gebhart/patrepeval huggingface dataset:
Systematic Analysis of Breast Cancer Morphology Uncovers Stromal Features Associated with Survival (2011)

The morphological interpretation of histologic sections forms the basis of diagnosis and prognostication for cancer. In the diagnosis of carcinomas, pathologists perform a semiquantitative analysis of a small set of morphological features to determine the cancer's histologic grade. Physicians use histologic grade to inform their assessment of a carcinoma's aggressiveness and a patient's prognosis. Nevertheless, the determination of grade in breast cancer examines only a small set of morphological features of breast cancer epithelial cells, which has been largely unchanged since the 1920s. A comprehensive analysis of automatically quantitated morphological features could identify characteristics of prognostic relevance and provide an accurate and reproducible means for assessing prognosis from microscopic image data. We developed the C-Path (Computational Pathologist) system to measure a rich quantitative feature set from the breast cancer epithelium and stroma (6642 features), including both standard morphometric descriptors of image objects and higher-level contextual, relational, and global image features. These measurements were used to construct a prognostic model. We applied the C-Path system to microscopic images from two independent cohorts of breast cancer patients [from the Netherlands Cancer Institute (NKI) cohort, n = 248, and the Vancouver General Hospital (VGH) cohort, n = 328]. The prognostic model score generated by our system was strongly associated with overall survival in both the NKI and the VGH cohorts (both log-rank P ≤ 0.001). This association was independent of clinical, pathological, and molecular factors. Three stromal features were significantly associated with survival, and this association was stronger than the association of survival with epithelial characteristics in the model. These findings implicate stromal morphologic structure as a previously unrecognized prognostic determinant for breast cancer.
Comparative genomics of the social amoebae Dictyostelium discoideum and Dictyostelium purpureum (2011)

The findings from this new genome sequence and comparative analysis shed light on the biology and evolution of the Dictyostelia.
Paper Electronics (2011)

Paper is ubiquitous in everyday life and a truly low-cost substrate. The use of paper substrates could be extended even further, if electronic applications would be applied next to or below the printed graphics. However, applying electronics on paper is challenging. The paper surface is not only very rough compared to plastics, but is also porous. While this is detrimental for most electronic devices manufactured directly onto paper substrates, there are also approaches that are compatible with the rough and absorptive paper surface. In this review, recent advances and possibilities of these approaches are evaluated and the limitations of paper electronics are discussed.
With Minimal Systemic T-Cell Expansion, CD8+T Cells Mediate Protection of Rhesus Macaques Immunized with Attenuated Simian-Human Immunodeficiency Virus SHIV89.6 from Vaginal Challenge with Simian Immunodeficiency Virus (2008)

The presence, at the time of challenge, of antiviral effector T cells in the vaginal mucosa of female rhesus macaques immunized with live-attenuated simian-human immunodeficiency virus 89.6 (SHIV89.6) is associated with consistent and reproducible protection from pathogenic simian immunodeficiency virus (SIV) vaginal challenge (18). Here, we definitively demonstrate the protective role of the SIV-specific CD8(+) T-cell response in SHIV-immunized monkeys by CD8(+) lymphocyte depletion, an intervention that abrogated SHIV-mediated control of challenge virus replication and largely eliminated the SIV-specific T-cell responses in blood, lymph nodes, and genital mucosa. While in the T-cell-intact SHIV-immunized animals, polyfunctional and degranulating SIV-specific CD8(+) T cells were present in the genital tract and lymphoid tissues from the day of challenge until day 14 postchallenge, strikingly, expansion of SIV-specific CD8(+) T cells in the immunized monkeys was minimal and limited to the vagina. Thus, protection from uncontrolled SIV replication in animals immunized with attenuated SHIV89.6 is primarily mediated by CD8(+) T cells that do not undergo dramatic systemic expansion after SIV challenge. These findings demonstrate that despite, and perhaps because of, minimal systemic expansion of T cells at the time of challenge, a stable population of effector-cytotoxic CD8(+) T cells can provide significant protection from vaginal SIV challenge.
Correlated and Uncorrelated Regions in Heart-Rate Fluctuations during Sleep (2000)

Healthy sleep consists of several stages: deep sleep, light sleep, and rapid eye movement (REM) sleep. Here we show that these sleep stages can be characterized and distinguished by correlations of heart rates separated by n beats. Using the detrended fluctuation analysis (DFA) up to fourth order we find that long-range correlations reminiscent to the wake phase are present only in the REM phase. In the non-REM phases, the heart rates are uncorrelated above the typical breathing cycle time, pointing to a random regulation of the heartbeat during non-REM sleep.
Upregulation of TRAF-3 by shear stress blocks CD40-mediated endothelial activation (2001)

Atherosclerosis is an inflammatory disease of large arteries that is initiated through the activation of endothelium by proinflammatory mediators. CD40 receptor stimulation has been implicated in the pathogenesis of atherosclerosis. One of the most important atheroprotective stimuli is the viscous drag (shear stress) generated by the streaming blood acting on the endothelial monolayer. Here, we demonstrate that shear stress prevents CD40 ligand-induced endothelial cell activation, and we identify upregulation of TNF receptor-associated factor-3 (TRAF-3) as a potent CD40-inhibitory mechanism. Shear stress specifically upregulates TRAF-3 in cultured endothelial cells. Moreover, in the endothelial cells overlying human atherosclerotic plaques, TRAF-3 expression is upregulated in areas with high shear stress. Overexpression of TRAF-3 inhibits endothelial expression of proinflammatory cytokines and tissue factor and blocks DNA-binding activity of the transcription factor AP-1; it thereby prevents CD40-induced endothelial activation. Thus, upregulation of TRAF-3 represents a novel mechanism for preserving the functional integrity of the endothelial monolayer.
Died of Wounds on the Battlefield: Causation and Implications for Improving Combat Casualty Care (2011)

Hemorrhage is a major mechanism of death in PS combat injuries, underscoring the necessity for initiatives to mitigate bleeding, particularly in the prehospital environment.
The 170 kDa glucose regulated stress protein is a large HSP70‐ HSP110‐like protein of the endoplasmic reticulum (1996)

The existence of a family of unusually large and highly diverged hsp70-like proteins (the hsp110/SSE family) has recently been described. The 170 kDa glucose regulated stress protein (grp170) is a retained endoplasmic reticulum glycoprotein that may be involved in immunoglobulin folding and/or assembly. We describe here the cloning of the cDNA for grp170 and show that it, like hsp110, is a large and highly diverged hsp70-like polypeptide which shares specific features with hsp70 (the dnaK family) and the hsp110/SSE family, while also differing from both. Grp170 contains an ATP binding domain and binds ATP, it possesses a carboxyl terminal NDEL sequence, and its mRNA is anoxia inducible.
Effort-based decision-making in major depressive disorder: A translational model of motivational anhedonia. (2012)

Anhedonia is a core feature of major depressive disorder (MDD), but the precise nature of anhedonic symptoms is unknown. Whereas anhedonia has traditionally been viewed as a deficit in the experience of pleasure, more recent evidence suggests that reduced anticipation and motivation may also be a core feature of this symptom. Here, we provide data from a study in MDD patients and healthy controls using a translational measure of reward motivation, the Effort Expenditure for Rewards Task (EEfRT or "effort"). This task offers subjects a series of trials where they may choose to expend more or less effort for the opportunity to win varying amounts of monetary rewards. We found that MDD patients were less willing to expend effort for rewards than controls. Additionally, we observed that patients were less able to effectively use information about magnitude and probability of rewards to guide their choice behavior. Finally, within the MDD patient group, duration of the current episode was a significant negative predictor of EEfRT task performance. These findings offer novel support for theoretical models proposing that anhedonia in MDD may reflect specific impairments in motivation and reward-based decision-making.
Inhibitory actions of procaterol, a beta-2 stimulant, on substance P-induced cough in normal subjects during upper respiratory tract infection. (1989)

We studied substance P (SP)-induced cough in normal subjects without and with colds, and the effects of orally administered procaterol on SP-induced cough in normal subjects with colds. SP aerosols caused cough at a concentration of approximately 10(-15) M in subjects with colds whereas it did not cause cough at a concentration of up to 10(-5) M in subjects without colds. Procaterol (50 micrograms) completely inhibited SP-induced cough in normal subjects with colds. These results suggest that cough response to SP remarkably increases during colds and that beta-2 stimulant may be a useful tool for treatment of cough during colds in normal subjects.
Computer-Controlled Measurement of Laboratory Areal Flood Saturation Distributions (1983)

ABSTRACT A microcomputer controlled microwave absorption instrument has been developed for automated measurement of laboratory linear and areal flood oil/water saturation distributions. The instrument design and performance characteristics are given in detail, and the roles of micro, mini and mainframe computers in data collection and analysis are described. Much of the design criteria and features are applicable to other oil recovery laboratory experimentation. An applications study is presented in a companion paper, SPE 12038. An error analysis study of experimental saturation distribution data is used to identify localized structured water present in a linear core at residual oil saturation to chemical flood. Comparison is made to the residual microemulsion phase predicted by a simulator study of the experiment.
Magnifying miniature displays with microlenslet arrays (2004)

Current technology trends are focused on miniaturizing displays, although for specific applications such as the use of head-mounted displays (HMD) this limits the advancements for a wider field-of-view (FOV) and a negligible overall weight of the optics. Due to the advancements of electronics that benefit from smaller miniature displays, universities and companies are focused on developing this technology to meet the growing demand of this global market. Higher resolution displays with added brightness are being developed, but these displays are decreasing in their viewable area. HMDs can benefit from these higher resolution and brighter displays but they will undergo an increased optical weight to compensate for the smaller display size. To overcome this hindrance in HMDs, we demonstrate in this paper how to incorporate microlenslet arrays as an optical relay system to magnify miniature displays. Microlenslet arrays provide respectively shorter focal length which yields a smaller overall object to image distance and an incremental overall weight compared to an otherwise increased optical lens assembly. The contribution of this paper is a patented concept of magnifying/demagnifying miniature displays with microlenslet arrays that can be integrated in a spaced limited area.
The biological relevance of FHL2 in tumour cells and its role as a putative cancer target. (2007)

The LIM-only protein FHL2 (four-and-a-half LIM-domain protein 2) belongs to the FHL protein family of transcriptional cofactors present in various cell lines. FHL2 interacts with a variety of transcription factors known to be involved in tumour development. Furthermore, FHL2 expression is often deregulated in cancer including overexpression and down-regulation in various types of tumours. The function of FHL2 in cancer is particularly intriguing, since it may act as an oncoprotein or as a tumour suppressor in a tissue-dependent fashion. This dual nature of FHL2 is also reflected by the finding that it can function as repressor or activator of transcriptional activity depending on the cell-type. The ability of FHL2 to exert functional diversity lies within its structural composition as a LIM-only protein. LIM-domains are enzymatically inactive protein-to-protein interaction domains, which determine the function of LIM-only proteins as adaptor molecules or scaffolding proteins. By selectively using different LIM-domains for protein-to-protein interactions, FHL2 is capable to interact with a broad spectrum of functionally unrelated proteins, thereby triggering different signalling pathways. In this review, the current knowledge of FHL2 expression in different cancers was summarized and the interaction of FHL2 with transcription factors and other proteins involved in cancer development was examined. Since transcription factors control all fundamental developmental and homeostatic processes, transcriptional cofactors like FHL2 are likely to contribute to human carcinogenesis and are of clinical importance in various forms of cancer.
Survival of conditionally immortalized hepatocytes in the spleen of syngeneic rats (2001)

Conditionally immortalized hepatocytes can survive in the spleen for a limited period, in spite of the growth stimulation, most likely because they undergo apoptosis in vivo as well as in vitro at a non-permissive temperature. These data suggest that the use of these cells in hepatocyte transplantation be limited to temporary hepatic support.
Assessment of Short Term Rainfall and Stream Flows in South Australia (2014)

The aim of this study is to assess the relationship between rainfall and stream flow at Broughton River in Mooroola, Torrance River in Mount Pleasant, and Wakefield River near Rhyine, in South Australia, from 1990 to 2010. Initially, we present a short term relationship between rainfall and stream flow, in terms of correlations, lagged correlations, and estimated variability between wavelet coefficients at each level. A deterministic regression based response model is used to detect linear, quadratic and polynomial trends, while allowing for seasonality effects. Antecedent rainfall data were considered to predict stream flow. The best fitting model was selected based on maximum adjusted R2 values (R2adj ), minimum sigma square (σ2), and a minimum Akaike Information Criterion (AIC). The best performance in the response model is lag rainfall, which indicates at least one day and up to 7 days (past) difference in rainfall, including offset cross products of lag rainfall. With the inclusion of antecedent stream flow as an input with one day time lag, the result shows a significant improvement of the R2adj values from 0.18, 0.26 and 0.14 to 0.35, 0.42 and 0.21 at Broughton River, Torrance River and Wakefield River, respectively. A benchmark comparison was made with an Artificial Neural Network analysis. The optimization strategy involved adopting a minimum mean absolute error (MAE).
High Sensitivity Micro-Thermal Conductivity Detector for Gas Chromatography (2009)

Design, fabrication and testing of a micro thermal conductivity detector (muTCD) with a detection limit of 260 parts per billion (hexane in helium), no excess dead-volume, low power consumption, fast response time (150 musec) and low sensitivity to flow rate is described herein. Significantly, this muTCD is shown to have a linear response and high sensitivity across a 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sup> -fold concentration range; to the best of our knowledge this linearity and sensitivity has not been previously shown for a muTCD. The thermal conduction properties of several configurations are examined to identify their influence on performance.
Using and Porting GNU CC (1998)

virtual classes provide somewhat similar facilities in standard C++. There are two main advantages to using signatures instead: 1. Subtyping becomes independent from inheritance. A class or signature type T is a subtype of a signature type S independent of any inheritance hierarchy as long as all the member functions declared in S are also found in T. So you can de ne a subtype hierarchy that is completely independent from any inheritance (implementation) hierarchy, instead of being forced to use types that mirror the class inheritance hierarchy. 2. Signatures allow you to work with existing class hierarchies as implementations of a signature type. If those class hierarchies are only available in compiled form, you're out of luck with abstract virtual classes, since an abstract virtual class cannot be retro tted on top of existing class hierarchies. So you would be required to write interface classes as subtypes of the abstract virtual class. There is one more detail about signatures. A signature declaration can contain member function de nitions as well as member function declarations. A signature member function with a full de nition is called a default implementation; classes need not contain that particular interface in order to conform. For example, a class C can conform to the signature signature T { int f (int); int f0 () { return f (0); }; }; whether or not C implements the member function `int f0 ()'. If you de ne C::f0, that de nition takes precedence; otherwise, the default implementation S::f0 applies. 170 Using and Porting GNU CC Chapter 8: gcov: a Test Coverage Program 171 8 gcov: a Test Coverage Program gcov is a tool you can use, together with GNU CC, to test code coverage in your programs. gcov is free software, but for the moment it is only available from Cygnus Support (pending discussions with the FSF about how they think Cygnus should really write it). This chapter describes version 1.5 of gcov. Jim Wilson wrote gcov, and the original form of this note. Pat McGregor edited the documentation. 8.
Discovery of Potent, Orally Available Vanilloid Receptor-1 Antagonists. Structure−Activity Relationship of N-Aryl Cinnamides (2004)

The vanilloid receptor-1 (TRPV1 or VR1) is a member of the transient receptor potential (TRP) family of ion channels and plays a role in regulating the function of sensory nerves. A growing body of evidence demonstrates the therapeutic potential of TRPV1 modulators, particularly in the management of pain. As a result of our screening efforts, we identified (E)-3-(4-tert-butylphenyl)-N-(2,3-dihydrobenzo[b][1,4]dioxin-6-yl)acrylamide (1), an antagonist that blocks the capsaicin-induced and pH-induced uptake of (45)Ca(2+) in TRPV1-expressing Chinese hamster ovary cells with IC(50) values of 17 +/- 5 and 150 +/- 80 nM, respectively. In this report, we describe the synthesis and structure-activity relationship of a series of N-aryl cinnamides, the most potent of which (49a and 49b) exhibit good oral bioavailability in rats (F(oral) = 39% and 17%, respectively).
Personal use of the genomic data: Privacy vs. storage cost (2013)

In this paper, we propose privacy-enhancing technologies for personal use of the genomic data and analyze the tradeoff between genomic privacy and storage cost of the genomes. First, we highlight the potential privacy threats on the genomic data. Then, focusing specifically on a disease-susceptibility test, we develop a new architecture (between the patient and the medical unit) and propose a privacy-preserving algorithm by utilizing homomorphic encryption. Assuming the whole genome sequencing is done by a certified institution, we propose to store patients' genomic data encrypted by their public keys at a Storage and Processing Unit (SPU). The proposed algorithm lets the SPU process the encrypted genomic data for medical tests while preserving the privacy of patients' genomic data. We extensively analyze the relationship between the storage cost (of the genomic data), the level of genomic privacy (of the patient), and the characteristics of the genomic data. Furthermore, we show via a complexity analysis the practicality of the proposed scheme.
High Rate of Induction of Human Autologous Cytotoxic T Lymphocytes against Renal Carcinoma Cells Cultured with an Interleukin Cocktail (1998)

A high rate of induction (9 of 10 cases) of human autologous cytotoxic T lymphocytes (CTL) was achieved in vitro from peripheral blood mononuclear cells of renal carcinoma patients by applying an interleukin (IL)-cocktail consisting of IL-1, -2, -4, and -6. The CTL specifically lysed their own target carcinoma cells within 24 h but did not kill neighboring autologous normal kidney cells or allogeneic renal cancer cell lines. In the case of TUHR4TKB, for which autologous CTL were not induced, no expression of MHC class-I molecules was observed on the surface of these carcinoma cells, although they were sensitive to autologous natural killer cells. The results imply that adoptive immunotherapy for metastasized renal carcinoma will be feasible with autologous CTL in combination with natural killer cells.
Stress-strain measurements of human and porcine corneas after riboflavin–ultraviolet-A-induced cross-linking (2003)

Riboflavin-UVA-induced collagen cross-linking led to an increase in mechanical rigidity in porcine corneas and an even greater increase in human corneas. As collagen cross-linking is maximal in the anterior 300 microm of the cornea, the greater stiffening effect in human corneas can be explained by the relatively larger portion of the cornea being cross-linked in the overall thinner human cornea.
Anticoagulant Efficacy and Immunogenicity of the Selective Factor Xa Inhibitor Antistasin Following Subcutaneous Administration in the Rhesus Monkey (1992)

The antithrombotic efficacy and duration of action of a single subcutaneous administration of the selective factor Xa inhibitor recombinant antistasin (rATS) was evaluated in a rhesus monkey model of mild disseminated intravascular coagulation. rATS (1 mg/kg) was shown to be fully effective and comparable to standard heparin (1,000 U/kg) in the suppression of thromboplastin-induced fibrinopeptide A generation for at least 5 h following a single subcutaneous administration. The absorption rate of rATS, as measured by ex vivo activated partial thromboplastin times (aPTT), mirrored that of standard heparin exhibiting peak anticoagulant activity between 1 and 2 h post administration. The anticoagulant effects of a single rATS dose lasted for longer than 30 h maintaining an aPTT value at least 2-fold higher than baseline. Repeated subcutaneous administrations of rATS resulted in the generation of fully neutralizing antibodies. These results suggest that specific factor Xa inhibition may be as effective as standard heparin in the treatment of venous thrombosis. Due to its antigenicity however, rATS is probably not suitable for chronic subcutaneous anticoagulant therapy.