gebhart/patrepeval huggingface dataset:
Association of Serum Lipocalin-Type Prostaglandin D Synthase Levels with Subclinical Atherosclerosis in Untreated Asymptomatic Subjects (2008)

Recent studies suggest that lipocalin-type prostaglandin (PG) D synthase (L-PGDS), which converts PGH2 to PGD2, is implicated in the pathogenesis of atherosclerosis. However, clinical evidence for the association between serum L-PGDS levels and atherosclerosis has not been reported. In this study, we measured the serum L-PGDS concentration using sandwich enzyme-linked immunosorbent assay (ELISA) and investigated the association with traditional cardiovascular risk factors and surrogate atherosclerotic indices, such as the maximum score of the intima-media complex thickness of the carotid artery (C-IMT(max)) and the brachial-ankle pulse wave velocity (ba-PWV), in 500 non-treated asymptomatic subjects. The serum concentration of L-PGDS was 0.56+/-0.01 (mean+/-SEM, range 0.25-1.27, median 0.54) mg/L. Serum L-PGDS levels increased with age and were higher in men than in women. Serum L-PGDS was higher in subjects with hypertension and increased with increasing numbers of the traditional atherosclerotic risk factors. When the subjects were divided into four groups according to the levels of serum L-PGDS, the age-adjusted values of C-IMT(max) and ba-PWV were significantly increased in subjects with higher serum L-PGDS levels (quartile 3 and quartile 4) compared to those in the lowest quartile (quartile 1), for both genders. Multiple regression analysis including risk factors revealed that serum L-PGDS was an independent determinant for ba-PWV (beta=0.130, p<0.001). Serum L-PGDS tended to associate with C-IMT(max) but was not statistically significant (beta=0.084, p=0.075). In conclusion, our results suggest that an increase in serum L-PGDS concentration is associated with the progression of atherosclerosis.
Exon-Level Microarray Analyses Identify Alternative Splicing Programs in Breast Cancer (2010)

Protein isoforms produced by alternative splicing (AS) of many genes have been implicated in several aspects of cancer genesis and progression. These observations motivated a genome-wide assessment of AS in breast cancer. We accomplished this by measuring exon level expression in 31 breast cancer and nonmalignant immortalized cell lines representing luminal, basal, and claudin-low breast cancer subtypes using Affymetrix Human Junction Arrays. We analyzed these data using a computational pipeline specifically designed to detect AS with a low false-positive rate. This identified 181 splice events representing 156 genes as candidates for AS. Reverse transcription-PCR validation of a subset of predicted AS events confirmed 90%. Approximately half of the AS events were associated with basal, luminal, or claudin-low breast cancer subtypes. Exons involved in claudin-low subtype-specific AS were significantly associated with the presence of evolutionarily conserved binding motifs for the tissue-specific Fox2 splicing factor. Small interfering RNA knockdown of Fox2 confirmed the involvement of this splicing factor in subtype-specific AS. The subtype-specific AS detected in this study likely reflects the splicing pattern in the breast cancer progenitor cells in which the tumor arose and suggests the utility of assays for Fox-mediated AS in cancer subtype definition and early detection. These data also suggest the possibility of reducing the toxicity of protein-targeted breast cancer treatments by targeting protein isoforms that are not present in limiting normal tissues.
Visualization of hepatic arteries with 3D ultrasound during intra-arterial therapies (2016)

Liver cancer represents the second most common cause of cancer-related mortality worldwide. The prognosis is poor with an overall mortality of 95%. Moreover, most hepatic tumors are unresectable due to their advanced stage at discovery or poor underlying liver function. Tumor embolization by intra-arterial approaches is the current standard of care for advanced cases of hepatocellular carcinoma. These therapies rely on the fact that the blood supply of primary hepatic tumors is predominantly arterial. Feedback on blood flow velocities in the hepatic arteries is crucial to ensure maximal treatment efficacy on the targeted masses. Based on these velocities, the intra-arterial injection rate is modulated for optimal infusion of the chemotherapeutic drugs into the tumorous tissue. While Doppler ultrasound is a well-documented technique for the assessment of blood flow, 3D visualization of vascular anatomy with ultrasound remains challenging. In this paper we present an image-guidance pipeline that enables the localization of the hepatic arterial branches within a 3D ultrasound image of the liver. A diagnostic Magnetic resonance angiography (MRA) is first processed to automatically segment the hepatic arteries. A non-rigid registration method is then applied on the portal phase of the MRA volume with a 3D ultrasound to enable the visualization of the 3D mesh of the hepatic arteries in the Doppler images. To evaluate the performance of the proposed workflow, we present initial results from porcine models and patient images.
Detecting sweethearting in retail surveillance videos (2009)

A significant portion of retail shrink is attributed to employees and occurs around the point of sale (POS). In this paper, we target a major type of retail fraud in surveillance videos, known as sweethearting (or fake scan), where a cashier intentionally fails to enter one or more items into the transaction in an attempt to get free merchandise for the customer. We first develop a motion-based algorithm to identify video segments as candidates for primitive events at the POS. We then apply spatio-temporal features to recognize true primitive events from the candidates and prune those falsely alarmed. In particular, we learn location-aware event models by Multiple-Instance Learning to address the location-sensitive issues that appear in our problem. Finally, we validate the entire transaction by combining primitive events according to temporal ordering constraints. We demonstrate the effectiveness of our approach on data captured from a real grocery store.
Factor Alignment Problems and Quantitative Portfolio Management (2012)

Quantitative equity portfolio management has evolved into an interdisciplinary activity that draws expertise from the fields of finance, statistics, econometrics, accounting, and optimization. Each one of these streams is a mature discipline in itself, having its own body of knowledge, and operates under assumptions that are usually well accepted within the respective communities. But when concepts from these diverse fields are applied in a common setting, there is bound to be friction among various assumptions that get further magnified due to the use of an optimizer. In this article, Ceria, Saxena, and Stubbs focus on the interaction of three key elements that are part of the quantitative portfolio management process, namely, the expected returns model, the risk model, and the constraints that are used to formulate the portfolio construction problem. They generally refer to the issues caused by this interaction as factor alignment problems. The authors present a detailed investigation of these alignment problems, survey some of their common sources, analyze and document their effects on the ex post performance of optimized portfolios, and conclude with a practical and effective remedy in the form of augmented risk models. <b>TOPICS:</b>Equity portfolio management, statistical methods, portfolio construction
Measuring collagen injury depth for burn severity determination using polarization sensitive optical coherence tomography (2022)

Determining the optimal treatment course for a dermatologic burn wound requires knowledge of the wound's severity, as quantified by the depth of thermal damage. In current clinical practice, burn depth is inferred based exclusively on superficial visual assessment, a method which is subject to substantial error rates in the classification of partial thickness (second degree) burns. Here, we present methods for direct, quantitative determination of the depth extent of injury to the dermal collagen matrix using polarization-sensitive optical coherence tomography (PS-OCT). By visualizing the depth-dependence of the degree of polarization of light in the tissue, rather than cumulative retardation, we enable direct and volumetric assessment of local collagen status. We further augment our PS-OCT measurements by visualizing adnexal structures such as hair follicles to relay overall dermal viability in the wounded region. Our methods, which we have validated ex vivo with matched histology, offer an information-rich tool for precise interrogation of burn wound severity and healing potential in both research and clinical settings.
The Thai Phase III HIV Type 1 Vaccine Trial (RV144) Regimen Induces Antibodies That Target Conserved Regions Within the V2 Loop of gp120 (2012)

The Thai Phase III clinical trial (RV144) showed modest efficacy in preventing HIV-1 acquisition. Plasma collected from HIV-1-uninfected trial participants completing all injections with ALVAC-HIV (vCP1521) prime and AIDSVAX B/E boost were tested for antibody responses against HIV-1 gp120 envelope (Env). Peptide microarray analysis from six HIV-1 subtypes and group M consensus showed that vaccination induced antibody responses to the second variable (V2) loop of gp120 of multiple subtypes. We further evaluated V2 responses by ELISA and surface plasmon resonance using cyclic (Cyc) and linear V2 loop peptides. Thirty-one of 32 vaccine recipients tested (97%) had antibody responses against Cyc V2 at 2 weeks postimmunization with a reciprocal geometric mean titer (GMT) of 1100 (range: 200-3200). The frequency of detecting plasma V2 antibodies declined to 19% at 28 weeks post-last injection (GMT: 110, range: 100-200). Antibody responses targeted the mid-region of the V2 loop that contains conserved epitopes and has the amino acid sequence KQKVHALFYKLDIVPI (HXB2 Numbering sequence 169-184). Valine at position 172 was critical for antibody binding. The frequency of V3 responses at 2 weeks postimmunization was modest (18/32, 56%) with a GMT of 185 (range: 100-800). In contrast, naturally infected HIV-1 individuals had a lower frequency of antibody responses to V2 (10/20, 50%; p=0.003) and a higher frequency of responses to V3 (19/20, 95%), with GMTs of 400 (range: 100-3200) and 3570 (range: 200-12,800), respectively. RV144 vaccination induced antibodies that targeted a region of the V2 loop that contains conserved epitopes. Early HIV-1 transmission events involve V2 loop interactions, raising the possibility that anti-V2 antibodies in RV144 may have contributed to viral inhibition.
Linearity Characteristics of Field Plated AlGaN/GaN HEMTs for Microwave Applications (2009)

Field-plated (FP) AlGaN/GaN high electron mobility transistor (HEMT) has been fabricated and characterized for microwave applications. After the implement of the FP structure, lower trans-conductance (Gm) was observed on DC and small signal characteristics of the GaN power HEMT. Even FP-HEMT showed lower linear gain, the devices still exhibited higher output power and higher power added efficiency than conventional HEMT. However, lower trans-conductance and higher gate-drain capacitance (Cgd) didn't influence the linearity characteristics of the FP-HEMT. Finally, a 100μm GaN power HEMT on sapphire was fabricated with linear gain of 15.39dB, outpout power of 25.36dBm, and power added efficiency of 43%. The device also demonstrated high linearity of -27.1dBc for IMD3 and 33.88dBc for ACPR when biased at drain voltage of 30V with current density of 15mA/mm at 2GHz.
Branched-chain analogs of luteinizing hormone-releasing hormone (1978)

Benzoyl-, acetylsalicylyl-, indomethacinyl-, pyroglutamylhistidyl-, and pyroglutamyl-D-phenylalanyl-D-tryptophanylseryltyrosyl groups were attached to a moderately active inhibitory analogue of LH-RH, [D-Phe2,D-Trp3-D-Lys6]-LH-RH, via the epsilon-amino group of the lysine residue. The resulting compounds were assayed for anti-LH-RH activity and for their ability to block ovulation in the rat. The decrease in polarity and increase in size of the lysine side chain resulting from addition of the aromatic acyl groups gave almost no increase in inhibitory activity. Addition of the dipeptide, less than Glu-His, also had little effect on potency. However, incorporation of the pentapeptide sequence to give a branched pentadecapeptide with essentially two N termini resulted in antiovulatory activity greater than the parent peptide or any other analogue thus far tested by us. The corresponding agonist peptide, [Nepsilon-(less than Glu-His-Trp-Ser-Tyr)-D-Lys6]-LH-RH, was also synthesized and tested for LH- and FSH-releasing activity. Surprisingly, it was no more active than [D-Lys6]-LH-RH itself, suggesting that an intact C terminus as well as an N terminus is necessary for the full expression of gonadotropin release.
Zeolite Membrane-Based Artificial Photosynthetic Assembly for Long-Lived Charge Separation (2005)

Photochemically generated long-lived charge separation is the key step in processes that aim for conversion of solar energy into chemical energy. In this study, we focus on a Ru polypyridyl complex [(bpy)(2)Ru(II)L, bpy = bipyridine, L = 1,2-bis[4-(4(')-2,2(')-bipyridyl) ethene] encapsulated on the surface of a pinhole-free zeolite membrane by quaternization of L and surrounded with intrazeolitic bipyridinium ions (N,N'-trimethyl-2,2'-bipyridinium ion, 3DQ(2+)). Visible-light irradiation of the Ru complex side of the membrane in the presence of a sacrificial electron donor led to formation of PVS(-*) on the other side. Pore-blocking disilazane-based chemistry allows for Na(+) to migrate through the membrane to maintain charge balance, while keeping the 3DQ(2+) entrapped in the zeolite. These results provide encouragement that the zeolite membrane based architecture has the necessary features for not only incorporating molecular assemblies with long-lived charge separation but also for ready exploitation of the spatially separated charges to store visible light energy in chemical species.
Fine Micro Patterning of Conductive Line by Using Direct Inkjet Printing (2006)

A novel selective metallization process to fabricate the fine conductive line based on drop-on-demand (DoD) inkjet printing was studied. Direct inkjet printing is an alternative and costeffective technology for patterning and fabricating objects directly from design or image files without making masks and patterns. The conductive ink used in this experiment consists of 1 to 50 nm silver particles that are homogeneously suspended in an organic carrier. A piezo-electric inkjet print head driven by a bipolar voltage signal is used to dispense 20-40μm diameter droplets. Repeatability of circuitry fabrication is closely related to the formation of steady, satellite-free droplets. Therefore, the ability to form small and stable droplets with a same size, constant velocity and the correct flight angle must be taken into consideration for fine and precise conductive lines. In this study, parameters affecting the pattern formation such as drop formation, drop placement accuracy and velocity deviation between each nozzle have been investigated. As a result, direct inkjet patterning systems equipped with several functioning modules and fine metallic patterns have been developed.
Faculty Opinions recommendation of Randomized phase II study of gemcitabine plus cisplatin or carboplatin [corrected], with or without cetuximab, as first-line therapy for patients with advanced or metastatic non small-cell lung cancer. (2008)

Read the full review for this Faculty Opinions recommended article: Randomized phase II study of gemcitabine plus cisplatin or carboplatin [corrected], with or without cetuximab, as first-line therapy for patients with advanced or metastatic non small-cell lung cancer.
Hierarchical self-assembly of amelogenin and the regulation of biomineralization at the nanoscale (2011)

Enamel is a highly organized hierarchical nanocomposite, which consists of parallel arrays of elongated apatitic crystallites forming an intricate three-dimensional microstructure. Amelogenin, the major extracellular matrix protein of dental enamel, regulates the formation of these crystalline arrays via cooperative interactions with forming mineral phase. Using cryoelectron microscopy, we demonstrate that amelogenin undergoes stepwise hierarchical self-assembly. Furthermore, our results indicate that interactions between amelogenin hydrophilic C-terminal telopeptides are essential for oligomer formation and for subsequent steps of hierarchical self-assembly. We further show that amelogenin assemblies stabilize mineral prenucleation clusters and guide their arrangement into linear chains that organize as parallel arrays. The prenucleation clusters subsequently fuse together to form needle-shaped mineral particles, leading to the formation of bundles of crystallites, the hallmark structural organization of the forming enamel at the nanoscale. These findings provide unique insight into the regulation of biological mineralization by specialized macromolecules and an inspiration for bottom-up strategies for the materials design.
Synthesis of poly(dimethylsiloxane) oligomers with pendant amine groups via co‐equilibration anionic polymerization reactions (1991)

Abstract The present study describes a method of incorporating amine functional groups on poly(dimethylsiloxane) chains as pendant groups on silicon atoms. This method allows for independent control of the molecular weight and the amine content of the oligomer. The new molecular design was achieved by co‐equilibration of the cyclic tetramer octamethylcyclotetrasiloxane (D 4 ) with a new cyclic siloxane monomer containing aliphatic amine substituents on the silicon atoms. The co‐equilibration of the two cyclic siloxanes was carried out in the presence of a silanolate catalyst, using the nonfunctionalized hexamethyldisiloxane as the end‐capper. The distribution of the molecular species at thermodynamic equilibrium and the efficiency of incorporation of siloxane units containing pendant amine functionalities into the poly(dimethylsiloxane) chains were investigated as a function of oligomer chemical composition and molecular weight.
High efficiency methylammonium lead triiodide perovskite solar cells: the relevance of non-stoichiometric precursors (2015)

Improved crystallinity and device performance of CH<sub>3</sub>NH<sub>3</sub>PbI<sub>3</sub> perovskite solar cells by using a non-stoichiometric PbI<sub>2</sub> : CH<sub>3</sub>NH<sub>3</sub>I precursor ratio.
Pinning fields in amorphous materials (1993)

The stress and field dependence of the pinning field Hp of ribbons of the composition Fe73.5Cu1Nb3Si13.5B9 and Co73.5Cu1Nb3Si13.5B9 is compared with that of the coercivity HC. The similar character of HC(σ) and Hp(σ) indicates a strong correlation between these two properties. At higher external stresses HC(σ) and Hp(σ) depend on a premagnetizing procedure. This can be explained assuming a different domain structure.
Development of Impedance Measurement of Lithium Ion Batteries Electrode using Terahertz Chemical Microscope (2021)

In recent years, with the spread of electric vehicles, improvement in the performance of lithium ion batteries has been required. Evaluation of the active material is important because the performance of the lithium ion battery is affected by the movement of lithium ions at the electrode active material-electrolyte interface. In this study, we fabricated a lithium ion battery with the sensing plate, which is a potential sensor, attached to the positive electrode, and evaluated lithium ion battery with a Terahertz Chemical Microscope. As a result, we succeeded in measuring the potential distribution of the positive electrode during charging and discharging, and the local impedance.
Ge on Si by novel heteroepitaxy for high efficiency near infrared photodetection (2006)

We report germanium-on-silicon MSM photodetectors with responsivities as high as 0.85A/W at 1.55μm and 2V reverse bias, and exhibit reverse dark currents of 100mA/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> and external quantum efficiency up to 68%.
The Angular Dependence of the Gradient Echo and Spin Echo Bold Signal Induced by Cortical Micro- and Macro- Vasculature (2018)

In recent investigations, the angular dependence of the BOLD signal with respect to the main magnetic field has been shown by Monte Carlo simulations and experimental approaches. This orientation dependence is often attributed to the contribution of large vessels (cortical surface and penetrating arteries/veins). However, the ability to resolve cortical layers and columns depends ultimately on the contribution of the MR signal generated by the capillary bed. In this work, we studied the MR signal attenuation generated by a vascular network model that was acquired from the parietal cortex of mice using a two-photon laser imaging techniques. We separately investigated the impact of macrovessels (&gt;5 µm in diameter) and microvessels (&lt; 5 µm in diameter) on the BOLD effect.
Neural Topic Modeling of Psychotherapy Sessions (2022)

In this work, we compare different neural topic modeling methods in learning the topical propensities of different psychiatric conditions from the psychotherapy session transcripts parsed from speech recordings. We also incorporate temporal modeling to put this additional interpretability to action by parsing out topic similarities as a time series in a turn-level resolution. We believe this topic modeling framework can offer interpretable insights for the therapist to optimally decide his or her strategy and improve psychotherapy effectiveness.
Antisense RNA-mediated Deficiency of the Calpain Protease, nCL-4, in NIH3T3 Cells Is Associated with Neoplastic Transformation and Tumorigenesis (2000)

We previously have described the use of an antisense RNA strategy termed random homozygous knock-out (RHKO) to identify negative regulators of cell proliferation. Here we report the discovery that RHKO-mediated deficiency of the nCL-4 calpain protease results in cellular transformation of and tumorigenesis by murine NIH3T3 fibroblasts. We isolated cell clones able to form colonies on 0.5% soft agar and found that these cells generated tumors when injected subcutaneously into nude mice. The gene inactivated by RHKO was identified as nCL-4 by genomic library screening, transcript analysis, and DNA sequencing. Anchorage-independent growth, as indicated by colony formation on soft agar, was reversed by reversal of antisense-mediated homozygous inactivation, but continued haplo-insufficiency of nCL-4 resulting from insertional mutagenesis of one nCL-4 allele was associated with persistent tumorigenesis. nCL-4 cDNA expressed in naive 3T3 cells in the antisense, but not sense, direction under control of the cytomegalovirus early promoter reproduced the anchorage-independent growth effects of RHKO. Our results implicate deficiency of the nCL-4 calpain protease in neoplastic transformation.