gebhart/patrepeval huggingface dataset:
The Ubiquitin Proteasome Pathway from Bench to Bedside (2005)

The validation of the ubiquitin-proteasome pathway as a target for therapy of hematological malignancies stands out as one salient example of the ability to translate laboratory-based findings from the bench to the bedside. Preclinical studies showed that proteasome inhibitors had significant activity against models of non-Hodgkin lymphoma and multiple myeloma, and identified some of the relevant mechanisms of action. These led to phase I through III trials of the first clinically available proteasome inhibitor, bortezomib, which confirmed its activity as a single agent in these diseases. Modulation of proteasome function was then found to be a rational approach to achieve both chemosensitization in vitro and in vivo, as well as to overcome chemotherapy resistance. Based on these findings, first-generation bortezomib-based regimens incorporating traditional chemotherapeutics such as alkylating agents, anthracyclines, immunomodulatory agents, or steroids have been evaluated, and many show promise of enhanced clinical anti-tumor efficacy. Further studies of the pro-and anti-apoptotic actions of proteasome inhibitors, and of their effects on gene and protein expression profiles, suggest that novel agents, such as those targeting the heat shock protein pathways, are exciting candidates for incorporation into these combinations. Phase I trials to test these concepts are just beginning, but have already shown some encouraging results. Finally, novel proteasome inhibitors are being developed with unique properties that may also have therapeutic applications. Taken together, these studies demonstrate the power of rational drug design and development to provide novel, effective therapies for patients with hematological malignancies.
Induction of pluripotent stem cells from mouse fibroblasts by four transcription factors (2007)

Abstract. Pluripotent stem cells, such as embryonic stem cells (ESCs), proliferate rapidly while maintaining pluripotency, namely, the ability to differentiate into various types of cells. Embryonic stem cells are promising donor sources for cell transplantation therapies. However, human ESCs are also associated with ethical issues regarding the use of human embryos and rejection reactions after allogenic transplantation. It may be possible to overcome these issues by generating pluripotent stem cells directly from a patient's somatic cells. That somatic cell nuclei acquire an embryonic stem‐like status by fusion with ESCs suggests the existence of ‘pluripotency‐inducing’ factors. Previous studies have recently shown that retrovirus‐mediated transfection with four transcription factors (Oct‐3/4, Sox2, KLF4 and c‐Myc), which are highly expressed in ESCs, into mouse fibroblasts has resulted in generation of induced pluripotent stem (iPS) cells. iPS cells are similar to ESCs in morphology, proliferation, and pluripotency, judged by teratoma formation and chimaera contribution. If iPS cells can be derived from human somatic cells, then such cells may thus lead to important drug discoveries and advances in regenerative medicine.
Structured Forests for Fast Edge Detection (2013)

Edge detection is a critical component of many vision systems, including object detectors and image segmentation algorithms. Patches of edges exhibit well-known forms of local structure, such as straight lines or T-junctions. In this paper we take advantage of the structure present in local image patches to learn both an accurate and computationally efficient edge detector. We formulate the problem of predicting local edge masks in a structured learning framework applied to random decision forests. Our novel approach to learning decision trees robustly maps the structured labels to a discrete space on which standard information gain measures may be evaluated. The result is an approach that obtains real time performance that is orders of magnitude faster than many competing state-of-the-art approaches, while also achieving state-of-the-art edge detection results on the BSDS500 Segmentation dataset and NYU Depth dataset. Finally, we show the potential of our approach as a general purpose edge detector by showing our learned edge models generalize well across datasets.
Studies on plasma transthyretin (prealbumin) in familial amyloidotic polyneuropathy, Portuguese type. (1983)

Amyloid deposits in several heredofamilial forms of amyloidosis are known to be chemically related to transthyretin (TTR, the plasma protein usually referred to as prealbumin). A genetic mutation, leading to an abnormal TTR, may be involved. Studies were conducted to investigate whether or not Portuguese patients with familial amyloidotic polyneuropathy (FAP) have an abnormal species of TTR circulating in their plasma and, if so, whether this might have any impact on vitamin A transport and retinol-binding protein (RBP) metabolism in these patients. The initial studies examined the plasma concentrations of TTR, RBP, and retinol in patients with FAP. Significantly reduced (p less than 0.005) levels of TTR were found in patients with FAP. The TTR levels in 24 FAP patients were approximately two thirds of those of a group of 18 control subjects from the same geographic area. In contrast, RBP levels were not reduced, nor was there an abnormality in the ratio of retinol to RBP, in the patients with FAP. Thus there does not appear to be an abnormality in vitamin A transport in Portuguese patients with FAP. There does, however, appear to be an abnormality of TTR metabolism, accounting for the reduced plasma levels of TTR. TTR was isolated from pooled sera of the FAP patients and was characterized in detail. FAP-TTR was indistinguishable from normal TTR with regard to a variety of parameters, including (1) electrophoretic mobility, (2) chromatographic behavior, (3) molecular weight, (4) stability of the TTR tetramer, (5) immunoreactivity in TTR radioimmunoassays using antisera prepared against both normal and FAP-TTR, (6) ability to form a protein-protein complex with RBP and affinity for RBP as assessed by polarization of fluorescence, and (7) overall amino acid composition. The possible explanations are as follows: (1) an abnormal TTR molecule is not produced in this form of FAP; (2) the abnormal molecule is present in only trace amounts (not detectable in the present study) in FAP plasma; or (3) the abnormal TTR is structurally almost identical to normal TTR and does not differ from normal TTR with regard to the various physical and chemical properties investigated in this study. Preliminary observations suggest that FAP patients do produce an abnormal form of TTR that selectively deposits in tissues as amyloid protein.
Detail Histologic Analysis of Nerve Plexus Invasion in Invasive Ductal Carcinoma of the Pancreas and Its Prognostic Impact (2007)

Nerve plexus invasion is regarded as one of the most important prognostic factors in invasive ductal carcinoma (IDC) of the pancreas, though nerve plexus invasion has not been evaluated in terms of prognostic impact on the basis of detailed histologic investigation. The purpose of this study was to precisely examine morphologic characteristics of nerve plexus invasion and analyze its prognostic predictive power compared with the well-known prognostic parameters of pancreatic IDCs. The outcome and histologic features of 75 patients with pancreatic IDC in the pancreas head were investigated, and 422 lesions of nerve plexus invasion were evaluated. Tumor cells invading nerve plexus showed a duct-forming differentiated feature and predominantly existed in the perineurium and perineural space. Multivariate analyses revealed that the important prognostic factors, in addition to invasive tumor size and tumor necrosis, were at long distances from nerve plexus invasion to pancreatic capsule and perineural invasion in nerve plexus invasion.
Effect of intravitreal anti-VEGF on choroidal thickness in patients with diabetic macular edema using spectral domain OCT (2016)

Over a 6-month period, the use of intravitreal anti-VEGF was associated with significant thinning of the choroid in patients with DME. The clinical significance of a thinner choroid in DME is currently unknown; however, it may contribute to long-term adverse effects on choroidal and retinal function, representing an area requiring future investigation.
t(11;14)(q23;q32) involving IGH and DDX6 in nodal marginal zone lymphoma (2012)

Nodal marginal zone lymphoma (NMZL) is a primary nodal B-cell lymphoma that shares morphological and immunophenotypic characteristics with extranodal and splenic marginal zone lymphoma. Data on altered genes and signaling pathways are scarce in this rare tumor entity. To gain further insights into the genetic background of NMZL, seven cases were investigated by microarray analysis, G-banding, and FISH. Chromosomal imbalances were observed in 3/7 cases (43%) with gains of chromosome arms 1q, 8q, and 12q being the most frequent findings. Furthermore, we identified a translocation t(11;14)(q23;q32) involving IGH and DDX6. Chromosomal walking, expression analysis, siRNA-mediated gene knockdown and a yeast two hybrid screen were performed for further characterization of the translocation in vitro. In siRNA experiments, DDX6 appeared not to be involved in NF-κB activation as frequently observed for genes promoting lymphomagenesis but was found to interfere with the expression of BCL6 and BCL2 in an NF-κB independent manner. In conclusion, we identified several unbalanced aberrations and a t(11;14) involving IGH and DDX6 providing evidence for a contribution of DDX6 to lymphomagenesis by deregulation of BCL6 in NMZL.
Recognising Trajectories of Facial Identities Using Kernel Discriminant Analysis (2001)

We present a comprehensive approach to address three challenging problems in face recognition: modelling faces across multi-views, extracting the nonlinear discriminating features, and recognising moving faces dynamically in image sequences. A multi-view dynamic face model is designed to extract the shape-and-pose-free facial texture patterns. Kernel discriminant analysis, which employs the kernel technique to perform linear discriminant analysis in a high-dimensional feature space, is developed to extract the significant nonlinear features which maximise the between-class variance and minimise the within-class variance. Finally, an identity surface based face recognition is performed dynamically from video input by matching object and model trajectories. q 2003 Elsevier B.V. All rights reserved.
Relation of lung function, maximal inspiratory pressure, dyspnoea, and quality of life with exercise capacity in patients with chronic obstructive pulmonary disease. (1994)

The results show that exercise capacity in patients with COPD with severe airways obstruction is more strongly related to inspiratory muscle strength and lung function than to dyspnoea and quality of life. The significant correlation between dyspnoea and the six minute walking test suggests that subjective variables are more strongly related to walking tests than to bicycle ergometer tests.
Surfactant-Assisted Processing of Carbon Nanotube/Polymer Composites (2000)

Interfacial interaction is one of the most critical issues in carbon nanotube/polymer composites. In this paper the role of nonionic surfactant is investigated. With the surfactant as the processing aid, the addition of only 1 wt % carbon nanotubes in the composite increases the glass transition temperature from 63 °C to 88 °C. The elastic modulus is also increased by more than 30%. In contrast, the addition of carbon nanotubes without the surfactant only has moderate effects on the glass transition temperature and on the mechanical properties. This work points to the pathways to improve dispersion and to modify interfacial bonding in carbon nanotube/polymer composites.
Differential expression of tissue-specific promoters by gene gun (2001)

Gene expression can be regulated by different promoters both in vivo and in cell culture. Based on the physiological expression of the different promoters, gene expression can be restricted to certain cell types, tissues and skin layers.
Electrochemical Planarization for Multilevel Metallization (1994)

We describe an electrochemical planarization technology involving electroplating followed by electropolishing, resulting in a very flat surface containing embedded conductors. Electrochemical planarization technology has been used to produce silicon substrate multichip modules.1 Both the electroplating and electropolishing processes have a thickness uniformity of better than ±2% (±3σ) across a 100 mm wafer.
Mitochondria Make A Comeback (1999)

It was more than 50 years ago that mitochondria first captured the attention of cell physiologists. Abundant, easy to purify, and a rich source of vital enzymes, these organelles were pivotal in the Nobel Prize-winning research that defined the fundamental principles of cellular energy metabolism. But over the years, as technological advances in molecular biology made nuclear functions more accessible to researchers, interest in mitochondria began to wane.
Protected Carotid Artery Stenting and Angioplasty via Transfemoral versus Transcervical Approaches (2005)

This prospective cohort study was taken to determine whether transcervical carotid artery stenting (CAS) with internal carotid artery (ICA) flow reversal is associated with a lower incidence of embolization and femoral access complication when compared with protected, transfemoral CAS in selected, high-risk patients. From 2002 to October 2004, the authors performed 55 carotid stentings and angioplasties. Among the 24 cases via transfemoral approach, 1 developed transient ischemic attack (TIA), 1 stroke, 1 asystolic cardiac arrest, 2 groin hematoma, 2 technical failure, and 1 restenosis. Among the 31 cases via transcervical approach, 2 patients developed TIAs, 4 bradycardia, 2 cervical hematoma, and 3 technical failures leading to open conversion and carotid endarterectomy. Transcervical CAS with ICA flow reversal eliminates the risk of aortic arch emboli, provides cerebral protection during predeployment manipulation across the carotid lesion, negates preprocedure mapping of the aortic arch configuration, and surpasses difficult aortic arch or transfemoral access.
What Has fMRI Taught Us About Object Recognition? (2009)

Humans can effortlessly recognize objects in a fraction of a second despite large variability in the appearance of objects (Thorpe et al. 1996). What are the underlying representations and computations that enable this remarkable human ability? One way to answer these questions is to investigate the neural mechanisms of object recognition in the human brain. With the advent of functional magnetic resonance imaging (fMRI) about 15 years ago, neuroscientists and psychologists began to examine the neural bases of object recognition in humans. Functional magnetic resonance imaging (fMRI) is an attractive method because it is a noninvasive technique that allows multiple measurements of brain activation in the same awake behaving human. Among noninvasive techniques, it provides the best spatial resolution currently available, enabling us to localize cortical activations in the spatial resolution of millimeters (as fine as 1 mm) and at a reasonable time scale (in the order of seconds).
Effects of particle's off-axis position, shape, orientation and entry position on resistance changes of micro Coulter counting devices (2011)

With the recent advance in micro/nano-fabrication technology, micro Coulter counters have been widely used in detecting and characterizing micro- and nanoscale objects. In this paper, the electrical resistance change during translocation of a non-conducting particle through a channel is studied numerically. The numerical results are validated by proven analytical results available in the literature. The effects of particle's off-axis position, shape and orientation, and entry position are studied for particles with a large dynamic range. From the numerical results, a new fitted correlation is proposed that can accurately predict the resistance change caused by off-axis spherical particles regardless of their size. The shape and orientation effects of the electrical resistance change are studied by changing the axis ratio of spheroid particles and their orientation angles. Results show that a particle's shape and orientation have a significant influence on the resistance change. Simulation of an entry effect indicates that a particle starts to induce a resistance change before it enters the channel and still causes a resistance change even after the particle exits the channel completely. This study will offer some guidelines in designing and implementing Coulter counting devices and experiments, and provide insights into explaining experimental results.
Molecular detection of micrometastases and circulating tumor cells in solid tumors. (1999)

The detection of circulating tumor cells and micrometastases may have important prognostic and therapeutic implications. Because their numbers can be very small, these tumor cells are not easily detected using conventional methods. In the last decade, molecular techniques have been widely used for the detection of occult tumor cells. The objective of this report is the application of these molecular tools to solid tumors. A systematic review of all related English-language articles published in the last 32 years was performed. The molecular detection of occult tumor cells can be accomplished by PCR amplification of tumor-specific abnormalities present in the DNA or mRNA of malignant cells. The other main PCR strategy for the detection of CTC and micrometastases involves amplification of tissue-specific mRNA. This latter method was often applied to solid tumors, whereas the former was occasionally used. PCR was shown to be superior to conventional techniques in detecting occult tumor cells, allowing the identification of 1 malignant cell mixed with 1 to 10 million normal cells. In some reports, PCR is shown to be a strong predictor of outcome. The molecular detection of circulating tumor cells and micrometastases in solid tumors can be accomplished using highly sensitive PCR assays. The central question of whether PCR reliably predicts relapse and survival remains unanswered for many types of solid tumor. If PCR-based assays are found to be a reliable tool, they will likely have a major impact on the management of these malignancies.
Oxidative Autoactivation of Latent Collagenase by Human Neutrophils (1985)

The pathological destruction of collagen plays a key role in the development of inflammatory disease states affecting every organ system in the human body. Neutrophils localized at inflammatory sites can potentially degrade collagen by releasing a metalloenzyme, collagenase, which is stored in a latent inactive form. Triggered human neutrophils were shown to release and simultaneously activate their latent collagenase. The activation of the latent enzyme was coupled to an oxidative process that required the generation of a highly reactive oxygen metabolite, hypochlorous acid. Oxidative regulation of latent collagenase activity may be important in the pathogenesis of connective tissue damage in vivo.
A highly efficient multiplication-free binary arithmetic coder and its application in video coding (2003)

A novel and highly efficient algorithm of multiplication-free binary arithmetic coding is proposed. Our proposed method relies on simple table lookups for performing the computationally critical operations of interval subdivision and probability estimation. Moreover, the underlying design principle provides a great flexibility for serving the different needs of all kind of coding applications where binary or binarized data have to be processed. A binary arithmetic coder of the type described in this paper has become part of the CABAC entropy coding scheme of the emerging H.264/AVC video coding standard. Experiments using this binary arithmetic coder in its native video coding environment demonstrate a superior coding efficiency as well as a significantly higher throughput rate in comparison to the MQ coder, which is currently being considered state-of-the-art in fast binary arithmetic coding.
Serum Levels of Total and Free Testosterone in Men Undergoing Hemodialysis (1998)

Serum concentrations of total and free testosterone were measured in 102 hemodialysis male patients and 45 healthy men. In hemodialysis patients, serum levels of total and free testosterone were significantly reduced compared to the controls (p < .001). Neither serum total nor free testosterone correlated with age in the controls. In contrast, both total and free testosterone in serum negatively correlated with age in hemodialysis patients (p < .05-.001). It would appear that testicular dysfunction becomes more severe with increasing age in hemodialysis patients.
Role of carcinoembryonic antigen in the progression of colon cancer cells that express carbohydrate antigen. (2001)

Carcinoembryonic antigen (CEA) has been reported to promote the metastatic potential in some experimental tumors. Adhesion molecules are known to play an important role in the process of metastasis. Cytokines, including interleukin 1beta (IL-1beta) and tumor necrosis factor-alpha (TNF-alpha), which are produced by Kupffer cells, induce endothelial cells to express adhesion molecules. As a result, the present study was designed to investigate whether the interaction between CEA and Kupffer cells accelerated the metastatic potential of tumors in the liver. Kupffer cells isolated from the liver of male BALB/c mice were cultured with CEA, either with or without the addition of a cytokine inhibitor. The levels of IL-1beta and TNF-alpha were examined in a culture medium. An adhesion assay of colon cancer cell lines to human umbilical vein endothelial cells was also performed. When CEA was added to the Kupffer cell culture medium, cytokines were produced. Elevated levels of cytokines appeared to lead to increased rates of adhesion of cancer cells to endothelial cells. However, these phenomena were blocked by the addition of cytokine inhibitors. CEA stimulated Kupffer cells to produce cytokines. An elevated number of cytokines have been proven to promote the expression of adhesion molecules in endothelial cells. These processes are therefore considered to contribute to the metastasis of malignant cells to the liver. These results suggest that cytokine inhibitors may therefore play an important role in the inhibition of hepatic metastasis.
Using ultra-sensitive next generation sequencing to dissect DNA damage-induced mutagenesis (2016)

Next generation sequencing (NGS) technologies have dramatically improved studies in biology and biomedical science. However, no optimal NGS approach is available to conveniently analyze low frequency mutations caused by DNA damage treatments. Here, by developing an exquisite ultra-sensitive NGS (USNGS) platform "EasyMF" and incorporating it with a widely used supF shuttle vector-based mutagenesis system, we can conveniently dissect roles of lesion bypass polymerases in damage-induced mutagenesis. In this improved mutagenesis analysis pipeline, the initial steps are the same as in the supF mutation assay, involving damaging the pSP189 plasmid followed by its transfection into human 293T cells to allow replication to occur. Then "EasyMF" is employed to replace downstream MBM7070 bacterial transformation and other steps for analyzing damage-induced mutation frequencies and spectra. This pipeline was validated by using UV damaged plasmid after its replication in lesion bypass polymerase-deficient 293T cells. The increased throughput and reduced cost of this system will allow us to conveniently screen regulators of translesion DNA synthesis pathway and monitor environmental genotoxic substances, which can ultimately provide insight into the mechanisms of genome stability and mutagenesis.