gebhart/patrepeval huggingface dataset:
A Si-Micromachined 162-Stage Two-Part Knudsen Pump for On-Chip Vacuum (2013)

This paper investigates a two-part architecture for a Knudsen vacuum pump with no moving parts. This type of pump exploits the thermal transpiration that results from the free-molecular flow in nonisothermal channels. For a high compression ratio, 162 stages are serially cascaded. The two-part architecture uses 54 stages designed for the pressure range from 760 to ≈ 50 Torr, and 108 stages designed for lower pressures. This approach provides greater compression ratio and speed than using a uniform design for each stage. Finite element simulations and analytical design analysis are presented. A five-mask single-wafer fabrication process is used for monolithic integration of the Knudsen pump that has a footprint of 12 × 15 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> . The pressure levels of each stage are measured by integrated Pirani gauges. Experimental evaluation shows that, using an input power of ≈ 0.39 W, the evacuated chamber is reduced from 760 to ≈ 0.9 Torr, resulting in a compression ratio of ≈ 844. The vacuum levels are sustained during 37 days of continuous operation.
Attachment of Cryptosporidium parvum sporozoites to MDCK cells in vitro (1994)

The initial attachment of Cryptosporidium parvum sporozoites to host cells in vivo may be a critical event in the pathogenesis of this infection. The molecular basis of attachment and the conditions influencing this host-parasite interaction have not been studied systematically. Therefore, we have developed a sporozoite attachment model by using paraformaldehyde-fixed Madin-Darby canine kidney (MDCK) cells. Attachment of sporozoites to fixed MDCK cells was quantitated by indirect immunofluorescence and confirmed by transmission electron microscopy. Attachment in this system was time, temperature (37 degrees C), and pH (7.2 to 7.6) dependent. Dose-response studies demonstrated that the attachment of sporozoites to fixed MDCK cells was a saturable process. Attachment was enhanced in the presence of 10 mM manganese, 1 mM calcium, and 1 to 10 mM zinc. Attachment of sporozoites to MDCK cells was inhibited in a dose-dependent manner by polyclonal anti-Cryptosporidium antisera and by purified immunoglobulin G (IgG). This model will be useful for the study of parasite and host cell molecules involved in the initial interaction of C. parvum sporozoites with their target cell.
Mouse model systems of autism spectrum disorder: Replicability and informatics signature (2020)

Phenotyping mouse model systems of human disease has proven to be a difficult task, with frequent poor inter- and intra-laboratory replicability, particularly in behavioral domains such as social and cognitive function. However, establishing robust animal model systems with strong construct validity is of fundamental importance as they are central tools for understanding disease pathophysiology and developing therapeutics. To complete our studies of mouse model systems relevant to autism spectrum disorder (ASD), we present a replication of the main findings from our two published studies of five genetic mouse model systems of ASD. To assess the intra-laboratory robustness of previous results, we chose the two model systems that showed the greatest phenotypic differences, the Shank3/F and Cntnap2, and repeated assessments of general health, activity and social behavior. We additionally explored all five model systems in the same framework, comparing all results obtained in this three-yearlong effort using informatics techniques to assess commonalities and differences. Our results showed high intra-laboratory replicability of results, even for those with effect sizes that were not particularly large, suggesting that discrepancies in the literature may be dependent on subtle but pivotal differences in testing conditions, housing enrichment, or background strains and less so on the variability of the behavioral phenotypes. The overall informatics analysis suggests that in our behavioral assays we can separate the set of tested mouse model system into two main classes that in some aspects lie on opposite ends of the behavioral spectrum, supporting the view that autism is not a unitary concept.
Design, Synthesis, and Biological Activity of Prazosin-Related Antagonists. Role of the Piperazine and Furan Units of Prazosin on the Selectivity for α1-Adrenoreceptor Subtypes (1998)

Prazosin-related quinazolines 4-20 were synthesized, and their biological profiles at alpha1-adrenoreceptor subtypes were assessed by functional experiments in isolated rat vas deferens (alpha1A), spleen (alpha1B), and aorta (alpha1D) and by binding assays in CHO cells expressing human cloned alpha1-adrenoreceptor subtypes. The replacement of piperazine and furan units of prazosin (1) by 1, 6-hexanediamine and phenyl moieties, respectively, affording 3-20, markedly affected both affinity and selectivity for alpha1-adrenoreceptor subtypes in functional experiments. Cystazosin (3), bearing a cystamine moiety, was a selective alpha1D-adrenoreceptor antagonist being 1 order of magnitude more potent at alpha1D-adrenoreceptors (pA2, 8.54 +/- 0.02) than at the alpha1A- (pA2, 7.53 +/- 0.01) and alpha1B-subtypes (pA2, 7.49 +/- 0. 01). The insertion of substituents on the furan ring of 3, as in compounds 4 and 5, did not improve the selectivity profile. The simultaneous replacement of both piperazine and furan rings of 1 gave 8 which resulted in a potent, selective alpha1B-adrenoreceptor antagonist (85- and 15-fold more potent than at alpha1A- and alpha1D-subtypes, respectively). The insertion of substituents on the benzene ring of 8 affected, according to the type and the position of the substituent, affinity and selectivity for alpha1-adrenoreceptors. Consequently, the insertion of appropriate substituents in the phenyl ring of 8 may represent the basis of designing new selective ligands for alpha1-adrenoreceptor subtypes. Interestingly, the finding that polyamines 11, 16, and 20, bearing a 1,6-hexanediamine moiety, retained high affinity for alpha1-adrenoreceptor subtypes suggests that the substituent did not give rise to negative interactions with the receptor. Finally, binding assays performed with selected quinazolines (2, 3, and 14) produced affinity results, which were not in agreement with the selectivity profiles obtained from functional experiments. This rather surprising and unexpected finding may be explained by considering neutral and negative antagonism.
Chapter 8. Photodynamic Therapy of Localized Infections in Animal Models (2011)

The rise of multi-drug resistant pathogenic microorganisms has led to searches for alternative antimicrobial therapies to treat infections. Photodynamic therapy (PDT) is a rapidly expanding approach to the treatment of infections because it may be able to eliminate infectious microbial cells without causing undue damage to host tissue and is thought to be unlikely to induce PDT resistance. In order to develop PDT as a new therapy for infections, we need to demonstrate that PDT can indeed accomplish these aims in living hosts. Animal models of infection represent a powerful tool to dissect the natural history of infection, investigate the pathogenicity and virulence of the microbes, as well as measure the efficacy of PDT. This chapter will discuss the use of animal models for evaluating PDT of various types of localized infections.
A TRIBUTE TO A LIVING LEGEND (Special Issue in Honor of the 70th Birthday of Dr. Atta-ur-Rahman) (2012)

The Editorial Board wishes to dedicate this issue of Current Medicinal Chemistry to the Editor-in-Chief of the journal, Prof. Dr. Atta-ur-Rahman, FRS, on his 70th birthday. The Editorial Board acknowledges the tremendous achievements of Prof. Rahman in the fields of Organic Chemistry in general and on bioactive natural products in particular. Prof. Rahman’s honors include: the first scientist from the Muslim world to have won the prestigious UNESCO Science Prize (1999) in the 35 year old history of the Prize; elected as Fellow of Royal Society (London) in July 2006; conferred honorary doctorate degrees from many prestigious universities, including the University of Cambridge. On a national level his services are acknowledged in the form of four prestigious civil awards of excellence, including: Nishan-e-Imtiaz (2002), Hilal-e-Imtiaz (1998), Sitara-e-Imtiaz (1991) and Tamgha-e-Imtiaz (1983). At an academic level, Prof. Rahman has 856 publications in several fields of organic chemistry including 658 research publications, 21 patents, 113 books and 65 chapters in books published largely by major U.S. and European presses. He is currently the Editor-in-Chief of 12 scientific journals in fields ranging from Medicinal Chemistry to Pharmaceutical Drug Design. Seventy six students have completed their Ph.D. degrees under his supervision. He chairs the Network of Academies of Sciences of Islamic Countries (NASIC) and is the Vice-President (Central & South Asia) of the Academy of Sciences for the Developing World (TWAS) Council, and Foreign Fellow of Korean Academy of Sciences. Prof. Atta-ur-Rahman was the President of the Pakistan Academy of Sciences (2003-2006) and was again elected as the President of the Academy from 1st of January 2011. In particular, as Editor-in-Chief, Prof. Rahman has made outstanding contribution to Current Medicinal Chemistry. The contributions of Prof. Rahman to the uplifting of science in Pakistan in his capacity as the Federal Minister for Science & Technology and later as Chairman Higher Education Commission were acknowledged by a high civil award of the government of Austria and TWAS prize for institution building as well as by four editorials in Nature. The Editorial board wishes health and prosperity to Prof. Atta-ur-Rahman in the years to come.
Orthogonal frequency division multiplexing (2008)

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Charge microheterogeneity of the β-trace proteins (lipocalin-type prostaglandin D synthase) in the cerebrospinal fluid of patients with neurological disorders analyzed by capillary isoelectrofocusing (2001)

Charge microheterogeneity of the beta-trace protein (beta-TP = lipocalin-type prostaglandin D synthase) in the cerebrospinal fluid (CSF) of patients with various neurological disorders was analyzed by capillary isoelectric focusing (CIEF). Under the conditions employed, beta-TP in the low-molecular-weight protein fraction of CSF was separated into at least four isoforms with different p/ values. An isoform with the pl value of 4.6-4.8 was usually the most abundant. The total beta-TP level in the CSF was determined by enzyme-linked immunosorbent assay (ELISA) to be elevated in patients recovering from organic damage to the CNS and those with pathological brain atrophy. Changes in the total beta-TP level in the CSF were occasionally accompanied by those in its charge microheterogeneity, as revealed by CIEF. Such quantitative and qualitative changes in beta-TP in human CSF indicated changes in its pathophysiological roles in association with various neurological disorders.
CD47-SIRPα Signaling Induces Epithelial-Mesenchymal Transition and Cancer Stemness and Links to a Poor Prognosis in Patients with Oral Squamous Cell Carcinoma (2019)

Of therapeutic relevance, CD47 knockdown enhanced the anti-OSCC effect of radiotherapy. Collectively, we showed an increased CD47 expression promoted the generation of CSCs and malignant OSCC phenotypes. Silencing CD47, in combination with radiation, could provide an alternative and improved therapeutic efficacy for OSCC patients.
Study of high power generation in UTC-PD at 110-210 GHz (2018)

We designed and fabricated a low-bias operational uni-travelling carrier photodiode (UTC-PD) structure, which can be operated at over 100 GHz. The main structure of the device consisted of p-doped InGaAs for the photo-absorption layer and non-doped InP for the carrier collector layer, to obtain both a high electron drift velocity at a low bias and a small CR time constant based on the pn-junction capacitance. Through an on-wafer probing test, the frequency response was measured up to 210 GHz using a 1 mm coaxial connecter type (DC-110GHz), W-band (75–110 GHz) and G-band (140–220 GHz) waveguide probe with a spectrum analyzer. In the measurement results, a large bandwidth of 10 MHz-110 GHz could be obtained with good flatness within &plusmn;1 dB. When the W-band and G-band performance were characterized, the high-power characteristic of -3.8 dBm could be achieved at 106 GHz. and the output power level of - 19.8 dBm could be confirmed at 210 GHz as well.
Cover Image, Volume 30, Issue 5 (2022)

The cover image is based on the Special Section Paper Utilizing advanced spatio-temporal backgrounds with dynamic test signals for high dynamic range display metrology by Timo Kunkel and Florian Friedrich., https://doi.org/10.1002/jsid.1125.
Circulating Tumor DNA Genomics Correlate with Resistance to Abiraterone and Enzalutamide in Prostate Cancer (2018)

Abstract Primary resistance to androgen receptor (AR)–directed therapies in metastatic castration-resistant prostate cancer (mCRPC) is poorly understood. We randomized 202 patients with treatment-naïve mCRPC to abiraterone or enzalutamide and performed whole-exome and deep targeted 72-gene sequencing of plasma cell-free DNA prior to therapy. For these agents, which have never been directly compared, time to progression was similar. Defects in BRCA2 and ATM were strongly associated with poor clinical outcomes independently of clinical prognostic factors and circulating tumor DNA abundance. Somatic alterations in TP53, previously linked to reduced tumor dependency on AR signaling, were also independently associated with rapid resistance. Although detection of AR amplifications did not outperform standard prognostic biomarkers, AR gene structural rearrangements truncating the ligand binding domain were identified in several patients with primary resistance. These findings establish genomic drivers of resistance to first-line AR-directed therapy in mCRPC and identify potential minimally invasive biomarkers. Significance: Leveraging plasma specimens collected in a large randomized phase II trial, we report the relative impact of common circulating tumor DNA alterations on patient response to the most widely used therapies for advanced prostate cancer. Our findings suggest that liquid biopsy analysis can guide the use of AR-targeted therapy in general practice. Cancer Discov; 8(4); 444–57. ©2018 AACR. See related commentary by Jayaram et al., p. 392. This article is highlighted in the In This Issue feature, p. 371
Polarization-Induced Local Pore-Wall Functionalization for Biosensing: From Micropore to Nanopore (2012)

The use of biological-probe-modified solid-state pores in biosensing is currently hindered by difficulties in pore-wall functionalization. The surface to be functionalized is small and difficult to target and is usually chemically similar to the bulk membrane. Herein, we demonstrate the contactless electrofunctionalization (CLEF) approach and its mechanism. This technique enables the one-step local functionalization of the single pore wall fabricated in a silica-covered silicon membrane. CLEF is induced by polarization of the pore membrane in an electric field and requires a sandwich-like composition and a conducting or semiconducting core for the pore membrane. The defects in the silica layer of the micropore wall enable the creation of an electric pathway through the silica layer, which allows electrochemical reactions to take place locally on the pore wall. The pore diameter is not a limiting factor for local wall modification using CLEF. Nanopores with a diameter of 200 nm fabricated in a silicon membrane and covered with native silica layer have been successfully functionalized with this method, and localized pore-wall modification was obtained. Furthermore, through proof-of-concept experiments using ODN-modified nanopores, we show that functionalized nanopores are suitable for translocation-based biosensing.
Nanoparticle-Based Metamaterials as Multiband Plasmonic Resonator Antennas (2011)

Plasmonic metamaterials based on metal-dielectric nanostructures exhibit unique optical properties such as high near-field enhancement, negative refractive indexing, and optical cloaking. In this paper, we present a plasmonic multiband metamaterial based on UT shaped nanoparticles. In order to understand the multispectral response, we analyze the near-field distributions at the corresponding resonance frequencies. In addition, we both numerically and experimentally, show the dependence of the spectral response on the geometrical parameters of the structure. By embedding the system in a dielectric cladding medium, we show strong sensitivities of the resonant behavior to the refractive index and thickness of the dielectric load. Due to its tunable multiband spectral characteristics, the proposed metamaterial antenna can be used for wide range of applications, such as wavelength-tunable active filters, optical modulators, ultrafast switching devices, and biosensing.
Molecular Design of Acid Generators for EB and ArF Excimer Laser Exposure Using Molecular Orbital Calculations. (1994)

Quantum chemical calculation is applied to investigate the reaction mechanism of sulfonyl acid generator and the transparency of the resist material. We have found that electron absorbed dimethylsulfone can be easily decomposed by relatively low energy (2.95 Kcallmol), reaching to the decomposed status of methyl radical and CH~SO2 (methyl sulfonyl anion). This was thought to bean initial step in the electron acid generation reaction of the sulfonyl compounds. The total molecular energy of dimethyl sulfone anion was found to be higher than that of the neutral dimethylsulfone. On the other hand, sulfone derivatives with electron-withdrawing groups, such as methyl sulfonyl acetonitrile, usually have higher energy (about 41 kcallmol) than those for their anion. This suggests that the electron withdrawing groups enhance the electron amity of the sulfone compounds, which are also considered to increase the efficiency of acid generation. Additionally, another quantum chemical study was carried out in order to improve transparency of the aromatic species in resist for ArF excimer laser. Using configuration interaction (CI) methods of molecular orbital theory, the substituent effects of W absorption in the aromatic compounds were investigated. As a result significant red sifts in Amax were observed in the conjugated romatic rings, which increases the transparency at 193 nm wavelength region.
Improving Grid Resilience Using High-Voltage dc: Strengthening the Security of Power System Stability (2019)

With a heavy dependence on electric power worldwide for critical services ranging from communication and banking to water treatment and medical care, the availability of reliable electricity proves essential for a productive society in the 21st century. Even short interruptions in service may result in significant lost revenue and widespread disruption in large grids serving tens of millions of customers. The combination of such dependence on electric power along with classical threats (e.g., severe weather) and modern concerns (e.g., cyberattacks) creates an imperative for grid resilience.
Hypoventilation After Inhaled Anesthesia Results in Reanesthetization (2014)

Reanesthetization from hypoventilation after inhaled anesthesia is possible. After initial emergence, muscle is a source of anesthetic and predisposes to reanesthetization while fat is a sink for anesthetic and fosters continued emergence. Severe hypoventilation will cause some degree of reanesthetization from anesthetic released from muscle after 4 hours of 1 MAC inhaled anesthesia with desflurane, sevoflurane, or isoflurane.
Stability Analysis of Tandem Riding on Motorcycles (2006)

&lt;div class="htmlview paragraph"&gt; This paper presents a stability analysis of tandem riding on a motorcycle, focusing especially on the effects of the passenger's positional behaviors. Firstly we experimentally investigate the motorcycle and rider control behavior after a posture change by the passenger. This is done by measuring the motorcycle's responses to posture changes by the passenger during straight running at low speed. The results reveal some characteristic behaviors. Second, we construct a multi-body model for a human-motorcycle system for tandem riding. By comparing experimental and simulated results, we have confirmed the validity of the model. Finally, we conduct simulations on some situations in which passenger properties are varied, and obtain the effects of these passenger characteristics. &lt;/div&gt;
Principal Component Analysis of Multimodal Neuromelanin MRI and Dopamine Transporter PET Data Provides a Specific Metric for the Nigral Dopaminergic Neuronal Density (2016)

The loss of dopaminergic (DA) neurons in the substantia nigra (SN) is a major pathophysiological feature of patients with Parkinson's disease (PD). As nigral DA neurons contain both neuromelanin (NM) and dopamine transporter (DAT), decreased intensities in both NM-sensitive MRI and DAT PET reflect decreased DA neuronal density. This study demonstrates that a more specific metric for the nigral DA neuronal density can be derived with multimodal MRI and PET. Participants were 11 clinically diagnosed PD patients and 10 age and gender matched healthy controls (HCs). Two quantities, the NM-related index (RNM) and the binding potential of the radiotracer [18F]FE-PE2I to DAT (BPND) in SN, were measured for each subject using MRI and PET, respectively. Principal component analysis (PCA) was applied to the multimodal data set to estimate principal components. One of the components, PCP, corresponds to a basis vector oriented in a direction where both BPND and RNM increase. The ability of BPND, RNM and PCP to discriminate between HC and PD groups was compared. Correlation analyses between the motor score of the unified Parkinson's disease rating scale and each metric were also performed. PCP, BPND and RNM for PD patients were significantly lower than those for HCs (F = 16.26, P<0.001; F = 6.05, P = 0.008; F = 7.31, P = 0.034, respectively). The differential diagnostic performance between the HC and PD groups as assessed by the area under the receiver-operating characteristic curve was best for PCP (0.94, 95% CI: 0.66-1.00). A significant negative correlation was found between the motor severity score and PCp (R = -0.70, P<0.001) and RNM (R = -0.52, P = 0.015), but not for BPND (R = -0.36, P = 0.110). PCA of multimodal NM-sensitive MRI and DAT PET data provides a metric for nigral DA neuronal density that will help illuminate the pathophysiology of PD in SN. Further studies are required to explore whether PCA is useful for other parkinsonian syndromes.
<title>Spectroscopic characterization of photorefractive materials for holographic storage applications</title> (1996)

In order for holographic storage applications to become more competitive, advances in recording materials are needed. To this end, two separate approaches for improving material properties are described, both of which involve various spectroscopic techniques for determining the efficacy of the approaches. First, post-growth high-temperature processing treatments are examined. These treatments combine oxidation/reduction for improved photosensitivity with hydrogen loading for efficient thermal fixing. Second, new rare earth dopants are considered for use in resonant two-photon recording with nondestructive readout.
Experimental and numerical investigation of effective area of all-solid photonic bandgap fiber for high power delivery (2012)

The effective area of a large-mode-area all-solid photonic bandgap fiber for high-power delivery is investigated numerically and experimentally. The new evaluation method of the effective area is proposed and discussed.