gebhart/patrepeval huggingface dataset:
Estrogen blocks M-CSF gene expression and osteoclast formation by regulating phosphorylation of Egr-1 and its interaction with Sp-1. (1998)

Central to the pathogenesis of osteoporosis is the ability of estrogen deficiency to increase osteoclast formation by enhancing stromal cell production of the osteoclastogenic cytokine macrophage colony-stimulating factor (M-CSF). We report that stromal cells from ovariectomized mice exhibit increased casein kinase II-dependent phosphorylation of the nuclear protein Egr-1. Phosphorylated Egr-1 binds less avidly to the transcriptional activator Sp-1 and the resulting higher levels of free Sp-1 stimulate transactivation of the M-CSF gene. Estrogen replacement fails to block M-CSF mRNA expression and osteoclast formation in ovariectomized mice lacking Egr-1, confirming the critical role played by this transcription factor in mediating the antiosteoclastogenic effects of estrogen. Thus, by downregulating formation of a novel Egr-1/Sp-1 complex in stromal cells, estrogen deficiency results in enhanced levels of free Sp-1 and increased M-CSF gene expression and osteoclast formation.
一位现代的折中主义者:理查德·古德温 (1986)

R.古德温是一位非凡人物.他一生的学术生涯经历3个时期,最初在美国哈佛大学讲授经济学(第二次世界大战期间在该校任物理学讲师),从1951年起他到英国剑桥大学讲学,后来被选为经济学讲师直到1979年退休为止,最后在意大利锡耶纳大学,终于脱颖而出,升任经济学教授.他是
Acidifier as an Alternative Material to Antibiotics in Animal Feed (2005)

Dietary acidifiers appear to be a possible alternative to feed antibiotics in order to improve performance of weaning pigs. It is generally known that dietary acidifiers lower gastric pH, resulting in increased activity of proteolytic enzymes, improved protein digestibility and inhibiting the proliferation of pathogenic bacteria in GI tract. It is also hypothesized that acidifiers could be related to reduction of gastric emptying rate, energy source in intestine, chelation of minerals, stimulation of digestive enzymes and intermediate metabolism. However, the exact mode of action still remains questionable. Organic acidifiers have been widely used for weaning pigs' diets for decades and most common organic acidifiers contain fumaric, citric, formic and/or lactic acid. Many researchers have observed that dietary acidifier supplementation improved growth performance and health status in weaning pigs. Recently inorganic acidifiers as well as organic acidifiers have drawn much attention due to improving performance of weaning pigs with a low cost. Several researchers introduced the use of salt form of acidifiers because of convenient application and better effects than pure state acids. However, considerable variations in results of acidifier supplementation have been reported in response of weaning pigs. The inconsistent responses to dietary acidifiers could be explained by feed palatability, sources and composition of diet, supplementation level of acidifier and age of animals. (
Human colon adenocarcinoma cell lines display infrared spectroscopic features of malignant colon tissues. (1992)

Seven human colon cell lines were studied by infrared spectroscopy including study of several spectral parameters under high pressure (pressure tuning spectroscopy). The results were compared to those obtained from the study of normal and malignant colon tissues (B. Rigas et al., Proc. Natl. Acad. Sci. USA, 87: 8140-8144, 1990; P. T. T. Wong and B. Rigas., Appl. Spectrosc., 44: 1715, 1990). The seven adenocarcinoma cell lines displayed almost all of the important spectroscopic features of colon cancer tissues: (a) increased hydrogen-bonding of the phosphodiester groups of nucleic acids; (b) decreased hydrogen-bonding of the C--OH groups of carbohydrates and proteins; (c) a prominent band at 972 cm-1; and (d) a shift of the band normally appearing at 1082 cm-1 to 1086 cm-1. These cell lines differed spectroscopically from the colon cancer tissues in that: (a) they displayed a band at 991 cm-1, which is weak in colon tissues; and (b) the packing and degree of disorder of membrane lipids were close to those observed in normal colonic tissues. These findings (i) establish IR spectroscopy, used in combination with pressure tuning, as a useful method to address problems of tumor biology in cell culture systems, (ii) indicate that these cell lines offer a useful experimental model to explore the origin of the spectroscopic changes that we observed in colon cancer tissues, and (iii) support the idea that the malignant colonocyte is the likely source of all or most spectroscopic abnormalities of human colon cancer.
Measurement of mitochondrial DNA synthesis in vivo using a stable isotope-mass spectrometric technique (2003)

We describe here a new stable isotope-mass spectrometric technique for measuring mitochondrial DNA (mtDNA) synthesis. Growing (2-4 mo old) and weight-stable (8-10 mo old) Sprague-Dawley rats were primed with (2)H(2)O (deuterated water) to 2.0-2.5% body water enrichment, via intraperitoneal injection, and then given 4% (2)H(2)O in drinking water for 3-11 wk. Mitochondria were isolated from cardiac and hindlimb muscle, and mtDNA was isolated and enzymatically hydrolyzed to deoxyribonucleosides. PCR confirmed the absence of nuclear DNA contamination. The isotopic enrichment of the deoxyribose moiety of deoxyadenosine was determined by GC-MS analysis, and percent new mtDNA was calculated by comparison to genomic DNA enrichments in a tissue with nearly complete turnover (bone marrow). Initial label incorporation into deoxyadenosine of mtDNA was linear, and turnover of mtDNA was observed in nongrowing adult female rats (1.1-1.3% new mtDNA per day in cardiac and skeletal muscle). Die-away curves of mtDNA after discontinuing (2)H(2)O administration gave a similar turnover rate constant. Human subjects were also given (2)H(2)O for up to 6 wk, and mitochondria from platelets were isolated. Incubation with DNase removed any contaminating genomic DNA; platelet mtDNA exhibited linear incorporation from (2)H(2)O and reached plateau values identical to those in genomic DNA from fully turned over cells (circulating monocytes). In conclusion, replication of mtDNA can be directly measured in vivo in rodents and humans without the use of radioactivity. Use of this technique may allow improved understanding of the regulation of mitochondrial biogenesis in health and disease.
Rch1, a protein that specifically interacts with the RAG-1 recombination-activating protein. (1994)

RAG1 and RAG2 are lymphoid-specific genes that together induce V(D)J recombinase activity in a variety of nonlymphoid cell types. While no other lymphoid-specific factors are required to induce recombination, other factors with more widespread expression patterns have been implicated in the reaction. However, none of these factors have been cloned, and their relationship to the RAG proteins is unclear. Using the yeast two-hybrid assay, we have identified RCH1, a gene encoding a protein of molecular weight 58,000 that interacts specifically with RAG-1. The predicted Rch1 protein sequence is 47% identical to yeast SRP1, a protein associated with the nuclear envelope. A truncated form of Rch1, which retains the ability to interact with RAG-1, reduces V(D)J recombination activity in HeLa cells.
p53 Mutation Analysis in Breast Tumors by a DNA Microarray Method (2006)

The p53 gene acts as a regulator of cell growth and DNA repair in normal cells; inactivation of the gene seems to lead to cancer. It is the most commonly mutated gene in human cancers, and a high-throughput sequencing method is needed for cancer etiology studies using large sample sets. In our population-based case-control study of breast cancer, the p53 gene was amplified by PCR for 392 subjects from seven hospitals in Western New York using the Affymetrix GeneChip technology. One hundred thirty-eight (35%) of the breast tumors had p53 mutations, of which 88% were located in exons 5 to 8. New hotspots were identified at codons 179, 195, 196, 213, 217, 249, 254, 278, 281, and 298, and previously reported hotspots were found at codons 175, 248, and 273. Manual sequencing for exons 5 to 9 of the p53 gene was done for 139 tumors to validate the Affymetrix assay. The two methods had 100% concordance for mutations detectable by the Affymetrix assay. We also successfully assayed paraffin-embedded breast and lung tumors from as early as 1958 and employed a nested PCR strategy to improve weak PCR amplification. To have statistical power, the investigation of gene environment interactions and cancer requires a large number of tumor analyses, which are frequently only available from archived tissue from multiple sources. We have shown the utility of the Affymetrix GeneChip method under these challenging conditions and provided new data for the mutational spectra of breast cancer in a population-based study.
Computers in imaging and guided surgery (2001)

The authors review the main technical issues in computer-integrated surgery (CIS) systems. They illustrate with examples of working systems the state of the art in the field and provide perspectives on deployment and future developments. They discuss the structure of CIS systems. At the core is a computer (or network of computers) running various modeling and analysis processes, including image and sensor processing, creation and manipulation of patient-specific anatomical models, surgical planning, visualization, monitoring, and control of surgical processes. After receiving information about the patient from medical imaging devices, some CIS systems act directly on the patient using specialized robots or other computer controlled therapy devices.
Structure of a Fibronectin Type III Domain from Tenascin Phased by MAD Analysis of the Selenomethionyl Protein (1992)

Fibronectin type III domains are found in many different proteins including cell surface receptors and cell adhesion molecules. The crystal structure of one such domain from the extracellular matrix protein tenascin was determined. The structure was solved by multiwavelength anomalous diffraction (MAD) phasing of the selenomethionyl protein and has been refined to 1.8 angstrom resolution. The folding topology of this domain is identical to that of the extracellular domains of the human growth hormone receptor, the second domain of CD4, and PapD. Although distinct, this topology is similar to that of immunoglobulin constant domains. An Arg-Gly-Asp (RGD) sequence that can function for cell adhesion is found in a tight turn on an exposed loop.
Carbonyl Reductase Expression and Its Clinical Significance in Non–Small-Cell Lung Cancer (2005)

Carbonyl reductase (CBR) is a cytosolic NADPH-dependent oxidoreductase metabolizing prostaglandins, steroids, quinines, and anthracycline antibiotics. Many experimental studies have shown that CBR plays important roles in the regulation of tumor progression, but clinical significance of CBR status remains unclear. Thus, we conducted a retrospective study on CBR mRNA expression in lung cancer. Tumor tissues obtained from 59 non-small-cell lung cancer patients were analyzed by quantitative real-time reverse transcription-PCR assay to reveal clinical significance of CBR expression. Angiogenesis was measured immunohistochemically as intratumoral microvessel density (IMVD) using anti-CD34 monoclonal antibody CD34-IMVD) and anti-CD105 monoclonal antibody (CD105-IMVD). CBR mRNA expression was significantly reduced along with progression of primary tumors (the mean CBR mRNA/GAPDH mRNA, 3.288x10(-2) for pT1, 1.628x10(-2) for pT2, and 1.175x10(-2) for pT3-4 disease, respectively; P=0.02). Moreover, CBR mRNA expression in tumor with nodal involvement seemed to be reduced as compared with that in tumor without nodal involvement (the mean CBR mRNA/GAPDH mRNA, 1.446x10(-2) and 2.531x10(-2), respectively), whereas the difference did not reach a statistical significance (P=0.09). The mean CD105-IMVD for CBR-high tumor was 59.2, which was significantly lower than that for CBR-low tumor (130.6, P=0.02), whereas no significant difference between the mean CD34-IMVDs for CBR-high tumor and CBR-low tumor was found. The 5-year survival rate of CBR-high patients was 68.3%, significantly higher than that of CBR-low patients (36.5%; P=0.03). A multivariate analysis confirmed that CBR-high expression was a significant factor to predict a favorable prognosis (P=0.04; relative risk, 0.39; 95% confidence interval, 0.16-0.98). Expression of CBR mRNA was a significant prognostic factor in non-small-cell lung cancer and was inversely associated with tumor progression and angiogenesis.
Molecular tools enabling pennycress (Thlaspi arvense) as a model plant and oilseed cash cover crop (2018)

Thlapsi arvense L. (pennycress) is being developed as a profitable oilseed cover crop for the winter fallow period throughout the temperate regions of the world, controlling soil erosion and nutrients run-off on otherwise barren farmland. We demonstrate that pennycress can serve as a user-friendly model system akin to Arabidopsis that is well-suited for both laboratory and field experimentation. We sequenced the diploid genome of the spring-type Spring 32-10 inbred line (1C DNA content of 539 Mb; 2n = 14), identifying variation that may explain phenotypic differences with winter-type pennycress, as well as predominantly a one-to-one correspondence with Arabidopsis genes, which makes translational research straightforward. We developed an Agrobacterium-mediated floral dip transformation method (0.5% transformation efficiency) and introduced CRISPR-Cas9 constructs to produce indel mutations in the putative FATTY ACID ELONGATION1 (FAE1) gene, thereby abolishing erucic acid production and creating an edible seed oil comparable to that of canola. We also stably transformed pennycress with the Euonymus alatus diacylglycerol acetyltransferase (EaDAcT) gene, producing low-viscosity acetyl-triacylglycerol-containing seed oil suitable as a diesel-engine drop-in fuel. Adoption of pennycress as a model system will accelerate oilseed-crop translational research and facilitate pennycress' rapid domestication to meet the growing sustainable food and fuel demands.
Diagnosis and diagnostic errors: time for a new paradigm (2013)

It looks like diagnosis triggers may be gaining traction. Building on their earlier efforts,1 ,2 a team of investigators based in Houston reports on their latest effort to apply electronic screens—so called ‘triggers’—to large clinical databases, to identify cases of potential diagnostic errors.3 They searched nearly 300 000 patients’ records over a 12-month period at two large health systems with comprehensive electronic health records. They sought patients who had one of four ‘red flag’ findings for prostate or colon cancer—elevated prostate specific antigen (PSA), positive fecal occult blood test (FOBT), rectal bleeding (haematochezia), and iron deficiency anaemia. They then used a refined electronic algorithm to cull out patients who (1) were already known to have prostate or colorectal cancer, or (2) had evidence of appropriate follow-up testing or referral. This process left roughly 1500 patients with one of the four red flags potentially unaddressed. Thus, searching an enormous haystack of 300 000 patients, they found roughly 1500 possible ‘needles’–patients who may have had their diagnosis of colon or prostate cancer delayed or overlooked entirely.

Their next step was manual chart review. They had hoped that the yield of their electronic screen for diagnostic failures (‘positive predictive value’) might approach 35%, meaning that at least one out of every three ‘screen positive’ charts would have evidence for care improvement opportunities. Instead they were pleasantly surprised that fully …
Prevention of cerebral edema and infarct in cerebral reperfusion injury by an antibody to interleukin-8. (1997)

Reperfusion after a transient ischemia is a frequently encountered clinical condition that often causes greater tissue damage than persistent ischemia itself. Reperfusion to rabbit brain, after a transient focal ischemia, induced neutrophil infiltration and aggregation--neither of which were observed in rabbit brain rendered ischemic alone for the same time interval--thereby leading to severe brain edema and infarct. Brain tissue levels of interleukin-8 (IL-8), a potent neutrophil chemotactic cytokine (chemokine), increased significantly at 6 hours after reperfusion, but without a noticeable elevation of plasma IL-8 levels. Moreover, we detected IL-8 protein immunohistologically in the vascular wall and, to a lesser degree, in infiltrated neutrophils, suggesting a local production of IL-8 in reperfused brain tissues. Furthermore, a neutralizing anti-IL-8 antibody significantly reduced brain edema and infarct size in comparison to rabbits receiving a control antibody. These results implicate locally produced IL-8 as a pivotal mediator of cerebral reperfusion and suggest that IL-8 is a novel target for the intervention of this injury.
Tissue Factor and VEGF Expression in Prostate Carcinoma: A Tissue Microarray Study (2009)

Tissue factor (TF) is the principal physiologic initiator of coagulation. It also plays an important role in tumor growth and metastasis possibly by contributing to angiogenesis. We evaluated the expression of TF in benign and malignant prostate tissue and correlated it with the expression of the pro-angiogenic protein, vascular endothelial growth factor (VEGF). We used a tissue microarray (TMA) constructed from 80 archival prostatectomy specimens. Core samples were collected from benign prostate tissue (BP) (n= 77), high-grade prostatic intraepithelial neoplasia (PIN) (n= 26), and carcinoma (PCa) (n= 93). TMA sections were stained with an immunopurified polyclonal TF antibody and a rabbit polyclonal VEGF. Two pathologists manually scored staining in epithelial cells using the German Immunoreactive Score. Positive staining for TF was seen predominantly in PCa with rare positive glands in BP and PIN. TF expression was significantly lower in BP versus PCa specimens (p< .001) and in PIN versus PCa specimens (p< .001). Positive staining for VEGF was seen in PCa, BP, and PIN. Rates of VEGF expression were also significantly lower in BP versus PCa specimens (p= .003) but not in PCa versus PIN (p= .430). The majority of PCa samples positive for TF were also positive for VEGF (p< .001). Our findings reinforce the link between angiogenesis and TF expression in PCa. We suggest further exploration of TF-mediated pathways leading to increased tumor aggressiveness in PCa, and the possible use of anti-TF agents in PCa.
Inflammation affects lipid metabolism during recovery from hyperinsulinaemia (2006)

Inflammation is an important contributor to lipid and glucose metabolism during recovery from hyperinsulinaemia.
Angiotensin II Receptor Subtypes and Cardiac Function (1994)

All the components of the renin-angiotensin system have been identified in the heart including the angiotensin II receptor subtypes AT1 and AT2. In the normal human heart, there is a decreasing receptor density from the right atrium to the left ventricle. In right atrial membranes prepared from pathological hearts, the percentage of AT1 receptor decreases with the severity of cardiac dysfunction whereas that of AT2 receptor increases. Treatment of hypertrophic rats with AT1 receptor antagonists inhibits cardiac hypertrophy and reverses the increase receptor density, indicating involvement of this Ang II receptor subtype. The role of the AT2 receptor is still largely unknown but it may be involved in cell growth and proliferation. The cloning of both AT1 and AT2 receptors as well as the availability of potent and selective antagonists will help us to understand better the functional role of Angiotensin II in cardiovascular disorders.
Differences in Patient Age Distribution between Influenza A Subtypes (2009)

Since the spring of 1977, two subtypes of influenza A virus (H3N2 and H1N1) have been seasonally infecting the human population. In this work we study the distribution of patient ages within the populations that exhibit the symptomatic disease caused by each of the different subtypes of seasonal influenza viruses. When the publicly available extensive information is pooled across multiple geographical locations and seasons, striking differences emerge between these subtypes. We report that the symptomatic flu due to H1N1 is distributed mainly in a younger population relative to H3N2. (The median age of the H3N2 patients is 23 years while H1N1 patients are 9 years old.) These distinct characteristic spectra of age groups, possibly carried over from previous pandemics, are consistent with previous reports from various regional population studies and also findings on the evolutionary dynamics of each subtype. Moreover, they are relevant to age-related risk assessments, modeling of epidemiological networks for specific age groups, and age-specific vaccine design. Recently, a novel H1N1 virus has spread around the world. Preliminary reports suggest that this new strain causes symptomatic disease in the younger population in a similar fashion to the seasonal H1N1 strains.
Identification of the sites in myelin basic protein that are phosphorylated by meiosis‐activated protein kinase p44mpk (1990)

Myelin basic protein serves as a convenient substrate for detection of a 44 kDa protein-serine/threonine kinase (p44mpk) that is activated near the time of germinal vesicle breakdown in maturing echinoderm and amphibian oocytes. In vitro phosphorylation by purified p44mpk from sea star oocytes was primarily on threonine residues on a single tryptic peptide of bovine brain myelin basic protein. Amino acid composition analysis of the isolated posphopeptide revealed that it was rich in proline residues. Automated solid-phase sequencing by Edman degradation identified the major site as Thr-97 in the sequence NIVTPRTPPPSQGK, which corresponds to residues 91-104 in bovine brain myelin basic protein. Thr-94 was also phosphorylated by p44mpk to a very minor extent.
Electric-Field Induced Degradation of Ionic Solids (2012)

Degradation of performance and life time of a functional material or device thereof is induced, to a great extent, by mass transfer in the material that is driven by various thermodynamic forces imposed intentionally or accidentally during its operation or service. The forces are any gradient of intensive thermodynamic variables, component chemical potentials, electrical potential, temperature, stresses, and the like. This paper reviews electric-field induced degradation phenomena in ionic solid compounds including insulation resistance degradation, crystal shift, microstructural alterations, compositional unmixing, and compound decomposition. Their inner workings are also discussed qualitatively.
Organizing ad hoc agents for human-agent service matching (2004)

Ambient intelligence, distributed agent systems, smart buildings and other emerging architectures leave the user lost between large amounts of autonomous entities or agents. With agents in cars, personal devices and other mobile systems, the set of agents available to the user can change rapidly, adding to the problems. We propose a set of agent relations to organize agents in an ad hoc situation. There are dynamic task-, location- and user relations, creating multiple relation hierarchies in agent space. These hierarchies allow robust, space- and task limited, context-sensitive search through agent space. We show how to use this structure to keep user interfaces near the user, and how it can be used to support the user in finding the agent he needs in a context-sensitive way.