gebhart/patrepeval huggingface dataset:
Tumor progression and metastasis (2000)

It is now widely accepted that cancer is attributed to the accumulation of genetic alterations in cells. Thus, to understand the molecular mechanisms of cancer metastasis, it is indispensable to identify the genes whose alterations accumulate during cancer progression as well as the genes whose expression is responsible for the acquisition of metastatic potential in cancer cells. Molecular analyses of cancer cells in various stages of progression have revealed that alterations in tumor suppressor genes and oncogenes accumulate during tumor progression and correlate with the clinical aggressiveness of cancer. Comparative analyses of gene expression profiles between metastatic and non-metastatic cells have revealed that various genes are differentially expressed in association with the metastatic potential of cancer cells. A number of genes have been also identified as having functions in inducing or suppressing metastasis in experimental models. However, the association between causative genetic alterations and resulting phenotypic alterations with respect to the metastatic potential of cancer cells is not fully understood. Therefore, elucidation of genotype-phenotype correlation will be required to further understand a complex process of metastasis. Here, I review the progress on molecular studies of tumor progression and metastasis of the past 20 years and discuss the future direction in this field of science.
T lymphocytes mediating protection and cellular cytolysis during the course of Mycobacterium tuberculosis infection. Evidence for different kinetics and recognition of a wide spectrum of protein antigens (1992)

Recent evidence suggests the existence of at least two pathways of acquired specific resistance to Mycobacterium tuberculosis infection; the first consisting of cytokine-mediated activation of parasitized host cells by protective T cells, and the second involving the lysis of these cells by cytolytic T cells. Evidence presented in this report shows that both of the above mechanisms are operative in experimentally infected mice, but that they differ markedly in terms of their kinetics of emergence and loss. It was found that protective T cell activity was acquired very early during the course of the infection, and was temporally associated with the onset of bacterial elimination; however, cytolytic activity did not peak until 10 to 20 days later. This report shows further that the target Ag of these effector T cell populations were apparently numerous with no evidence for preferential recognition of a few immunodominant Ag. In view of the preponderance of target proteins in the bacterial filtrate, we present the hypothesis that such proteins secreted or otherwise leaked from the dividing mycobacterium are pinocytosed from the phagosome and used by the infected macrophage as the key protective Ag leading to T cell sensitization. This hypothesis thus explains the preferential requirement for the viable bacterium in the generation of specific resistance, and further explains why protective immunity is generated even while the organism is still multiplying in an apparently unrestrained manner.
Improved biological activity of Gly2- and Ser2-substituted analogues of glucose-dependent insulinotrophic polypeptide (2003)

The therapeutic potential of glucagon-like peptide-1 (GLP-1) in improving glycaemic control in diabetes has been widely studied, but the potential beneficial effects of glucose-dependent insulinotropic polypeptide (GIP) have until recently been almost overlooked. One of the major problems, however, in exploiting either GIP or GLP-1 as potential therapeutic agents is their short duration of action, due to enzymatic degradation in vivo by dipeptidylpeptidase IV (DPP IV). Therefore, this study examined the plasma stability, biological activity and antidiabetic potential of two novel NH2-terminal Ala2-substituted analogues of GIP, containing glycine (Gly) or serine (Ser). Following incubation in plasma, (Ser2)GIP had a reduced hydrolysis rate compared with native GIP, while (Gly2)GIP was completely stable. In Chinese hamster lung fibroblasts stably transfected with the human GIP receptor, GIP, (Gly2)GIP and (Ser2)GIP stimulated cAMP production with EC(50) values of 18.2, 14.9 and 15.0 nM respectively. In the pancreatic BRIN-BD11 beta-cell line, (Gly2)GIP and (Ser2)GIP (10(-8) M) evoked significant increases (1.2- and 1.5-fold respectively; P<0.01 to P<0.001) in insulinotropic activity compared with GIP. In obese diabetic ob/ob mice, both analogues significantly lowered (P<0.001) the glycaemic excursion in response to i.p. glucose. This enhanced glucose-lowering ability was coupled to a significantly raised (P<0.01) and more protracted insulin response compared with GIP. These data indicate that substitution of the penultimate Ala2 in GIP by Gly or Ser confers resistance to plasma DPP IV degradation, resulting in enhanced biological activity, therefore raising the possibility of their use in the treatment of type 2 diabetes.
Controversies in reproductive immunology. (1991)

Nine areas of current controversy in the field of immunology of reproduction have been selected for discussion: (1) do antisperm antibodies cause infertility; (2) does cell mediated immunity cause infertility; (3) do antibodies cause spontaneous abortion; (4) is abortion due to rejection of the "fetal allograft"; (5) is altered antigen expression crucial for survival of the "fetal allograft"; (6) is abortion mediated by graft rejection mechanisms; (7) does locoregional suppression prevent abortion; (8) does immunization to prevent abortion and promote pregnancy act via immunotropism and cytokine cross-talk; (9) do immune responses prevent spontaneous abortion in humans? The reasons for debate and uncertainty are reviewed and current data considered in an attempt to arrive at the most likely answer to each question. Directions for future research are proposed where appropriate.
Lifetime History of Depression and Anxiety Disorders as a Predictor of Quality of Life in Midlife Women in the Absence of Current Illness Episodes (2012)

A history of both depression and anxiety has the most robust negative effect on HRQOL in women during midlife, an association not explained by VMS or sleep disturbance. For the depression-alone group, sleep disturbance may partially explain the negative impact of previous affective illness on HRQOL. Sleep disturbance remains an independent correlate of low HRQOL.
Impact of RTS,S/AS02A and RTS,S/AS01B on Genotypes of P. falciparum in Adults Participating in a Malaria Vaccine Clinical Trial (2009)

It is concluded that both RTS,S/AS vaccines reduce multiplicity of infection. Our results do not support the hypothesis that RTS,S/AS vaccines elicit preferential effects against pfcsp alleles with sequence similarity to the 3D7 pfcsp sequence employed in the vaccine construct.
Specificity of a protective memory immune response against Mycobacterium tuberculosis (1993)

We have investigated the memory T-cell immune response to Mycobacterium tuberculosis infection. C57BL/6J mice infected with M. tuberculosis were found to generate long-lived memory immunity which provided a heightened state of acquired resistance to a secondary infection. The T-cell response of memory immune mice was directed to all parts of the bacilli, i.e., both secreted and somatic proteins. Major parts of the memory T-cell repertoire were maintained in a highly responsive state by cross-reactive restimulation with antigens present in the normal microbiological environment of the animals. A resting non-cross-reactive part of the memory repertoire was restimulated early during a secondary infection to expand and produce large amounts of gamma interferon. The molecular target of these T cells was identified as a secreted mycobacterial protein with a molecular mass of 3 to 9 kDa.
Modifiers of Radiation Action on DNA Screened by Analytical Ultracentrifugation (1982)

The effect of daunomycin, chromomycin A/sub 3/, anthramycin, cis-dichlorodiammineplatinum(II) (cisplatin), mitomycin C, and chloroquine on the frequency of radioninduced strand breaks in X-irradiated aqueous solutions of DNA was studied primarily by analytical ultracentrifugation using the sedimentation velocity method. The results show a potent radiosensitizing effect for daunomycin and chromomycin, a protective action for chloroquine and mitomycin, and a nonmodifying effect for anthramycin. Cisplatin forms a highly aggregated complex with DNA which prevents this kind of study.
Automatic composition of transition-based semantic web services with messaging (2005)

Abstract: In this paper we present Colombo, a framework in which web services are characterized in terms of (i) the atomic processes (i.e., operations) they can perform; (ii) their impact on the “real world ” (modeled as a relational database); (iii) their transition-based behavior; and (iv) the messages they can send and receive (from/to other web services and “human ” clients). As such, Colombo combines key elements from the standards and research literature on (semantic) web services. Using Colombo, we study the problem of automatic service composition (synthesis) and devise a sound, complete and terminating algorithm for building a composite service. Specifically, the paper develops (i) a technique for handling the data, which ranges over an infinite domain, in a finite, symbolic way, and (ii) a technique to automatically synthesize composite web services, based on Propositional Dynamic Logic. 1
Welfare Dynamics of Mature Age Customers: An Analysis Using the FaCS Longitudinal Data Set (2002)

This paper examines the welfare dynamics of a subgroup of income support customers aged between 50 to 60 years using FaCS fortnightly longitudinal data covering the period June 1995 - March 2000. It analyses this subgroup's socioeconomic characteristics, duration, spells and pathways on welfare over the sample period. It also explores the factors that influence churning and exit from welfare. It is found that mature age customers experience longer average duration on benefits relative to prime age customers. Customers on Newstart Allowance (NSA) payments are more likely to exit from welfare compared to non-NSA customers. Some attachment to the labour market substantially increases the likelihood of churning while presence of earned and unearned income, being of ATSI origin, being older, renting and having more children reduce the probability of exit from welfare.
La décompression des kystes des maxillaires (2017)

Les kystes des maxillaires sont des lesions intra-osseuses, de nature odontogeniques ou non. Ils se developpent progressivement en raison d'une combinaison de pression osmotique, de la liberation de facteurs de croissance et de prostaglandines. Ce travail montre l’interet de la technique de decompression face a une lesion kystique etendue. La premiere partie expose les differentes strategies therapeutiques des kystes des maxillaires dont l’enucleation chirurgicale, qui peut etre un acte tres invasif. La deuxieme partie decrit les principes de la decompression. La troisieme partie detaille le protocole operatoire de la decompression a l’aide d’un drain. Un cas clinique de decompression illustre la derniere partie.
Pharmacologic Targeting or Genetic Deletion of Mitochondrial Cyclophilin D Protects from NSAID-Induced Small Intestinal Ulceration in Mice (2010)

Small intestinal ulceration is a frequent and potentially serious condition associated with nonselective cyclooxygenase 1/2 inhibitors (nonsteroidal anti-inflammatory drugs, NSAIDs) including diclofenac (DCF). An initial topical effect involving mitochondria has been implicated in the pathogenesis, but the exact mechanisms of NSAID-induced enteropathy are unknown. We aimed at investigating whether DCF caused enterocyte demise via the mitochondrial permeability transition (mPT) and whether inhibition of critical mPT regulators might protect the mucosa from DCF injury. Cultured enterocytes (IEC-6) exposed to DCF readily underwent mPT-mediated cell death. We then targeted mitochondrial cyclophilin D (CypD), a key regulator of the mPT, in a mouse model of NSAID enteropathy. C57BL/6J mice were treated with an ulcerogenic dose of DCF (60 mg/kg, ip), followed (+ 1 h) by a non-cholestatic dose (10 mg/kg, ip) of the CypD inhibitor, cyclosporin A (CsA). CsA greatly reduced the extent of small intestinal ulceration. To avoid potential calcineurin-mediated effects, we used the non-immunosuppressive cyclosporin analog, D-MeAla(3)-EtVal(4)-cyclosporin (Debio 025). Debio 025 similarly protected the mucosa from DCF injury. To exclude drug-drug interactions, we exposed mice genetically deficient in mitochondrial CypD (peptidyl-prolyl cis-trans isomerase F [Ppif(-/-)]) to DCF. Ppif-null mice were largely protected from the ulcerogenic effects of DCF, whereas their wild-type littermates developed typical enteropathy. Enterocyte injury was preceded by upregulation of the proapoptotic transcription factor C/EBP homologous protein (Chop). Chop-null mice were refractory to DCF enteropathy, suggesting a critical role of endoplasmic reticulum stress induced by DCF. In conclusion, mitochondrial CypD plays a key role in NSAID-induced enteropathy, lending itself as a potentially new therapeutic target for cytoprotective intervention.
Enumeration of CD34+ cells in cord blood: A variation on a single‐platform flow cytometric method based on the ISHAGE gating strategy (2001)

Single-platform flow cytometric absolute cell counting protocols provide increased robustness for CD34+ cell enumeration by limiting potential sources of imprecision. However, samples with any cellular fragmentation or debris, such as cord blood samples, provide challenges for these assays. We describe a simple, robust absolute CD34+ cell counting protocol, suitable for cord blood, using TRUCOUNT absolute count tubes (BD Biosciences, San Jose, CA) and a modified ISHAGE (International Society for Hematotherapy and Graft Engineering) gating strategy. An advantage of TRUCOUNT tubes is that each tube is supplied with a known number of lyophilized fluorescent beads. The method includes no-wash fixative-free ammonium chloride red blood cell lysis and the viability dye, 7-amino actinomycin D, to exclude dead cells. The threshold was set on CD45 expression in the FL1 channel and an exclusion gate in the forward scatter channel reduced debris. No manual adjustment of the gating regions was required, even for samples in less than optimal condition. Comparison of the TRUCOUNT-ISHAGE protocol with the original dual-platform ISHAGE assay (n = 30) and the single-platform ISHAGE protocol using Flow-Count Fluorospheres (Beckman Coulter, Fullerton, CA; n = 22) showed high correlation (R(2) = 0.949 and 0.989, respectively) and no significant difference or bias for samples ranging from 22 to 600 CD34+ cells per microliter. Results are presented that demonstrate the detrimental effect of a fixative-containing lysis reagent when used in a lyse-and-wash procedure. The TRUCOUNT-ISHAGE protocol combines the attributes of TRUCOUNT tubes and the ISHAGE gating strategy to provide a single-platform protocol capable of achieving readily standardization of CD34+ cell enumeration.
A Minimal Model of Ribosome Allocation Dynamics Captures Trade-offs in Expression between Endogenous and Synthetic Genes (2016)

Cells contain a finite set of resources that must be distributed across many processes to ensure survival. Among them, the largest proportion of cellular resources is dedicated to protein translation. Synthetic biology often exploits these resources in executing orthogonal genetic circuits, yet the burden this places on the cell is rarely considered. Here, we develop a minimal model of ribosome allocation dynamics capturing the demands on translation when expressing a synthetic construct together with endogenous genes required for the maintenance of cell physiology. Critically, it contains three key variables related to design parameters of the synthetic construct covering transcript abundance, translation initiation rate, and elongation time. We show that model-predicted changes in ribosome allocation closely match experimental shifts in synthetic protein expression rate and cellular growth. Intriguingly, the model is also able to accurately infer transcript levels and translation times after further exposure to additional ambient stress. Our results demonstrate that a simple model of resource allocation faithfully captures the redistribution of protein synthesis resources when faced with the burden of synthetic gene expression and environmental stress. The tractable nature of the model makes it a versatile tool for exploring the guiding principles of efficient heterologous expression and the indirect interactions that can arise between synthetic circuits and their host chassis because of competition for shared translational resources.
Chemical Composition on the Seeds and Oil of Sesame (Sesamum indicum L.) Grown in Congo-Brazzaville (2009)

Proximate composition and physicochemical analyses were carried out on the seed and Sesame oil (Sesamum indicum L.). The results showed that the seed contained 5.7% moisture, 20% crude protein, 3.7% ash, 3.2% crude fiber, 54% fat and 13.4% carbohydrate. The seeds were found to be good sources of minerals. Potassium (851.35±3.44 mg/100g) was the highest, followed in descending order by Phosphorus (647.25±3.52 mg/100g), Magnesium (579.53±0.42 mg/100g), Calcium (415.38±3.14 mg/100g) and Sodium (122.50±4.21 mg/100g). The physical properties of the oil extracts showed the state to be liquid at room temperature. The oil was found to contain high levels of unsaturated fatty acids, especially oleic (up to 38.84%) and linoleic (up to 46.26%). Sesamum indicum L. oil can be classified in the oleic-linoleic acid group. The dominant saturated acids were palmitic (up to 8.58%) and stearic (up to 5.44%). The oil extracts exhibited good physicochemical properties and could be useful as edible oils and for industrial applications.
Magnetic resonance imaging and spectroscopy of the intervertebral disc (2006)

Intervertebral disc disease is an emerging health concern and has a considerable negative effect on the economy and on society. MRI has a critical role in assessing the disc, but it is still a challenge to objectively correlate disc health and pain with images. In this paper, a review of MR disc imaging techniques including grading, relaxation time measurements, diffusion, and contrast perfusion is presented. In addition, high-resolution magic-angle spinning methods to correlate in vitro disc degeneration (with pain, etc) are discussed. With the potential for gaining morphological and biochemical information, MRI shows promise for quantitative assessment of disc health.
HER 2/neu expression and gene amplification in colon cancer (2003)

HER 2/neu is an important oncogene in breast cancer, but the prevalence and significance of HER 2/neu gene amplification in colon cancer have been poorly documented. We have evaluated HER 2/neu gene amplification and protein overexpression in a series of colon cancers to assess the frequency, concordance and clinical significance of these events. HER 2/neu gene copy number was measured in 154 primary colon tumors, 15 liver metastases and matched normal tissues using a quantitative PCR/ligase detection reaction (LDR) technique developed and validated in our laboratory. HER 2/neu copy number was confirmed by fluorescent in situ hybridization (FISH) in all tumors found to have gene amplification. In an independent and blinded fashion, HER 2/neu expression was assessed in paraffin sections from 139 of the tumor specimens using the HercepTest kit. HER 2/neu gene amplification was observed in 4 (2.4%) of the 169 tumor specimens and in none of the normal tissues. There was no apparent association with stage of disease, tumor grade or patient survival. Among 139 cases evaluated by immunohistochemistry (IHC), HER 2/neu overexpression was seen in 5 cases (3.6%). There was extremely high concordance (kappa = 0.852) between gene amplification and protein overexpression. The low prevalence of HER 2/neu gene amplification and protein overexpression suggests that this oncogene plays an infrequent role in the development and progression of colon cancer. These data indicate that the primary mechanism of dysregulated HER 2/neu expression in colon cancer, as in breast cancer, is gene amplification.
Screening for Colorectal Cancer (2009)

A healthy 76-year-old woman presents as a new patient for primary care. She reports having one daily bowel movement and no rectal bleeding. She has no family history of colorectal cancer. She reports having negative stool-card tests during gynecologic examinations, most recently at 65 years of age. Would you advise this patient to undergo colon-cancer screening, and if so, what test would you recommend?
The Engineering Design of the STRETCH Computer (1959)

The Stretch Computer project was started in order to achieve two orders of magnitude of improvement in performance over the then existing 704. Although this computer, like the 704, is aimed at scientific problems such as reactor design, hydrodynamics problems, partial differential equations etc., its instruction set and organization are such that it can handle with ease data-processing problems normally associated with commercial applications, such as processing of alphanumeric fields, sorting, and decimal arithmetic.
An augmented reality system using a real-time vision based registration (2002)

Describes a prototype of an augmented reality system using vision-based registration. In order to build an augmented reality system with video see-through image composition, camera parameters for generating virtual objects must be obtained at video-rate. The system estimates camera parameters from four known markers in an image sequence captured by a small CCD camera mounted on a HMD (head mounted display). Virtual objects are overlaid upon a captured image sequence in real-time.
Bijels: a new class of soft materials (2008)

Bicontinuous interfacially jammed emulsion gels (‘bijels’) were proposed in 2005 as a hypothetical new class of soft materials in which interpenetrating, continuous domains of two immiscible fluids are maintained in a rigid state, by a jammed layer of colloidal particles at their interface. Such gels should have unusual material properties relevant to catalysis and other applications. Although initially proposed on the basis of computer simulation, the existence of bijels has since been confirmed in the laboratory. However, a wide gap remains between the simulated and the experimental systems. This leaves room for continuing debate on the cause of stability in these materials; in particular, it is not known whether an attraction between the colloidal particles is essential for stability.
A Peptide Conjugate of Vitamin E Succinate Targets Breast Cancer Cells with High ErbB2 Expression (2007)

Overexpression of erbB2 is associated with resistance to apoptosis. We explored whether high level of erbB2 expression by cancer cells allows their targeting using an erbB2-binding peptide (LTVSPWY) attached to the proapoptotic alpha-tocopheryl succinate (alpha-TOS). Treating erbB2-low or erbB2-high cells with alpha-TOS induced similar levels of apoptosis, whereas alpha-TOS-LTVSPWY induced greater levels of apoptosis in erbB2-high cells. alpha-TOS rapidly accumulated in erbB2-high cells exposed to alpha-TOS-LTVSPWY. The extent of apoptosis induced in erbB2-high cells by alpha-TOS-LTVSPWY was suppressed by erbB2 RNA interference as well as by inhibition of either endocytotic or lysosomal function. alpha-TOS-LTVSPWY reduced erbB2-high breast carcinomas in FVB/N c-neu transgenic mice. We conclude that a conjugate of a peptide targeting alpha-TOS to erbB2-overexpressing cancer cells induces rapid apoptosis and efficiently suppresses erbB2-positive breast tumors.