gebhart/patrepeval huggingface dataset:
Toward a more complete recognition of immunoreactive antigens in squamous cell lung carcinoma (2002)

There is very limited knowledge about the antibody response against tumor-expressed antigens in lung cancer. To arrive at a more complete picture of lung cancer antigens, we generated 2 cDNA libraries from squamous cell lung carcinoma and isolated 15 immunogenic antigens using autologous sera. Among the antigens most frequently identified were the lymphoid blast crisis oncogene (LBC), an unknown hypothetical protein and the p53-binding protein (TP53 BP), which have already been associated with tumor development. Of the immunogenic antigens, 6 map to chromosomes that are frequently altered in squamous cell lung carcinoma. SEREX database analysis showed that 7 of the identified immunogenic antigens have been associated with the humoral immune response in other human tumors. Screening with heterologous sera of patients with lung carcinoma identified 4 antigens, including human protein kinase C and TP53 BP, which have also been found by autologous screening. Only 1 of the 15 identified antigens reacted with any of the 36 control sera, which were taken from individuals without known disease. Sera from adenocarcinoma and large cell carcinoma of the lung were not reactive for the antigens. In summary, using 2 newly established cDNA libraries, we isolated 15 novel antigens, which were subsequently evaluated for the frequency of their corresponding antibodies in autologous, normal and heterologous sera; their chromosomal localization; and their correlation with survival after surgery.
A six-month systems toxicology inhalation/cessation study in ApoE−/− mice to investigate cardiovascular and respiratory exposure effects of modified risk tobacco products, CHTP 1.2 and THS 2.2, compared with conventional cigarettes (2019)

Smoking is one of the major modifiable risk factors in the development and progression of chronic obstructive pulmonary disease (COPD) and cardiovascular disease (CVD). Modified-risk tobacco products (MRTP) are being developed to provide substitute products for smokers who are unable or unwilling to quit, to lessen the smoking-related health risks. In this study, the ApoE<sup>-/-</sup> mouse model was used to investigate the impact of cigarette smoke (CS) from the reference cigarette 3R4F, or aerosol from two potential MRTPs based on the heat-not-burn principle, carbon heated tobacco product 1.2 (CHTP1.2) and tobacco heating system 2.2 (THS 2.2), on the cardiorespiratory system over a 6-month period. In addition, cessation or switching to CHTP1.2 after 3 months of CS exposure was assessed. A systems toxicology approach combining physiology, histology and molecular measurements was used to evaluate the impact of MRTP aerosols in comparison to CS. CHTP1.2 and THS2.2 aerosols, compared with CS, demonstrated lower impact on the cardiorespiratory system, including low to absent lung inflammation and emphysematous changes, and reduced atherosclerotic plaque formation. Molecular analyses confirmed the lower engagement of pathological mechanisms by MRTP aerosols than CS. Both cessation and switching to CHTP1.2 reduced the observed CS effects to almost sham exposure levels.
Massively Parallel Reporter Assays in Cultured Mammalian Cells (2014)

The genetic reporter assay is a well-established and powerful tool for dissecting the relationship between DNA sequences and their gene regulatory activities. The potential throughput of this assay has, however, been limited by the need to individually clone and assay the activity of each sequence on interest using protein fluorescence or enzymatic activity as a proxy for regulatory activity. Advances in high-throughput DNA synthesis and sequencing technologies have recently made it possible to overcome these limitations by multiplexing the construction and interrogation of large libraries of reporter constructs. This protocol describes implementation of a Massively Parallel Reporter Assay (MPRA) that allows direct comparison of hundreds of thousands of putative regulatory sequences in a single cell culture dish.
Changes of Quality of Life in Gastric Cancer Patients After Curative Resection (2012)

Our findings show that there are various functional and symptomatic problems, which health care providers need to manage during the postsurgical period. We need to continuously address fatigue, diarrhea, dysphagia, eating restrictions, body image disturbance, and cognitive functioning. In addition, it would be necessary to inform patients about possible QOL outcomes while they are receiving information about surgery and signing informed consent for surgery.
Congenital diaphragmatic hernia candidate genes derived from embryonic transcriptomes (2012)

Congenital diaphragmatic hernia (CDH) is a common (1 in 3,000 live births) major congenital malformation that results in significant morbidity and mortality. The discovery of CDH loci using standard genetic approaches has been hindered by its genetic heterogeneity. We hypothesized that gene expression profiling of developing embryonic diaphragms would help identify genes likely to be associated with diaphragm defects. We generated a time series of whole-transcriptome expression profiles from laser captured embryonic mouse diaphragms at embryonic day (E)11.5 and E12.5 when experimental perturbations lead to CDH phenotypes, and E16.5 when the diaphragm is fully formed. Gene sets defining biologically relevant pathways and temporal expression trends were identified by using a series of bioinformatic algorithms. These developmental sets were then compared with a manually curated list of genes previously shown to cause diaphragm defects in humans and in mouse models. Our integrative filtering strategy identified 27 candidates for CDH. We examined the diaphragms of knockout mice for one of the candidate genes, pre-B-cell leukemia transcription factor 1 (Pbx1), and identified a range of previously undetected diaphragmatic defects. Our study demonstrates the utility of genetic characterization of normal development as an integral part of a disease gene identification and prioritization strategy for CDH, an approach that can be extended to other diseases and developmental anomalies.
Surface analysis of tissue paper using laser scanning confocal microscopy and micro-computed topography (2020)

Abstract Tissue paper softness relies on two major factors, the bulk softness, which can be indicated by the elasticity of the sheet, and surface softness. Measurement of surface softness is complicated and often requires a multi-step process. A key parameter defining surface softness is the topography of the surface, particularly the crepe structure and its periodicity. Herein, we present a novel approach to measure and quantify the tissue paper surface crepe structure and periodicity based on the detection of waviness along the sample using laser scanning confocal microscopy (LSM) and X-ray tomography (XRT). In addition, field emission scanning electron microscope (FESEM) was used to characterize the tissue paper surface. We demonstrate that surface topography is directly correlated to the erosion of the doctor blade, which is used to remove the dry tissue paper from the Yankee cylinder. Because of its accuracy and simplicity, the laser confocal microscopy method has the potential to be used directly on the production line to monitor the production process of the tissue paper. XRT revealed more structural details of the tissue paper structure in 3D, and it allowed for the reconstruction of the surface and the internal structure of the tissue paper. Graphic abstract
Transcriptome profiling and sequencing of differentiated human hematopoietic stem cells reveal lineage-specific expression and alternative splicing of genes (2011)

Hematopoietic differentiation is strictly regulated by complex network of transcription factors that are controlled by ligands binding to cell surface receptors. Disruptions of the intricate sequences of transcriptional activation and suppression of multiple genes cause hematological diseases, such as leukemias, myelodysplastic syndromes, or myeloproliferative syndromes. From a clinical standpoint, deciphering the pattern of gene expression during hematopoiesis may help unravel disease-specific mechanisms in hematopoietic malignancies. Herein, we describe a human in vitro hematopoietic model system where lineage-specific differentiation of CD34(+) cells was accomplished using specific cytokines. Microarray and RNAseq-based whole transcriptome and exome analysis was performed on the differentiated erythropoietic, granulopoietic, and megakaryopoietic cells to delineate changes in expression of whole transcripts and exons. Analysis on the Human 1.0 ST exon arrays indicated differential expression of 172 genes (P < 0.0000001) and significant alternate splicing of 86 genes during differentiation. Pathway analysis identified these genes to be involved in Rac/RhoA signaling, Wnt/B-catenin signaling and alanine/aspartate metabolism. Comparison of the microarray data to next generation RNAseq analysis during erythroid differentiation demonstrated a high degree of correlation in gene (R = 0.72) and exon (R = 0.62) expression. Our data provide a molecular portrait of events that regulate differentiation of hematopoietic cells. Knowledge of molecular processes by which the cells acquire their cell-specific fate would be beneficial in developing cell-based therapies for human diseases.
Cereal products derived from wheat, sorghum, rice and oats alter the infant gut microbiota in vitro (2017)

The introduction of different nutrient and energy sources during weaning leads to significant changes in the infant gut microbiota. We used an in vitro infant digestive and gut microbiota model system to investigate the effect of four commercially available cereal products based on either wheat, sorghum, rice or oats, on the gut microbiota of six infants. Our results indicated cereal additions induced numerous changes in the gut microbiota composition. The relative abundance of bacterial families associated with fibre degradation, Bacteroidaceae, Bifidobacteriaceae, Lactobacillaceae, Prevotellaceae, Ruminococcaceae and Veillonellaceae increased, whilst the abundance of Enterobacteriaceae decreased with cereal additions. Corresponding changes in the production of SCFAs showed higher concentrations of acetate following all cereal additions, whilst, propionate and butyrate varied between specific cereal additions. These cereal-specific variations in the concentrations of SCFAs showed a moderate correlation with the relative abundance of potential SCFA-producing bacterial families. Overall, our results demonstrated clear shifts in the abundance of bacterial groups associated with weaning and an increase in the production of SCFAs following cereal additions.
Supplementary Data from Fluorescence-Based Codetection with Protein Markers Reveals Distinct Cellular Compartments for Altered MicroRNA Expression in Solid Tumors (2023)

&lt;p&gt;Supplementary Figures S1-S7 and Supplementary Tables S1-S3.&lt;/p&gt;
Artificial neural networks in mammography: application to decision making in the diagnosis of breast cancer. (1993)

The authors investigated the potential utility of artificial neural networks as a decision-making aid to radiologists in the analysis of mammographic data. Three-layer, feed-forward neural networks with a back-propagation algorithm were trained for the interpretation of mammograms on the basis of features extracted from mammograms by experienced radiologists. A network that used 43 image features performed well in distinguishing between benign and malignant lesions, yielding a value of 0.95 for the area under the receiver operating characteristic curve for textbook cases in a test with the round-robin method. With clinical cases, the performance of a neural network in merging 14 radiologist-extracted features of lesions to distinguish between benign and malignant lesions was found to be higher than the average performance of attending and resident radiologists alone (without the aid of a neural network). The authors conclude that such networks may provide a potentially useful tool in the mammographic decision-making task of distinguishing between benign and malignant lesions.
Temperature-dependent spin susceptibility in a two-dimensional metal (2005)

We consider a two-dimensional electron system with Coulomb interaction between particles at a finite temperature $T$. We show that the dynamic Kohn anomaly in the response function at $2{k}_{F}$ leads to a nonanalytic, linear-in-$T$ correction to the spin susceptibility, $\ensuremath{\delta}\ensuremath{\chi}(T)=aT$, the same as in systems with short-range interaction. We show that the singularity of the Coulomb interaction at $q=0$ does not invalidate the expansion of the prefactor $a$ in powers of ${r}_{s}$, but makes the expansion nonanalytic.
Determination of the reduced matrix of the piezoelectric, dielectric and elastic material constants for a piezoelectric material with C<inf>&#x221E;</inf> symmetry (2010)

We present a procedure for determining the reduced piezoelectric, dielectric and elastic coefficients for a C <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">∞</sub> material, including losses, from a single disk sample. Measurements have been made on a Navy III PZT (Channel 5804) ceramic sample and the reduced matrix of coefficients for this material is presented.
Quantum gates with controlled adiabatic evolutions (2015)

We introduce a class of quantum adiabatic evolutions that we claim may be interpreted as the equivalents of the unitary gates of the quantum gate model. We argue that these gates form a universal set and may therefore be used as building blocks in the construction of arbitrary ``adiabatic circuits,'' analogously to the manner in which gates are used in the circuit model. One implication of the above construction is that arbitrary classical boolean circuits as well as gate model circuits may be directly translated to adiabatic algorithms with no additional resources or complexities. We show that while these adiabatic algorithms fail to exhibit certain aspects of the inherent fault tolerance of traditional quantum adiabatic algorithms, they may have certain other experimental advantages acting as quantum gates.
Catabolism of Fibrinogen in Pregnant Rabbits before and after Delivery (1978)

16 non-pregnant female and 19 pregnant rabbits were injected with purified rabbit 125I-fibrinogen in order to study the catabolism of fibrinogen before and after delivery. The half-life time (T 1/2) of the clottable 125I-radioactivity in pregnant rabbits during the last third of gestation was 27.3 +/- 5.3 hr in comparison to 54.4 +/- 3.7 hr in non-pregnant rabbits. After delivery, T 1/2 returned to normal values of 47.9 +/- 10.9 hr. The fractional catabolic rate (FCR) of the clotabble 125I-radioactivity was 67.1% X d-1 +/- 8.6 before and 41.6% X d-1 after delivery whereas FCR in non-pregnant rabbits amounted to 44.7% X d-1 +/- 4.8. These figures demonstrate a pronounced increase in fibrinogen catabolism during the last third of gestation in pregnant rabbits and a normalization immediately after delivery. Although in pregnant rabbits the elimination of fibrinogen from the circulating blood was pronouncedly increased, the plasma fibrinogen concentration did not change. Only after delivery did the fibrinogen concentration increase when the fibrinogen catabolism had already normalized.
Eosinophils, tissue eosinophilia, and eosinophil-derived transforming growth factor alpha in hamster oral carcinogenesis. (1992)

Eosinophilia in tissues and/or circulating blood is known to be associated with a wide variety of malignancies but the role of the eosinophil in neoplastic conditions is not known. Using the cheek pouch of the Syrian hamster as an experimental model for oral carcinogenesis, it has recently been shown that eosinophils at sites of developing oral cancer express the multifunctional cytokine, transforming growth factor alpha (TGF-alpha). This study investigated the time course of eosinophil infiltration, tissue eosinophilia associated with malignant epithelium, and eosinophil-derived TGF-alpha mRNA during the 16-week 7,12-dimethylbenz[a]anthracene (DMBA)-induced oral cancer development process. The results reveal that the occasional eosinophil is normally present in the lamina propria of hamster oral mucosa. With progressive DMBA treatments, there is an increase of eosinophils infiltrating into the lamina propria. By weeks 12-16, the number of eosinophils is significantly higher in DMBA-treated pouches than in control pouches treated with the vehicle mineral oil alone. Analysis of the infiltrating eosinophils into fully developed hamster oral carcinomas reveals that tissue eosinophilia is associated with 78% of the stromal areas associated with malignant epithelium, while only 7% of sites associated with non-tumor oral epithelium (normal, hyperplastic-dysplastic) exhibited eosinophilia. Furthermore, the majority of the eosinophils associated with malignant epithelium were found to contain TGF-alpha mRNA. The number of TGF-alpha mRNAs containing eosinophils associated with malignant oral epithelium is significantly higher than that associated with nonmalignant oral epithelium. Together, these results suggest that eosinophils are recruited to tumor-developing sites, that they predominantly associate with malignant epithelium, and that most tumor-associated eosinophils express the cytokine TGF-alpha.
Project Zephyrus: Developing a rapidly reusable high-altitude flight test platform (2018)

Reusable, inexpensive, and rapid testing of payloads in near-space conditions is an unfilled niche that could speed development of flight-ready projects. With growing availability of commercial off-the-shelf (COTS) hardware and open source software, high-altitude ballooning (HAB) has become a viable option for rapid prototyping of ideas in near-space conditions. A product of the Jet Propulsions Laboratory's (JPL) collaborative Innovation to Flight (i2F) program, the Zephyrus system is a proposed HAB solution for high-altitude testing and atmospheric observation, a cheaper and easy-to-use alternative to traditional HAB systems. The Zephyrus system permits testing of small-to mid-sized instruments in the upper atmosphere (approximately 35,000 m maximum altitude) using a reusable common architecture. Over the summer of 2017, the i2F team demonstrated all of these key features of the Zephyrus platform via four test flights. Zephyrus I, II, III, and IV were successfully launched, tracked, and recovered over groundtracks of up to approximately 50 km and altitudes of approximately 30,000 m by a team averaging eight individuals, while accomplishing a majority of the intended science. This included a turnaround time of less than two weeks between two flight tests with differing instrumentation. Lessons from the Zephyrus I flight were successfully used in the Zephyrus II flight to speed up launch time and operations procedures (e.g. rigorous pre-launch preparation). Likewise, the Zephyrus III flight brought the cost of relaunching a mid-sized payload to 28,500 m down significantly. Many diverse instruments and experiments were tested during the Zephyrus missions (e.g. inflatable origami reflectors, flexible solar panels), demonstrating the system's versatility. From concept to first flight of Zephyrus I in just five weeks, followed by turnarounds as short as two weeks, the team demonstrated that it is entirely possible to bring to bear cost-effective, hobbyist HAB techniques in meaningful high-altitude testing using a new reusable test platform.
Autonomous docking ground demonstration (1991)

The Autonomous Docking Ground Demonstration is an evaluation of the laser sensor system to support the docking phase (12 ft to contact) when operated in conjunction with the guidance, navigation, and control (GN&C) software. The docking mechanism being used was developed for the Apollo/Soyuz Test Program. This demonstration will be conducted using the 6-DOF Dynamic Test System (DTS). The DTS simulates the Space Station Freedom as the stationary or target vehicle and the Orbiter as the active or chase vehicle. For this demonstration, the laser sensor will be mounted on the target vehicle and the retroflectors will be on the chase vehicle. This arrangement was chosen to prevent potential damage to the laser. The laser sensor system, GN&C, and 6-DOF DTS will be operated closed-loop. Initial conditions to simulate vehicle misalignments, translational and rotational, will be introduced within the constraints of the systems involved.
An embedded core for the 2D wavelet transform (2002)

We present a new architecture for the wavelet transform based on the lifting scheme. We present the advantages of the lifting scheme compared to the filter-bank method and propose an architecture that allows a high processing rate and has a very small memory requirement. A new way of managing the transposition buffer using FIFO and delay lines allows the 2D decomposition of an image in real time on-the-fly. The proposed architecture is therefore very compact and is adapted for an implementation as a macrocell inside a system-on-a-chip.
Renal artery origins: location and distribution in the transverse plane at CT. (1997)

In the transverse plane, the location of the origin of the right renal artery tended to be anterolateral and of the left renal artery tended to be posterolateral or lateral. The variation in location and distribution width was great.
The effect of changing intraocular pressure on the corneal and scleral curvatures in the fresh porcine eye (2006)

The elastic moduli of the cornea and sclera are independent of IOP. The modulus of elasticity of the sclera is higher than that of the cornea. Elevation of IOP changes the curvature of the sclera but not that of the cornea. Porcine scleral rigidity is similar to human scleral rigidity. Scleral curvature could be a novel method for measuring IOP.
Interaction Models for Multiagent Reinforcement Learning (2008)

This article proposes and compares different interaction models for reinforcement learning based on multi-agent system. The cooperation during the learning process is crucial to guarantee the convergence to a good policy. The exchange of rewards among the agents during the interaction is a complex task and if it is inadequate it may cause delays in learning or generate unexpected transitions, making the cooperation inefficient and con-verging to a non-satisfactory policy. In order to allow the interactive discovery of high quality policies we have developed several cooperation models based on the ex-change of action policies between the agents. Experimental results have shown that the proposed cooperation models are able to speed up the convergence of the agents while achieving optimal action policies even in high-dimensional environments (e.g. traffic), outperforming the standard Q-learning algorithm.