gebhart/patrepeval huggingface dataset:
Immunolocalization and Quantitation of Transforming Growth Factor Alpha in Hydatidiform Mole (1999)

Complete hydatidiform mole (CHM), a condition related to abnormal gestation, occurs predominantly in the young reproductive age group and has a high prevalence rate in the Trivandrum region, occurring in 1.2% of deliveries. Transforming growth factor alpha (TGF-alpha) is an important growth regulatory molecule, the location and function of which at the human fetomaternal interface in CHM remains to be determined. The present study examined the presence of TGF-alpha in the normal and complete molar placenta and decidua throughout gestation. A total of 149 complete molar placental tissue samples and 96 normal placental tissue samples were evaluated for TGF-alpha expression by immunohistochemistry and 50 each of CHM and normal placental tissue for TGF-alpha concentration by radioimmunoassay. The peptide was localized immunocytochemically with a monoclonal anti-TGF-alpha antibody on paraffin-embedded tissue using the avidin-biotin complex peroxidase technique with aminoethyl carbazole as the chromogen. In molar placenta, villous trophoblast cells (syncytiotrophoblasts and cytotrophoblasts) showed intense cytoplasmic staining at all gestational ages compared to normal placenta of the same gestational age. The tissue concentration of TGF-alpha was highly overexpressed in the molar placenta (10-1000 fold) compared to that in the normal placenta. The results indicate that TGF-alpha is present in trophoblasts throughout human gestation and may provide additional growth advantage to maintenance of the hyperproliferative condition in trophoblastic tumors.
Development of Novel Enkephalin Analogues that Have Enhanced Opioid Activities at Both μ and δ Opioid Receptors (2007)

Enkephalin analogues with a 4-anilidopiperidine scaffold have been designed and synthesized to achieve therapeutic benefit for the treatment of pain due to mixed mu and delta opioid agonist activities. Ligand 16, in which a Dmt-substituted enkephalin-like structure was linked to the N-phenyl-N-piperidin-4-yl propionamide moiety, showed very high binding affinities (0.4 nM) at mu and delta receptors with an increased hydrophobicity (aLogP = 2.96). This novel lead compound was found to have very potent agonist activities in MVD (1.8 nM) and GPI (8.5 nM) assays.
The miR-124 - Sox9 paramutation: RNA-mediated epigenetic control of embryonic and adult growth (2009)

The size of the mammalian body is determined by genetic and environmental factors differentially modulating pre- and postnatal growth. We now report a control of growth acting in the mouse from the first cleavages to the postnatal stages. It was evidenced by a hereditary epigenetic modification (paramutation) created by injection of a miR-124 microRNA into fertilized eggs. From the blastocyst to the adult, mouse pups born after microinjection of this miRNA showed a 30% increase in size. At the blastocyst stage, frequent duplication of the inner cell mass resulted in twin pregnancies. A role of sperm RNA as a transgenerational signal was confirmed by the giant phenotype of the progeny of transgenic males expressing miR-124 during spermiogenesis. In E2.5 to E8.5 embryos, increased levels of several transcripts with sequence homology to the microRNA were noted, including those of Sox9, a gene known for its crucial role in the progenitors of several adult tissues. A role in embryonic growth was confirmed by the large size of embryos expressing a Sox9 DNA transgene. Increased expression in the paramutants was not related to a change in miR-124 expression, but to the establishment of a distinct, heritable chromatin structure in the promoter region of Sox9. While the heritability of body size is not readily accounted for by Mendelian genetics, our results suggest the alternate model of RNA-mediated heritable epigenetic modifications.
Zebrafish to humans: evolution of the 3-chain of type IV collagen and emergence of the autoimmune epitopes associated with Goodpasture syndrome (2005)

Goodpasture syndrome is an autoimmune vascular disease associated with kidney and lung failure, with pathogenic circulating autoantibodies targeted to a set of discontinuous epitope sequences within the noncollagenous domain-1 (NC1) of the alpha3 chain of type IV collagen (alpha3(IV)NC1), the Goodpasture autoantigen. We demonstrate that basement membrane extracted NC1 domain preparations from Caenorhabditis elegans, Drosophila melanogaster, and Danio rerio do not bind Goodpasture autoantibodies, while Xenopus laevis, chicken, mouse and human alpha3(IV)NC1 domains bind autoantibodies. The alpha3(IV) chain is not present in C elegans and Drosophila melanogaster, but is first detected in the Danio rerio. Interestingly, native Danio rerio alpha3(IV)NC1 does not bind Goodpasture autoantibodies. Next, we cloned, sequenced, and generated recombinant Danio rerio alpha3(IV)NC1 domain. In contrast to recombinant human alpha3(IV)NC1 domain, there was complete absence of autoantibody binding to recombinant Danio rerio alpha3(IV)NC1. Three-dimensional molecular modeling from existing x-ray coordinates of human NC1 domain suggest that evolutionary alteration of electrostatic charge and polarity due to the emergence of critical serine, aspartic acid, and lysine residues, accompanied by the loss of asparagine and glutamine, contributes to the emergence of the 2 major Goodpasture epitopes on the human alpha3(IV)NC1 domain, as it evolved from the Danio rerio over 450 million years.
Cavity QED, Single-Photon Nonlinear Optics and Quantum Information Processing with Quantum Dots in Photonic Crystals (2008)

We have performed coherent probing of a strongly coupled quantum dot-photonic crystal cavity system, and employed this platform to demonstrate effects including controlled phase shift at the single photon level and photon blockade.
Harmonic Analysis of Microbeams with PZT On-Chip Actuating and Sensing (2004)

Two groups of microbeams with different top electrode patterns are designed as PZT on-chip actuating and sensing devices. The results of hamonic analysis reveal that such microbeams present high Qs (>500 in air) in certain ranges of frequency, which provides the design basis for various applications.
Void-Free Filling of HAR TSVs Using a Wet Alkaline Cu Seed on CVD Co as a Replacement for PVD Cu Seed (2010)

The results of a wet alkaline seed deposition process directly on a thin adhesion promoter film, such as chemical vapor deposition (CVD) Co, are presented. This solution has been successfully used for copper plating on blanket and patterned through-silicon-via (TSVs) wafers covered with either silicon oxide/physical vapor deposition (PVD) Ta/CVD Co or silicon oxide/PVD Ti/CVD Co stacks. Such direct plated films were used as seed layers for subsequent copper plating from an in-house-made acidic Cu bath with model additives poly(ethylene glycol) (PEG), bis(3-sulfopropyl) disulfide (SPS), and Janus Green B (JGB). We report the impact of the directly plated stack composition and thicknesses on the integration of the wet alkaline seed in TSVs with width and high aspect ratio (HAR) as high as 8:1. The conformal wet seed layer enables the achievement of a successful void-free filling using an in-house made acidic Cu bath with model additives (SPS, PEG, and JGB).
How molecular advances may improve the diagnosis and management of PTCL patients (2023)

Peripheral T-cell lymphomas (PTCL) comprised more than 30 rare heterogeneous entities, representing 10 to 15% of adult non-Hodgkin lymphomas. Although their diagnosis is still mainly based on clinical, pathological, and phenotypic features, molecular studies have allowed for a better understanding of the oncogenic mechanisms involved and the refinement of many PTCL entities in the recently updated classifications. The prognosis remains poor for most entities (5-year overall survival < 30%), with current conventional therapies based on anthracyclin-based polychemotherapy regimen, despite many years of clinical trials. The recent use of new targeted therapies appears to be promising for relapsed/refractory patients, such as demethylating agents in T-follicular helper (TFH) PTCL. However further studies are needed to evaluate the proper combination of these drugs in the setting of front-line therapy. In this review, we will summarize the oncogenic events for the main PTCL entities and report the molecular targets that have led to the development of new therapies. We will also discuss the development of innovative high throughput technologies that aid the routine workflow for the histopathological diagnosis and management of PTCL patients.
Synthesis and conversion kinetics of some new “Durham” polyacetylene precursors (1994)

Abstract A new “Durham” polyacetylene precursor monomer (substituted tricyclo[4.2.2.0 2,5 ]deca‐3,7,9‐triene) was synthesized, and improved synthetic pathways to two existing precursor monomers were developed. Polymers of these three precursor monomers, as well as a bis‐trifluoro substituted precursor monomer, were synthesized using ring opening metathesis polymerization (ROMP) with a tungsten alkylidine initiator. The kinetics of conversion (precursor polymer to polyacetylene) were studied for each of the four precursor polymers using differential scanning calorimetry (DSC). Percent age conversion vs. time data were fit to the Avrami expression often used to describe the kinetics of bulk of crystallization of polymers. The parameter K of the Avrami expression was assumed to depend on temperature according to an Arrhenius expression. In this way, an equation with three constants was obtained that completely describes the kinetics of conversion of a particular polyacetylene precursor polymer. Values for the constants depended on the type of substituent on the precursor polymer. Because the kinetics are well described by the Avrami expression, it is proposed that “nucleation” and “propagation” processes are involved in the conversion of the precursor polymers to polyacetylene.
Integrated Nano-hole Array Surface Plasmon Resonance Biochemical Sensor (2010)

We have demonstrated a super-periodic metallic nano-hole array surface plasmon device for integrated biochemical sensing. The super-periodic nano-hole array device combines functions of sensing and surface plasmon resonance spectral analysis on a single device.
Azithromycin Modulates Murine Immune Responses to Pneumococcal Conjugate Vaccine and Inhibits Nasal Clearance of Bacteria (2004)

Macrolide antibiotics, including azithromycin, have been implicated in the modulation of host immune responses, independently of their antimicrobial properties. The present work was designed to study the effect that azithromycin has on protective humoral immune responses induced by a 7-valent, polysaccharide, pneumococcal conjugate vaccine (PCV7). By use of a murine vaccination/challenge model, it was found that inoculation with azithromycin led to significantly lower primary antibody responses, decreased recall proliferative responses, and, in nasal cavities, impaired clearance of Streptococcus pneumoniae serotype 14 from the nasal cavities. The results demonstrate that azithromycin can be inhibitory with regard to protective immune responsiveness.
Contact behavior evolution induced by damage growth in radio-frequency microelectromechanical system switches (2015)

This study provides a two-contact-event model to explain the evolution of the contact behavior of microelectromechanical system (MEMS) switches through their lifetime. The succession of two dynamic contact events is carefully considered during actuation inspired by experimental observations. The contact between the MEMS switch tip and the drain can be treated as an effective contact between an elastic hemisphere and a rigid plane. If the first contact event results in elastic deformation, the effective hemisphere will fully recover. Consequently, the subsequent contact event also produces elastic deformation. If, on the other hand, the first contact event induces elastoplastic or plastic deformation, a residual depth will be produced between the hemisphere and the rigid plane. The contact force of the subsequent contact event can be significantly reduced due to this additional residual depth. With the growth of residual depth during the switch cycling process, the modeling results show three possible situations of contact radius evolution: (1) The contact radius increases to a maximum value and then decreases to zero; (2) the contact radius increases to one local maximum value; then decreases to a local minimum value; subsequently increases again to another maximum value, and finally decreases to zero; and (3) the contact radius increases to one maximum value and then decreases to zero; after an intermittent response, the contact radius increases again to another maximum value and finally decreases to zero. Furthermore, the Maxwell spreading formula is applied to determine the contact resistance which is inversely proportional to the contact radius. Three situations of contact resistance evolution corresponding to the evolution of contact radius are obtained. All three situations are also observed and validated by the experimental results.
Nuts and bolts of the salt-inducible kinases (SIKs) (2021)

The salt-inducible kinases, SIK1, SIK2 and SIK3, most closely resemble the AMP-activated protein kinase (AMPK) and other AMPK-related kinases, and like these family members they require phosphorylation by LKB1 to be catalytically active. However, unlike other AMPK-related kinases they are phosphorylated by cyclic AMP-dependent protein kinase (PKA), which promotes their binding to 14-3-3 proteins and inactivation. The most well-established substrates of the SIKs are the CREB-regulated transcriptional co-activators (CRTCs), and the Class 2a histone deacetylases (HDAC4/5/7/9). Phosphorylation by SIKs promotes the translocation of CRTCs and Class 2a HDACs to the cytoplasm and their binding to 14-3-3s, preventing them from regulating their nuclear binding partners, the transcription factors CREB and MEF2. This process is reversed by PKA-dependent inactivation of the SIKs leading to dephosphorylation of CRTCs and Class 2a HDACs and their re-entry into the nucleus. Through the reversible regulation of these substrates and others that have not yet been identified, the SIKs regulate many physiological processes ranging from innate immunity, circadian rhythms and bone formation, to skin pigmentation and metabolism. This review summarises current knowledge of the SIKs and the evidence underpinning these findings, and discusses the therapeutic potential of SIK inhibitors for the treatment of disease.
Comparing magnetic resonance imaging/ultrasound-fusion biopsy and systemic 12-core transrectal ultrasound biopsy for whole gland pathology. (2014)

84 Background: Historically, pathologic findings from standard 12-core prostate biopsies are upgraded in 25 to 33% of patients after radical prostatectomy (RP). MRI/US fusion prostate biopsy has been shown to upgrade prostate cancer compared to standard 12-core biopsy in 32% of patients. MRI/US fusion biopsy may offer a more accurate representation of whole gland pathology. We evaluate the rate of pathologic upgrade in standard 12-core biopsy and MRI/US fusion biopsy when compared with whole gland pathology from RP. Methods: Patients who underwent random prostate biopsy, fusion biopsy and subsequently RP for prostate cancer from 2012 to 2013 were included. Pathology was reviewed by a single pathologist. The cohort was divided into clinically significant high-grade (Gleason score 4+3 or higher) and clinically insignificant low-grade (Gleason score 3+4 or lower) sub cohorts. Pathological upgrade was defined as any increase in Gleason sum or primary Gleason score. McNemar’s test was used to compare the proportion of patients who were upgraded from random biopsy to RP versus the proportion that were upgraded from fusion biopsy to RP. Results: Sixty eight patients underwent 12-core and fusion prostate biopsy then subsequently RP. Mean prostate-specific antigen was 9.2ng/ml. There are total of 43 patients with clinically insignificant low-grade and 25 patients with clinically significant high-grade. Fusion biopsy upgraded 19 patients (28%) compared to 12-core biopsy, eight of these patients had negative 12-core biopsy. Pathology on the RP specimen upgraded 18 of the 12-core results (26%) compare to only eight fusion biopsy results (11%). (p =0.0095) 14 patients (20%) who had clinically insignificant low-grade disease on 12-core biopsy were upgraded to clinically significant high-grade on RP. Only two patients (3%) with clinically insignificant low-grade from fusion biopsy were upgraded on RP. (p&lt; 0.0005) Conclusions: Prostate cancer detected on MRI/US fusion prostate biopsy has significantly lower rates of pathologic upgrade than standard 12-core biopsy when both were compared to prostatectomy specimens. MRI/US fusion biopsy may represent whole gland pathology more accurately compared to 12-core biopsy.
Microcantilever‐Based Sensors (2011)

This chapter contains sections titled: Basic Modes of Operation Thermal and Vapor Sensing Sensing in Liquid Environment References
Liquid crystal photonic bandgap fiber components (2007)

Liquid crystal photonic bandgap fibers represent a promising platform for the design of all-in-fiber optical devices, which show a high degree of tunability and exhibit novel optical properties for the manipulation of guided light. In this review paper we present tunable fiber devices for spectral filtering, such as Gaussian filters and notch filters, and devices for polarization control and analysis, such as birefringence control devices and switchable and rotatable polarizers.
Human blood PIG‐A mutation and micronucleated reticulocyte flow cytometric assays: Method optimization and evaluation of intra‐ and inter‐subject variation (2020)

We previously described flow cytometry-based methods for scoring the incidence of micronucleated reticulocytes (MN-RET) and PIG-A mutant phenotype reticulocytes (MUT RET) in rodent and human blood samples. The current report describes important methodological improvements for human blood analyses, including immunomagnetic enrichment of CD71-positive reticulocytes prior to MN-RET scoring, and procedures for storing frozen blood for later PIG-A analysis. Technical replicate variability in MN-RET and MUT RET frequencies based on blood specimens from 14 subjects, intra-subject variability based on serial blood draws from 6 subjects, and inter-subject variation based on up to 344 subjects age 0 to 73 years were quantified. Inter-subject variation explained most of the variability observed for both endpoints (≥77%), with much lower intra-subject and technical replicate variability. The relatively large degree of inter-subject variation is apparent from mean and standard deviation values for MN-RET (0.15 ± 0.10%) and MUT RET (4.7 ± 5.0 per million, after omission of two extreme outliers). The influences of age and sex on inter-subject variation were investigated, and neither factor affected MN-RET whereas both influenced MUT RET frequency. The lowest MUT RET values were observed for subjects <11 years old, and males had moderately higher frequencies than females. These results indicate that MN-RET and MUT RET are automation-compatible biomarkers of genotoxicity that bridge species of toxicological interest to include human populations. These data will be useful for appropriately designing future human studies that include these biomarkers of genotoxicity, and highlight the need for additional work aimed at identifying the sources of inter-individual variability reported herein.
Effects of crystallinity and point defects on optoelectronic applications of β-Ga_2O_3 epilayers (2013)

This study evaluates the effect of crystallinity and point defects on time-dependent photoresponsivity and the cathodoluminescence (CL) properties of β-Ga₂O₃ epilayers. A synchrotron high-resolution X-ray technique was used to understand the crystalline structure of samples. Rutherford backscattering spectroscopy was used to determine the net chemical composition of the samples to examine the type and ratio of their possible point defects. The results show that in functional time-dependent photoresponsivity of photodetectors based on β-Ga₂O₃ epilayers, point defects contribution overcomes the contribution of crystallinity. However, the crystalline structure affects the intensities and emission regions of CL spectra more than point defects.
Extracting hierarchical data points and tables from scanned contracts. (2013)

We present a technique for developing systems to automatically extract information from scanned semi-structured contracts. Such contracts are based on a template, but have different layouts and clientspecific changes. While the presented technique is applicable to all kinds of such contracts we specifically focus on so called ISDA credit support annexes. The data model for such documents consists of 150 individual entities some of which are tables that could span multiple pages. The information extraction is based on the Apache UIMA framework. It consists of a collection of small and simple Analysis Components that extract increasingly complex information based on earlier extractions. This technique is applied to extract individual data points and tables. Experiments show an overall precision of 97% with a recall of 93% regarding individual/simple data points and 89%/81% for table cells measured against manually entered ground truth. Due to its modular nature our system can be easily extended and adapted to other collections of contracts as long as some data model can be formulated.
P1–104: Assessing the effects of memantine in APP/PS1 transgenic mice by behavioral studies and ex vivo imaging of amyloid plaques using gadolinium labeled amyloid β peptides and micromri (2006)

Memantine, a moderate affinity uncompetitive NMDA receptor antagonist, has been shown to improve learning and memory in several preclinical models of Alzheimer's disease (AD) and is widely used clinically to treat AD. Memantine has also been shown to reduce the levels of amyloid precursor protein (APP), Aβ1–40 and Aβ1–42 peptides in human neuroblastoma cells and in the rat primary cortical neurons, and provide neuroprotection against Aβ neurotoxicity. In this study, we sought to determine whether memantine's memory enhancing effects could be correlated with its effects on amyloid plaque levels in APP/PS1 transgenic mice using object discrimination and MRI imaging. We used mice expressing both APP (KM670/671NL) and PS1 (L166P) mutations on the same transgene (APP/PS1–Tg); these mice develop amyloid deposits from the age of about 2 months. Two groups of 7 APP/PS1 Tg mice were treated either with memantine (10 mg/kg; i.p.) or vehicle for a period of 4 months starting at 3 months of age. At the end of this period the Tg mice were subject to an object discrimination test. We found that memantine–treated Tg mice performed the same as wild–type mice, while the performance of vehicle–treated Tg mice was significantly impaired (P=.0081 one–way ANOVA). The mice were then subject to ex vivo μMRI and histological examination of amyloid burden. μMRI was performed in memantine– and vehicle–treated Tg mice following intracarotid injection with gadolinium–DTPA–Aβ1–40(co–injected with mannitol to permeabilize the blood brain barrier). For μMR imaging, a gradient echo sequence sensitized to the presence of either iron or targeted magnetic contrast agent labeling plaques was used to provide both 2D T2* maps and 3D T2*–weighted image data sets with acquisition times of 55 min and 115 min, respectively. Analysis of whether the observed behavioral improvement by memantine can be correlated with μMRI and histological evaluations of amyloid burden are underway.