gebhart/patrepeval huggingface dataset:
Prediction of genetically-evaluated tumour responses to chemotherapy from breast MRI using machine learning with model selection (2021)

Abstract Genetic tests can provide prognostic information in breast cancer for both diagnosis and treatment planning. However, the cost of a genetic test is still high. In this study, we developed a radiogenomics method to predict genetically-evaluated responses to chemotherapy for breast cancer using our machine-learning technology coupled with model selection. Our proposed method consists of feature extraction, model selection, and prediction by the selected model. In the feature extraction, 318 morphological and texture features were extracted from a tumour region. In the model selection module, there are two major components: (1) selection of imaging biomarkers based on our original sequential forward floating selection (SFFS) feature selection and (2) building of a support vector machine (SVM) classifier including kernel function selection and hyperparameter optimization. The optimized feature set, i.e. imaging biomarkers, coupled with an SVM classifier were chosen by maximizing the area under curve (AUC) of corresponding receiver-operating-characteristic curve (ROC). After the model selection, the optimized SVM classifier operated on the selected imaging biomarkers for prediction. We applied our proposed method to 118 breast MRI studies from 118 patients for predicting genetically-evaluated responses to chemotherapy for breast cancer that evaluated by the genetic test of IRSN-23. We achieved an AUC value of 0.96 using the optimized SVM classifier model coupled with 24 selected imaging biomarkers in predicting the results of IRSN-23 in a five-fold cross-validation procedure.
Low Loss MMI Couplers for High Performance MZI Modulators (2010)

Optical splitters and combiners which can provide precise splitting with low loss, high thermal stability, large optical bandwidth, high compactness, and insensitivity to fabrication tolerances are essential components for high performance Mach-Zehnder Interferometers (MZI)-based optical modulators. In this letter, we theoretically and experimentally investigate the multimode interference (MMI) based structure and the reduction in optical loss achievable through the use of linear tapers at the input and output ports. Our data shows that losses can be reduced to below 1 dB/MMI without affecting the static extinction when employed in MZIs.
Arterial secondary blood flow patterns visualized with vector flow ultrasound (2011)

This study presents the first quantification and visualization of secondary flow patterns with vector flow ultrasound. The first commercial implementation of the vector flow method Transverse Oscillation was used to obtain in-vivo, 2D vector fields in real-time. The hypothesis of this study was that the rotational direction is constant within each artery. Three data sets of 10 seconds were obtained from three main arteries in healthy volunteers. For each data set the rotational flow patterns were identified during diastole. Each data set contains a 2D vector field over time using the vector angles and velocity magnitudes the blood flow patterns were visualized using streamlines in Matlab (Mathworks, Natick, MA, USA). The rotational flow was quantified by the angular frequency for each cardiac cycle, and the mean rotational frequencies and standard deviations were calculated for the abdominal aorta {−1.3±0.4;−1.0±0.3;−0.9±0.2}Hz, the common iliac artery {−0.4±0.1;−1.0±0.2;−0.4±0.1}Hz, and the common carotid artery {0.8±0.3;1.4±0.3;0.4±0.1}Hz. A positive sign indicates an anti-clockwise rotation, and a negative sign indicates clockwise rotation. The sign of the rotational directions within each artery were constant.
Fully-Integrated CMOS-Compatible Q-Switched Laser at 1.9µm Using Thulium-Doped Al2O3 (2017)

A fully-integrated Q-switched laser is demonstrated at 1.9 µm using thulium-doped aluminum oxide waveguides, with the potential for achieving an on-chip passively mode-locked laser. All components of the laser are fabricated in a CMOS-compatible silicon photonics process.
A backup appliance composed of high-capacity disk drives (2005)

Disk drives are now available with capacity and price per capacity comparable to nearline tape systems. Because disks have superior performance, density and maintainability characteristics, it seems likely that they will soon overtake tapes as the backup medium of choice. The authors outline the potential advantages of a backup system composed of high-capacity disk drives and describe what implications such a system would have for backup software.
Regioselective Preparation of 1,6- and 1,8-Dihydroxy-9,10-anthraquinones from the Common Intermediates: Synthesis of Aloesaponarin I and K1115A (2000)

Abstract Treatment of 3-acyl-2-[(2,2-dimethyl-6-oxo-1,3-dioxin-4-yl)methyl]-5-methoxy-1,4-naphthoquinones with K2CO3 in an alcohol brought about the intramolecular condensation to give 1-alkyl-3-hydroxy-8-methoxy-9,10-anthraquinone-2-carboxylates in good yields, while the same naphthoquinone gave 1-hydroxy-8-methoxy-9,10-anthraquinone-3-acetic acid in good yield by treatment with KHMDS.
Sleep Quality, Psychologic Profiles, Cardiac Activity, and Salivary Biomarkers in Young Subjects with Different Degrees of Rhythmic Masticatory Muscle Activity: A Polysomnography Study (2019)

In otherwise healthy subjects presenting normal physiologic variables, neither significant nor consistent differences in sleep architecture, psychologic states, heart rate variability, or salivary biomarkers in relation to the frequency of RMMA were found.
Spectral analysis of flow cytometric data: Design of a special‐purpose low‐pass digital filter (1987)

Spectral decomposition of flow cytometric datafiles of arbitrary dimension reveal information of both the signal and the noise components that constitute the histograms. This spectral information is used to construct a low-pass digital filter, which removes the high-frequency noise from the actual data. It is shown that this procedure guarantees non-trivial smoothing of the flow cytometric data in accordance with the local experimental situation. As a consequence optimal reconstruction of the signal is possible, which facilitates unambiguous interpretation of the data files and mathematical estimation of the statistical parameters.
Topology optimized RF MEMS switches (2013)

Topology optimization is a rigorous and powerful method that should become a standard MEMS design tool - it can produce unique and non-intuitive designs that meet complex objectives and can dramatically improve the performance and reliability of MEMS devices. We present successful uses of topology optimization for an RF MEM capacitive switch. Extensive experimental data confirms that the switches perform as designed by the optimizations, and that our simulation models are accurate. A subset of measurements are presented here. Broader results have been submitted in full journal format.
Development of a Monitoring System to Assess the Internal Environment of Bagged Grain in Storage (2022)

Highlights A temperature and relative humidity monitoring system for bagged grain was developed. Continuous monitoring of condition of bagged corn and paddy was done for four months. Temperature and relative humidity within bagged grain followed the ambient conditions. Equilibrium moisture content of the stored grain increased by 1.2% during storage. Abstract. Most farmers in African countries produce small amounts of grain per season and use polypropylene bags for grain storage. Little published information is available on the temperature and moisture change of bagged grain even though high losses are observed. Commercially available moisture meters are expensive and not suitable for providing real-time information on the condition of bagged grain. A monitoring system was developed to assess the internal environment of bagged grain stored in warehouses. The system has eight on-board integrated temperature and relative humidity sensors connected to a custom Arduino-based data acquisition system which recorded a time stamp, temperature, and relative humidity onto a microSD card. Four units were deployed in two warehouses in Nigeria from 3 May 2019 to 9 September 2019. There were 54 bags of corn in Ilorin, and 4000 bags of paddy rice in Tede. Average monthly temperatures recorded at various locations in the warehouse were significantly different (p&amp;lt;0.05). The errors in temperature and relative humidity measurement were 0.2°C and 3.7%, respectively. Equilibrium moisture content of bagged corn and paddy increased by 1.1 and 1.2 percentage points (wet basis), respectively. Data acquired by the system can be used to monitor the condition of bagged grain and detect potential spoilage. This system would help warehouse managers make informed decisions to reduce storage losses. Keywords: EMC, Grain bag storage, Loss management, Moisture, Resilience, Temperature.
Staphylococcus aureus vaccines: Deviating from the carol (2016)

Staphylococcus aureus, a commensal of the human nasopharynx and skin, also causes invasive disease, most frequently skin and soft tissue infections. Invasive disease caused by drug-resistant strains, designated MRSA (methicillin-resistant S. aureus), is associated with failure of antibiotic therapy and elevated mortality. Here we review polysaccharide-conjugate and subunit vaccines that were designed to prevent S. aureus infection in patients at risk of bacteremia or surgical wound infection but failed to reach their clinical endpoints. We also discuss vaccines with ongoing trials for combinations of polysaccharide-conjugates and subunits. S. aureus colonization and invasive disease are not associated with the development of protective immune responses, which is attributable to a large spectrum of immune evasion factors. Two evasive strategies, assembly of protective fibrin shields via coagulases and protein A-mediated B cell superantigen activity, are discussed as possible vaccine targets. Although correlates for protective immunity are not yet known, opsonophagocytic killing of staphylococci by phagocytic cells offers opportunities to establish such criteria.
Abstract 2439: HSulf-1 loss in ovarian cancer cells induces lipid droplet biogenesis (2014)

Abstract We have previously shown that a frequent loss of endosulfatase HSulf-1 in ovarian cancer enhances the heparin binding growth factor signaling which subsequently induces and potentiates tumorigenesis. Our recent data indicate that knockdown of HSulf-1 in ovarian cancer cells significantly alter levels of several metabolites which is comparable to the deranged metabolite profiles in primary ovarian tumors. Here we report that the metabolites associated with lipid metabolism are altered in such a way that the cells start manifesting a “lipogenic phenotype” characterized by an increased fatty acid synthesis, storage and mitochondrial beta oxidation. The lipogenic phenotype is associated with an accumulation of cytoplasmic lipid droplets (LDs) in a stably HSulf-1 knockdown cells [OV202 (Sh1/2) and OV2223 cells]. Presence of LDs is evidenced by BODIPY staining and transmission electron microscopy (TEM) analysis in Sh1/2 and a non-transduced control (NTC) cells. Conversely, enhanced expression of HSulf-1 in TOV21G, SKOV3, and C13 cells also resulted in reducing the number of LDs. More importantly, MEFs (mouse embryonic fibroblasts) from HSulf-1 knockout mice also showed an increased LD biogenesis compared to the wild type MEFs. Microarray analysis identified cytoplasmic phospholipase A2 (cPLA2; an enzyme involved in LD biogenesis) as one of the genes that was significantly upregulated in OV202 Sh1 and Sh2 cells. We found that Sh1 and Sh2 cells show an increased phosphorylation (ser505) of cytoplasmic phospholipase A2 (p-cPLA2) compared to NTC cells. Phosphorylation at ser505 is vital for the enzyme activity of cPLA2 and also necessary for LD biogenesis. We inhibited the LD biogenesis in Sh1 cells by a pharmacological inhibitor of cPLA2 (AACOCF3 and MAFP) as well by shRNA mediated knockdown of endogenous cPLA2. Further, we stimulated NTC and Sh1 cells with heparin binding growth factor (50ng/ml) for different time points and found an elevated phosphorylation of cPLA2 and extracellular signal related kinase (ERK), which is also inhibited by a pre-treatment of cells with cPLA2 inhibitor. Interestingly, inhibition of phospho-ERK by U0126 (MEK inhibitor) also inhibits the phosphorylation of cPLA2. These findings strongly suggest that loss of HSulf-1 promotes lipid metabolism in the ovarian cancer cells via activation of cPLA2 via an ERK dependent pathway. The present work highlights a novel role HSulf-1 in regulating lipid metabolism which could lead to a better understanding of tumorigenesis and identification of new targets for tumor therapy. Citation Format: Debarshi Roy, Xiaoping He, Ashwani Khurana, Susmita Mondal, Deok-Beom Jung, Sung Kim, Thomas Dierks, Clifford Folmes, Andre Terzic, Viji Shridhar. HSulf-1 loss in ovarian cancer cells induces lipid droplet biogenesis. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 2439. doi:10.1158/1538-7445.AM2014-2439
Practical implementation of PN scrambler for PAPR reduction in OFDM systems for range extension and lower power consumption (2008)

Orthogonal Frequency Division Modulation (OFDM) is an efficient multi-carrier modulation scheme. It is used in many wireless communication systems due to its robustness towards fading channel behavior and a relative ease of implementation coming from computationally efficient Inverse Fast Fourier Transforms (IFFT). However, the OFDM waveform has a very large Peak-to-Average Power Ratio (PAPR). Therefore, to avoid clipping plus nonlinear distortion, the Power Amplifier (PA) needs to be backed off significantly. This paper proposes a novel implementation and analysis of a Pseudorandom Noise (PN) scrambling technique allowing a significant reduction of the OFDM signalpsilas PAPR. The theoretical basis for the technique is presented, and a particular implementation of the technique for the IEEE 802.11a standard is discussed. Both simulations and measurements demonstrate significant benefits of the proposed technique in longer range wireless communications applications that use OFDM.
[Echocardiographic observation of appearance and progression of mitral annular calcification in a patient with familial obstructive hypertrophic cardiomyopathy]. (1998)

A 37-year-old man with familial hypertrophic obstructive cardiomyopathy (HOCM) developed mitral annular calcification (MAC) during the follow-up period. At the age of 23 years, a systolic murmur and electrocardiographic abnormality including giant T wave inversion were detected incidentally. His elder brother also had HOCM. Catheterization disclosed a left ventricular outflow pressure gradient of 25 mmHg and thickened interventricular septum. Echocardiography showed asymmetric septal hypertrophy and systolic anterior motion of the mitral valve. The patient was followed up by repeated echocardiography from age 37 years and the onset of MAC (2 mm in thickness) was found at age 48 years. One year later, the MAC had progressed markedly (5 mm) without other remarkable changes in the M-mode echocardiogram, except mitral regurgitation (at age 41 years), left ventricular apical as well as posterior wall hypertrophy (age 43 years) and left atrial enlargement (age 46 years). The left ventricular inflow velocity at the atrial contraction period decreased significantly concomitantly with MAC. MAC is a rare complication in young and middle aged patients. The onset and progression of MAC is still obscure in HOCM. This patient showed that sudden onset and rapid progression of MAC can occur in young patients with HOCM.
Coherent multi-photon interference and compensation of polarization dispersion (2001)

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2001.
Polydentate Amines as CVD Precursor Ancillary Ligands. Epitaxial MgO Thin-Film Growth Using a Highly Volatile, Thermally and Air-Stable Magnesium Precursor (2000)

A superior monomeric MOCVD precursor for epitaxial MgO growth is described.The complex (see Figure) can be readily prepared using commercially available reagents via a simple aqueous route under ambient laboratory conditions. Clean and complete volatilization with no loss of coordinated ligands is observed by TGA and high-quality epitaxial films were grown using the precursor.
A survey of Asian Eye Institutions on perioperative antibiotic prophylaxis in cataract surgery (2023)

There are variations in antimicrobial prophylaxis approaches to preoperative, intra-operative and postoperative regimens in cataract surgery in Asia. More evidence-based research is needed to support the development of detailed guidelines for perioperative antibiotic prophylaxis to reduce postoperative infections.
Supplementary Figures 1-3 from Armed Antibodies Targeting the Mucin Repeats of the Ovarian Cancer Antigen, MUC16, Are Highly Efficacious in Animal Tumor Models (2023)

Supplementary Figures 1-3 from Armed Antibodies Targeting the Mucin Repeats of the Ovarian Cancer Antigen, MUC16, Are Highly Efficacious in Animal Tumor Models
Reliability Analysis of Ultra Low-Temperature Polycrystalline Silicon Thin-Film Transistors (2007)

We investigated the reliability of polycrystalline silicon (poly-Si) thin-film transistors (TFTs) fabricated by an ultra low-temperature process below 200 °C. Their comparatively high reliability was confirmed. It was found by emission observation that hot carriers were hardly generated under the drain avalanche condition. The Joule heating effect was also hardly observed under DC stress at high drain and gate voltage stress. These results show that the hot carrier and Joule heating effects are not the predominant causes of the degradation of ultra low-temperature TFTs. The new degradation mode of the threshold voltage shift by a vertical electric field was found to be dominant in ultra low-temperature TFT.
Abstract 15826: SCUBE1 Controls BMPR2-relevant Pulmonary Endothelial Function: Implications for Diagnostic Marker Development in Pulmonary Arterial Hypertension (2020)

Introduction: Pulmonary arterial hypertension (PAH) is a morbid vascular disease where mutations of bone morphogenetic protein receptor 2 (BMPR2) control pulmonary endothelial pathophenotypes. Transcriptomic screening from endothelial cells (ECs) derived from hereditary BMPR2-driven disease offers an opportunity to identify novel effectors in PAH pathogenesis. Methods: Public RNA-sequencing data were analyzed from inducible pluripotent stem (iPS) cell-derived endothelial cells with and without BMPR2 mutations. Candidate genes were assessed in cultured pulmonary arterial ECs (PAECs) and in rodent and human PAH. Correlations were assessed of human plasma expression with clinical disease indices. Results: Signal Peptide CUB-EGF-Domain Containing Protein 1 (SCUBE1), a putative binding partner to BMPR2, was differentially expressed in ECs carrying BMPR2 mutations. SCUBE1 was enriched in PAECs, dependent on hypoxia inducible factor-1α, and downregulated by PAH triggers, including BMPR2 knockdown, hypoxia, and IL-1β exposure. In vitro analyses defined SCUBE1 as a pathogenic effector activating BMPR2-associated SMAD1/5/9, thus regulating endothelial angiogenic potential, proliferation, and apoptosis. SCUBE1 was decreased specifically in plasma and lungs in rodents and patients with PAH but not in those with pulmonary hypertension due to left heart disease, or in the patients of other acute and chronic cardiopulmonary pathologies, including pneumonia, acute lung injury, chronic obstructive pulmonary disease, ischemic heart disease, and cardiomyopathy. An optimal plasma SCUBE1 cut point of 5.02 ng/mL was defined to diagnose PAH from control cohort with a sensitivity of 0.65 and a specificity of 0.82. In PAH patients, plasma SCUBE1 levels negatively correlated with pulmonary arterial pressure, pulmonary vascular resistance, and right ventricular dysfunction. Conclusions: Guided by iPSC-EC sequencing, SCUBE1 was identified as a downregulated secreted factor in PAH, controlling endothelial pathophenotypes and correlated with disease indices. Clinically, SCUBE1 is a sensitive and specific PAH diagnostic marker. It may also serve as a therapeutic target given its inherent links to controlling PAH predisposition and severity.
Phase I trial of pod-intravaginal rings delivering antiretroviral agents for HIV-1 prevention: Rectal drug exposure from vaginal dosing with tenofovir disoproxil fumarate, emtricitabine, and maraviroc (2018)

The concentrations of FTC and MVC in rectal fluids obtained in two exploratory clinical trials of IVRs delivering ARV combinations exceeded levels associated with in vitro efficacy in HIV inhibition. Unexpectedly, MVC appeared to depress the distribution of TFV and FTC into the rectal lumen. Here we show that vaginal delivery of ARV combinations may provide adherence and coitally independent dual-compartment protection from HIV infection during both vaginal and receptive anal intercourse.
Wet Removal of Post-Etch Residues by a Combination of UV Irradiation and a SC1 Process (2012)

In back-end of line processing (BEOL), the polymer deposited on the dielectric sidewalls during the etch process must be removed prior to subsequent processing steps to achieve high adhesion and good coverage of materials deposited in the etched features [1, . Typically, this is done by a combination of a short plasma treatment and a diluted wet clean, or by wet cleans alone. On the one hand, for porous dielectric stacks, a mild plasma treatment that preserves the integrity of the low- k dielectrics would not be sufficient to effectively remove this residue. With regard to wet clean, diluted aqueous solutions (e.g. HF-based) are not efficient for polymer removal without etching the underlying dielectric to lift off the polymer, leading to unacceptable critical dimension (CD) loss. In addition, analytical techniques available for direct characterization of sidewall residues are limited. For a fast screening of potential chemistries capable of dissolving/removing polymer residues generated during the low- k etch, a model fluoropolymer was deposited on a blanket, checkerboard low- k substrate. The present study mainly focused on the characterization of model polymer after deposition (as-deposited) and after immersion in aqueous and solvent-based cleaning solutions. The polymer removal efficiency was influenced/ improved by UV treatments prior to wet clean processes. In the second part of the study, selected UV treatment conditions and cleaning solutions were applied to low- k patterned structures using Angle-resolved X-ray photoelectron spectroscopy (AR-XPS) to characterize the dielectric sidewall before and after UV modification and the subsequent cleaning process.
Abstract 14297: A Mouse Model of Recurrent Myocardial Infarction Reports Diminished Emergency Hematopoiesis and Cardiac Inflammation (2019)

Recurrent myocardial infarction is common in patients with coronary artery disease and associated with high mortality. Here we describe a surgical mouse model in which two subsequent infarcts affec...