bias that lung cancer is untreatable or an inevitable consequence of smoking may be operating. Citation Format: Norma F. Kanarek, Craig M. Hooker, Luckson Mathieu, Hua-Ling Tsai, Charles M. Rudin, James G. Herman, Malcolm V. Brock. Referral delay after community diagnosis of non-small cell lung cancer impairs survival. [abstract]. In: Proceedings of the Fifth AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2012 Oct 27-30; San Diego, CA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2012;21(10 Suppl):Abstract nr B78.
Development and Repetitive-Compensated PID Control of a Nanopositioning Stage With Large-Stroke and Decoupling Property (2017)

Piezoelectric-actuator-driven nanopositioning stages, with large stroke and low crosstalk, are quite appealing for fulfilling the through-silicon via lithography etching task. The motivation of this paper is to combine the ability to enable the nanopositioning stage running in a manner of millimeter scale workspace and nanometer scale positioning accuracy. Two pairs of flexure-guided kinematic modules with high displacement amplification ratio are adopted to construct a 4-PP (P is prismatic) XY nanopositioning stage. A new decoupling design is implemented to realize the decoupling behavior between the input actuators and output compliant limbs, respectively. Kinematics modeling including output compliance, input stiffness, displacement amplification ratio modeling, and workspace determination are carried out. After a series of mechanism dimension optimizations via particle swarm optimization algorithm, the performance of the optimized mechanism is analyzed and assessed by using the ANSYS workbench. Then, a repetitive-compensated PID controller and a single-input and single-output closed-loop control strategy are designed. Finally, a series of experimental tests in terms of crosstalk test, frequency characteristic analysis, damping property analysis, dynamic hysteresis nonlinearity characterization, signal trajectory tracking, workspace determination, and Bode diagram plotting are carried out in details. It indicates that the workspace of fabricated prototype has reached to 1.035 mm × 1.035 mm, the crosstalk ratio is kept within 0.5%, and the closed-loop positioning accuracy is determined as 400 nm.
Verapamil reduces incidence of reentry during ventricular fibrillation in pigs (2014)

The characteristics of reentrant circuits during short duration ventricular fibrillation (SDVF; 20 s in duration) and the role of Ca(++) and rapid-activating delayed rectifier potassium currents during long duration ventricular fibrillation (LDVF; up to 10 min in duration) were investigated using verapamil and sotalol. Activation mapping of the LV epicardium with a 21 × 24 electrode plaque was performed in 12 open-chest pigs. Pigs were given either verapamil (0.136 mg/kg) or sotalol (1.5 mg/kg) and verapamil. Reentry patterns were quantified for SDVF, and, for LDVF, activation patterns were compared with our previously reported control LDVF data. Verapamil significantly increased conduction velocity around the reentrant core by 10% and reduced the reentrant cycle length by 15%, with a net reduction in reentry incidence of 70%. Sotolol had an opposite effect of decreasing the conduction velocity around the core by 6% but increasing the reentrant cycle length by 13%, with a net reduction of reentry incidence of 50%. After 200 s of VF, verapamil significantly slowed wavefront conduction velocity and activation rate compared with control data. Verapamil decreased the incidence of reentry in SDVF by accelerating conduction velocity to increase the likelihood of conduction block, possibly through increased sympathetic tone. The drug slowed activation rate and conduction velocity after 200 s of VF, suggesting that L-type Ca(++) channels remain active and may be important in the maintenance of LDVF. Sotalol in addition to verapamil caused no additional antiarrhythmic effect.
Modern Advances in Wireless Power Transfer Systems for Roadway Powered Electric Vehicles (2016)

Wireless power transfer system (WPTS)-based wireless electric vehicles, classified into roadway-powered electric vehicles (RPEVs) and stationary charging electric vehicles (SCEVs), are in the spotlight as future mainstream transportations. RPEVs are free from serious battery problems such as large, heavy, and expensive battery packs and long charging time because they get power directly from the road while moving. The power transfer capacity, efficiency, lateral tolerance, electromagnetic field, air-gap, size, weight, and cost of the WPTSs have been improved by virtues of innovative semiconductor switches, better coil designs, roadway construction techniques, and higher operating frequency. Recent advances in WPTSs for RPEVs are summarized in this review paper. The fifth- and sixth-generation online electric vehicles, which reduce infrastructure cost for commercialization, and the interoperability between RPEVs and SCEVs are addressed in detail in this paper. Major milestones of the developments of other RPEVs are also summarized. The rest of this paper deals with a few important technical issues such as coil structures, power supply schemes, and segmentation switching techniques of a lumped inductive power transfer system for RPEVs.
Supplementary Table 2 from RKI-1447 Is a Potent Inhibitor of the Rho-Associated ROCK Kinases with Anti-Invasive and Antitumor Activities in Breast Cancer (2023)

&lt;p&gt;PDF file, 58K, Percent tumor volume change after mouse treatment with vehicle. ErbB2 mammary tumor transgenic mice were treated with Vehicle (20% HPCD) as described under Materials and Methods. Percent change in tumor volume was calculated for each tumor using the following formula; (Vf-V0)/V0*100; where V0= Initial volume (at the beginning of treatment) and Vf= Final volume (at the end of treatment).&lt;/p&gt;
Large‐Scale Synthesis (2010)

Abstract The capability to fulfill drug substance requirements to support the various elements of pharmaceutical development is an essential component of the overall drug development process. The preparation of bulk materials for toxicology, formulation development, and clinical supplies can represent a significant challenge, depending on such factors as the molecular complexity of the drug candidate, the quantities of materials required, and the state of development of the synthetic process. As a drug candidate proceeds through the various stages of drug development and into commercial launch, the challenge of process development is to ensure the uninterrupted supply of drug substance without compromising the ability to ultimately supply a commercially viable chemical process. This chapter provides a general overview of the issues and requirements associated with the development and scale‐up of chemical processes for bulk active drug substances. An account of the nevirapine process development efforts at Boehringer Ingelheim is also provided as an example of the evolution of a chemical process from the initial efforts in medicinal chemistry to commercial‐scale operations.
1,3-Dioxolane-Based Ligands as a Novel Class of α1-Adrenoceptor Antagonists (2003)

1,3-Dioxolane-based compounds (2-14) were synthesized, and the pharmacological profiles at alpha(1)-adrenoceptor subtypes were assessed by functional experiments in isolated rat vas deferens (alpha(1A)), spleen (alpha(1B)), and aorta (alpha(1D)). Compound 9, with a pA(2) of 7.53, 7.36, and 8.65 at alpha(1A), alpha(1B), and alpha(1D), respectively, is the most potent antagonist of the series, while compound 10 with a pA(2) of 8.37 at alpha(1D) subtype and selectivity ratios of 162 (alpha(1D)/alpha(1A)) and 324 (alpha(1D)/alpha(1B)) is the most selective. Binding assays in CHO cell membranes expressing human cloned alpha(1)-adrenoceptor subtypes confirm the pharmacological profiles derived from functional experiments, although the selectivity values are somewhat lower. Therefore, it is concluded that 1,3-dioxolane-based ligands are a new class of alpha(1)-adrenoceptor antagonists.
Cell Biology of Laryngeal Epithelial Defenses in Health and Disease: Further Studies (2003)

This is the second annual report of an international collaborative research group that is examining the cellular impact of laryngopharyngeal reflux (LPR) on laryngeal epithelium. The results of clinical and experimental studies are presented. Carbonic anhydrase (CA), E-cadherin, and MUC gene expression were analyzed in patients with LPR, in controls, and in an in vitro model. In patients with LPR, we found decreased levels of CAIII in vocal fold epithelium and increased levels in posterior commissure epithelium. The experimental studies confirm that laryngeal CAIII is depleted in response to reflux. Also, cell damage does occur well above pH 4.0. In addition, E-cadherin (transmembrane cell surface molecules, which have a key function in epithelial cell adhesion) was not present in 37% of the LPR laryngeal specimens. In conclusion, the laryngeal epithelium lacks defenses comparable to those in esophageal epithelium, and these differences may contribute to the increased susceptibility of laryngeal epithelium to reflux-related injury.
SEM overlay target design using e-beam simulation (2023)

Current SEM target design methodology relies on knowledge and experience with previous designs. This experience-based method can break down in cases of significant architectural or material changes, requiring a “best guess” approach for a new target. Validation of this guess is only available once wafers are created and measured. Using electron interaction simulations in the target design process enables waferless evaluation of targets. Simulations can also identify the necessary imaging conditions to generate a high-quality SEM image, indicating the required tool conditions for successful metrology. The work in this paper demonstrates a correlation between simulation and results on wafers.
Brain activity during landmark and line bisection tasks (2009)

Neglect patients bisect lines far rightward of center whereas normal subjects typically bisect lines with a slight leftward bias supporting a right hemisphere bias for attention allocation. We used fMRI to assess the brain regions related to this function in normals, using two complementary tasks. In the Landmark task subjects were required to judge whether or not a presented line was bisected correctly. During the line bisection task, subjects moved a cursor and indicated when it reached the center of the line. The conjunction of BOLD activity for both tasks showed right lateralized intra-parietal sulcus and lateral peristriate cortex activity. The results provide evidence that predominantly right hemisphere lateralized processes are engaged in normal subjects during tasks that are failed in patients with unilateral neglect and highlight the importance of a right fronto-parietal network in attention allocation.
Evaluation of Exopolysaccharide Production by Leuconostoc mesenteroides Strains Isolated from Wine (2008)

Exopolysaccharide (EPS)-producing lactic acid bacteria are responsible for the alteration of wine and other fermented beverages. The potential to produce EPS was investigated for Leuconostoc mesenteroides strains isolated from Spanish grape must and wine. Most strains were able to produce EPS from sucrose containing media. Based on their EPS-producing phenotype and on their EPS monosaccharide composition, the L. mesenteroides strains analyzed could be arranged in 2 groups. One group comprises mucoid strains producing a glucan polymer, and the other group includes strains producing a fructan polymer. The presence of a glucosyltransferase encoding gene in the glucan producing L. mesenteroides strains was assayed by PCR. Two primer sets, PF1-PF8 and GTFF-GTFR, were used to amplify internal fragment of known glucosyltransferase genes. None of the glucan-producing strains gave a positive amplicon by the primer sets used. Therefore, new tools need to be developed to broaden the range of potentially spoiling agents detected by PCR in fermented beverages.
Amyloid ß and Tau Alzheimer¿s disease related pathology is reduced by toll-like receptor 9 stimulation (2014)

Alzheimer’s disease (AD) is the most common cause of dementia, and currently, there is no effective treatment. The major neuropathological lesions in AD are accumulation of amyloid β (Aβ) as amyloid plaques and congophilic amyloid angiopathy, as well as aggregated tau in the form of neurofibrillary tangles (NFTs). In addition, inflammation and microglia/macrophage function play an important role in AD pathogenesis. We have hypothesized that stimulation of the innate immune system via Toll-like receptor 9 (TLR9) agonists, such as type B CpG oligodeoxynucleotides (ODNs), might be an effective way to ameliorate AD related pathology. We have previously shown in the Tg2576 AD model that CpG ODN can reduce amyloid deposition and prevent cognitive deficits. In the present study, we used the 3xTg-AD mice with both Aβ and tau related pathology. The mice were divided into 2 groups treated from 7 to 20 months of age, prior to onset of pathology and from 11 to 18 months of age, when pathology is already present. We demonstrated that immunomodulatory treatment with CpG ODN reduces both Aβ and tau pathologies, as well as levels of toxic oligomers, in the absence of any apparent inflammatory toxicity, in both animal groups. This pathology reduction is associated with a cognitive rescue in the 3xTg-AD mice. Our data indicate that modulation of microglial function via TLR9 stimulation is effective at ameliorating all the cardinal AD related pathologies in an AD mouse model suggesting such an approach would have a greater chance of achieving clinical efficacy.
Comparative Analysis of the Effects of Neurotrophic Factors CDNF and GDNF in a Nonhuman Primate Model of Parkinson’s Disease (2016)

Cerebral dopamine neurotrophic factor (CDNF) belongs to a newly discovered family of evolutionarily conserved neurotrophic factors. We demonstrate for the first time a therapeutic effect of CDNF in a unilateral 6-hydroxydopamine (6-OHDA) lesion model of Parkinson's disease in marmoset monkeys. Furthermore, we tested the impact of high chronic doses of human recombinant CDNF on unlesioned monkeys and analyzed the amino acid sequence of marmoset CDNF. The severity of 6-OHDA lesions and treatment effects were monitored in vivo using 123I-FP-CIT (DaTSCAN) SPECT. Quantitative analysis of 123I-FP-CIT SPECT showed a significant increase of dopamine transporter binding activity in lesioned animals treated with CDNF. Glial cell line-derived neurotrophic factor (GDNF), a well-characterized and potent neurotrophic factor for dopamine neurons, served as a control in a parallel comparison with CDNF. By contrast with CDNF, only single animals responded to the treatment with GDNF, but no statistical difference was observed in the GDNF group. However, increased numbers of tyrosine hydroxylase immunoreactive neurons, observed within the lesioned caudate nucleus of GDNF-treated animals, indicate a strong bioactive potential of GDNF.
Structure‐Activity and Mechanism Studies on Silicon Phthalocyanines with Plasmodium falciparum in the Dark and Under Red Light (1997)

Syntheses for the new photosensitizers HOSiPcOSi(CH3)2(CH2)3N(CH1)1 or 3(CH3)2, Pc 34 and Pc 25, have been developed and the order of activity of these photosensitizers and the previously reported photosensitizer Pc 4, HOSiPcOSi(CH3)2(CH2)3N(CH3)2, in the dark and with broad-band red light toward Plasmodium falciparum in red blood cell (RBC) suspensions has been studied. The order of activity has been found to be Pc 4 > Pc 34 > Pc 25. Thus, the activity of the photosensitizers under both sets of conditions is inversely proportional to the length of their terminal amino alkyl chains. The 50% inhibition dye concentration (IC50) in the dark for the parasites in RBC suspension with Pc 4 is 24 nM and the dye concentration and light fluence that yield > or = 3 log10 of parasite inactivation with Pc 4 are 2 microM and 3 J/cm2, respectively. The synthesis of DNA and proteins by the parasites in culture was strongly inhibited by Pc 4 in the dark while parasite lactate dehydrogenase (pLDH) activity was unaffected. With Pc 4 and light, DNA and protein synthesis of the parasites in culture was strongly inhibited, pLDH activity of the parasites was moderately inhibited and ribosome density of the parasite cells was reduced. Gel electrophoresis studies showed that synthesis of all parasite proteins was inhibited to a similar extent. These results suggest that Pc 4 both in the dark and with light inactivates the cells by disturbing their machinery for the synthesis of not just one but a whole series of proteins. It is concluded that Pc 4 and light may be able to serve as a practical sterilization combination not only for HIV and other viruses but also for malaria parasites in RBC concentrates, and that Pc 4 by itself may have potential as a chemotherapeutic agent toward malaria.
Crash Test and Evaluation of the TxDOT T631 Bridge Rail (2014)

In August 2010, Midwest Roadside Safety Facility (MwRSF) developed and crash tested a low-cost, energy-absorbing bridge rail for the Manual for Assessing Safety Hardware (MASH) TL-3 applications. This low-cost bridge rail was designed to be compatible with the Midwest Guardrail System (MGS) such that an approach transition would not be required between the two barriers. It was desired that the system minimize bridge deck and rail costs. As part of this project, several concepts for an energy-absorbing bridge post were developed and tested. These concepts included strong-post systems designed with plastic hinges and weak-post systems designed to bend near the attachment to the bridge deck. The final post concept incorporated S3 × 5.7 steel sections designed to yield at their bases. These posts were located on 6 ft-3 in. on center. A W-beam section was used as the rail element and was attached to the posts with a bolt designed to break during and impact event. Two full-scale crash tests were performed according to the TL-2 impact conditions provided in MASH. The new bridge rail system successfully met all the safety performance criteria for MASH TL-2. The Texas Type T631 Bridge Rail was developed as a low-cost, energy absorbing bridge rail system for TL-2 applications. Many of the features used for the system tested at Midwest Roadside Safety Facility for TL-3 were incorporated into the design developed for this project for MASH TL-2 application. The Texas Department of Transportation (TxDOT) Type T631 Bridge Rail designed and developed for this project was evaluated under MASH TL-2.
The absence of a surface protease, OmpT, determines the intercellular spreading ability of Shigella: the relationship between the ompT and kcpA loci (1993)

A large plasmid-encoded protein, VirG, on the bacterial surface is essential for the spreading of Shigella by eliciting polar deposition of filamentous actin in the cytoplasm of epithelial cells. VirG expression from the large plasmid is diminished greatly when it is introduced into Escherichia coli K-12 from Shigella. In an attempt to identify factors affecting VirG expression, we found that the absence of the ompT gene, encoding outer membrane protease OmpT, restored full production of VirG protein to E. coli K-12. Conversely, upon introduction of the ompT gene of E. coli K-12 into Shigella, spreading ability was completely abolished, probably because of the proteolytic degradation of VirG protein by OmpT. Analysis of the DNA sequence of the ompT region indicated that the absence of the ompT gene occurred in Shigella and enteroinvasive E. coli strains, and that the absent DNA segment corresponded to a remnant lambdoid phage structure found in E. coli K-12, which encompasses a 21 kb DNA segment spanning from argU through to the ompT genes. Since ompT is located near purE in E. coli K-12 and a virulence locus for provoking keratoconjunctivitis in the eyes of guinea-pigs, named kcpA, is located near purE in S. flexneri, and the two loci are involved in VirG expression, the KcpA- mutants of S. flexneri 2a constructed were examined for correlation between acquisition of ompT and VirG degradation. Our data suggest that the previous recognition of a kcpA locus in S. flexneri is the result of transfer of the ompT gene from E. coli K-12, giving rise to a KcpA- phenotype. These results indicate that the lack of OmpT protease confers upon Shigella the ability to spread into adjacent epithelial cells.