gebhart/patrepeval huggingface dataset:
Altered Cholesterol Ester Cycle in Skin Fibroblasts from Patients with Alzheimer's Disease (2009)

Intracellular cholesterol metabolism was reported to modulate amyloid-beta (Abeta) generation in Alzheimer's disease (AD). Results presented herein demonstrated that, like brain cells, cultured skin fibroblasts from AD patients contained more cholesterol esters than fibroblasts from healthy subjects. Particularly, Oil Red-O, Nile Red, and filipin staining highlighted higher levels of neutral lipids which responded to inhibitors of acyl-coenzyme A:cholesterol acyl-transferase (ACAT-1), associated with an increase in free cholesterol. ACAT-1 mRNA levels increased significantly in AD fibroblasts, whereas those of sterol regulatory element binding protein-2, neutral cholesterol ester hydrolase, and ATP-binding cassette transporter member 1 were markedly down-regulated. Instead, mRNA levels of low-density lipoprotein receptor, hydroxy-methyl-glutaryl-coenzyme A reductase, caveolin-1, and amyloid-beta protein precursor (AbetaPP) were virtually unchanged. Notably, mRNA levels of both beta-site AbetaPP-cleaving enzyme 1 (BACE1) and neprilysin were significantly down-regulated. An increase in Abeta(40) and Abeta(42) immunostaining and a decrease in BACE1 active form were also found in AD versus control fibroblasts. Altogether, these findings support the hypothesis that the derangement of cholesterol homeostasis is a systemic alteration involving central but also peripheral cells of AD patients, and point to cholesterol ester levels in AD fibroblasts as an additional metabolic hallmark useful in the laboratory and clinical practice.
Coherent view of non-Hodgkin's lymphoma. (1995)

The subtypes of primary B-lineage nodal lymphoma include low-grade (small lymphocytic, lymphoplasmacytic-lymphoplasmacytoid, follicular small cleaved cell, and follicular mixed small cleaved and large cell), intermediate-grade (follicular large cell, diffuse small cleaved or mixed, and intermediate lymphocytic), and high-grade (diffuse large cell, immunoblastic, and small noncleaved cell) neoplasms. The less common lymphomas of T lineage and lymphomas that arise in extranodal sites are placed in separate subdivisions. This subdivision serves as a guide to prognosis and treatment.
Manufacturing of half-tone phase-shift masks III: inspection, repair, and quality assurance (1994)

Half-tone phase shift masks with Cr-based shifters have been developed for i-line lithography. The printability of defects is determined with test marks for the four categories of defects: clear defects (pinholes and intrusions) and opaque defects (pinspots and extrusions) under the conditions that a normal hole of 0.40-micrometers width is formed by an i-line stepper with NA equals 0.57. The detectability with a KLA219HRL-PS and that of a KLA331 are also evaluated. The minimum detectable defect size is found to be smaller than the minimum intolerable defect size for each category. Clear defects are repairable by covering them with carbon patches deposited by a focused-ion-beam repair system. On the basis of the consideration of both the shielding effect and the halo effect of the patch, the deposition conditions are optimized: the thickness is 150 nm and the patch edge should be placed just on the hole edge. Opaque defects are repairable by removing them with a laser repair system without any printable damage. A KLA219HRL-PS is used for inspection both before repair and before shipment. It is confirmed that the well repaired (i.e., unprintable) defects are undetectable. Quality assurance tools are summarized.
[Significance of pedography in the diagnosis and treatment of the diabetic foot syndrome]. (2004)

Pedographic systems are now in use in many research centers and hospitals throughout the world. The platform system permits rapid and accurate static and dynamic measurement of the local pressure loading on the plantar surface of the foot, and also permits a functional assessment of the roll-over process in the bare foot. The in-shoe system employing an insole measures the pressure distribution within an orthopedic shoe and enables an accurate comparison of the loading situation before and after fitting. As an additional diagnostic tool, pedography improves preventive measures and the quality of the orthopedic treatment of the diabetic foot.
The wild thing! (2005)

Suppose you are on a mobile device with no keyboard (e.g., a cell or PDA). How can you enter text quickly? T9? Graffiti? This demo will show how language modeling can be used to speed up data entry, both in the mobile context, as well as the desk-top. The Wild Thing encourages users to use wildcards (*). A language model finds the k-best expansions. Users quickly figure out when they can get away with wildcards. General purpose trigram language models are effective for the general case (unrestricted text), but there are important special cases like searching over popular web queries, where more restricted language models are even more effective.
Webster, Augusta (2015)

Augusta Webster was an accomplished translator and prolific poet who was well regarded by Victorian readers. Webster wrote in many genres: she published translations of Prometheus Bound and Medea , seven books of poetry, two novels, three plays, and numerous essays and reviews. In addition to her literary career, Webster was politically active in feminist causes. Many of her poems focus on women's lives and experience. Today she is best known as the author of “A Castaway,” a dramatic monologue about a prostitute, and for a posthumous sequence of sonnets celebrating maternal love.
Rosacea: An Update (2005)

Rosacea is a common chronic cutaneous disorder of unknown etiology which occurs most commonly in middle-aged individuals. Cutaneous manifestations include transient or persistent facial erythema, telangiectasia, edema, papules and pustules that are usually confined to the central portion of the face. The National Rosacea Society's Expert Committee on the Classification and Staging of Rosacea identified four subtypes of rosacea: erythematotelangiectatic, papulopustular, phymatous and ocular. Recently, a standard grading system for assessing gradations of the severity of rosacea has been reported. Little is known about the cause of rosacea. Genetic, environmental, vascular, inflammatory factors and microorganisms such as Demodex folliculorum and Helicobacter pylori have been considered. Topical metronidazole and azelaic acid have been demonstrated to be effective treatments for rosacea. Severer or persistent cases may be treated with oral metronidazole, tetracyclines or isotretinoin.
PLAC1, a trophoblast-specific cell surface protein, is expressed in a range of human tumors and elicits spontaneous antibody responses. (2007)

Identification of genes that are upregulated in tumors, and whose normal expression excludes adult somatic tissues but includes germline and/or embryonic tissues, has resulted in a rich variety of cancer antigens that are attractive targets for cancer vaccine and other therapeutic approaches. In the present study, we extended this approach to include genes strongly and restrictively expressed in the placenta by mining publicly available SAGE and EST databases. We identified a number of genes with high expression in placenta and different cancer types but with relatively restricted expression in normal tissues. The gene with the most distinctive expression pattern was found to be PLAC1, which encodes a putative cell surface protein that is highly expressed in placenta, testis, cancer cell lines and lung tumors. Hence we have designated it CT92. We found by ELISA that PLAC1 is immunogenic in a subset of cancer patients and healthy women. Its physical and expression characteristics render it a potential target for both active and passive cancer immunotherapeutic strategies.
Apolipoprotein E element 4 association with dementia in a population-based study (1996)

Apolipoprotein E type 4 allele (apoE epsilon4) is associated with Alzheimer's disease (AD) in the late-onset familial form and in sporadic cases, but the age-associated risk in a randomly sampled elderly population is not established. We examined the association of apoE epsilon4 with AD and other dementias (mainly multi-infarct or dementia following stroke) in 1,030 persons aged 71 to 100 years in the population-based Framingham Study cohort. Kaplan-Meier survival analysis revealed that 55% of the apoE epsilon4/epsilon4 homozygotes developed AD by age 80, whereas 27% of apoE epsilon3/epsilon4 heterozygotes developed AD by age 85, and 9% of those without a 4 allele developed AD by age 85 years. In comparison with persons without a 4 allele, the risk ration for AD was 3.7 (95% CI = 1.9 to 7.5) for apoE epsilon3/epsilon4 heterozygotes and 30.1 (95% CI = 10.7 to 84.4) for apoE epsilon4 homozygotes. ApoE epsilon2 (2/2, 2/3, or 2/4 genotypes) was associated with an absence of AD. One-half (n=21) of the 43 AD patients were either homozygous or heterozygous for apoE epsilon4. We found evidence for an association of apoE epsilon4 with other dementia, primarily multi-infarct dementia and stroke. The risk ratio was 2.3 (95% CI = 0.9 to 6.1) for non-AD dementias among persons with apoE epsilon3/epsilon4. Although the apoE epsilon4 allele is a potent risk factor for AD and may be associated with other forms of dementia, most apoE epsilon4 carriers do not develop dementia, and about one-half of AD is not apoE epsilon4 associated. The low positive predictive value of this marker (0.10) suggest that use of apoE genotyping as a screening test for AD is not supported.
Onset of TCR-beta gene rearrangement and role of TCR-beta expression during CD3-CD4-CD8- thymocyte differentiation. (1994)

TCR-beta gene rearrangement or expression is necessary and sufficient for the progression of early alpha beta thymocyte differentiation from the CD3-CD4-CD8- triple negative (TN)3 to the CD4+CD8+ double positive stage. The onset of TCR-beta rearrangement is currently thought to occur gradually. Some thymocytes were reported to be rearranged at the earliest (CD44+CD25-) TN stage, whereas other thymocytes did not initiate TCR-beta rearrangement until the latest (CD44-CD25-) TN stage. Here, we have isolated subsets of TN thymocytes on the basis of surface expression of CD44 and CD25, with c-kit as an additional marker. We present a revised model of early T cell development in which TCR-beta and TCR-gamma rearrangements occur abruptly, at the CD44lowCD25+ c-kitlowTN stage. A high level of c-kit expression defines pro-T cells which have not yet rearranged their TCR genes. Germ-line TCR-beta transcripts, and transcripts of recombination activating genes (RAG)-1 and 2, are detected before TCR-beta gene rearrangement. Analyses of TN thymocytes of RAG-1 mutant mice, and of various TCR mutant and TCR transgenic RAG-1 mutant mice, indicate the existence of a control point at the CD44-CD25+TN stage at which cells expressing a productively rearranged TCR-beta chain are selected for further differentiation.
Genetic Control of Extracellular Protease Synthesis in the Yeast Yarrowia lipolytica (2002)

Abstract Depending on the pH of the growth medium, the yeast Yarrowia lipolytica secretes an acidic protease or an alkaline protease, the synthesis of which is also controlled by carbon, nitrogen, and sulfur availability, as well as by the presence of extracellular proteins. Previous results have indicated that the alkaline protease response to pH was dependent on YlRim101p, YlRim8p/YlPalF, and YlRim21p/YlPalH, three components of a conserved pH signaling pathway initially described in Aspergillus nidulans. To identify other partners of this response pathway, as well as pH-independent regulators of proteases, we searched for mutants that affect the expression of either or both acidic and alkaline proteases, using a YlmTn1-transposed genomic library. Four mutations affected only alkaline protease expression and identified the homolog of Saccharomyces cerevisiae SIN3. Eighty-nine mutations affected the expression of both proteases and identified 10 genes. Five of them define a conserved Rim pathway, which acts, as in other ascomycetes, by activating alkaline genes and repressing acidic genes at alkaline pH. Our results further suggest that in Y. lipolytica this pathway is active at acidic pH and is required for the expression of the acidic AXP1 gene. The five other genes are homologous to S. cerevisiae OPT1, SSY5, VPS28, NUP85, and MED4. YlOPT1 and YlSSY5 are not involved in pH sensing but define at least a second protease regulatory pathway.
Architecture-independent parallel computation (1990)

The major parallel architecture classes are considered: single-instruction multiple-data (SIMD) computers, tightly coupled multiple-instruction multiple-data (MIMD) computers, hypercuboid computers and constant-valence MIMD computers. An argument that the PRAM model is universal over tightly coupled and hypercube systems, but not over constant-valence-topology, loosely coupled-system is reviewed, showing precisely how the PRAM model is too powerful to permit broad universality. Ways in which a model of computation can be restricted to become universal over less powerful architectures are discussed. The Bird-Meertens formalism (R.S. Bird, 1989), is introduced and it is shown how it is used to express computations in a compact way. It is also shown that the Bird-Meertens formalism is universal over all four architecture classes and that nontrivial restrictions of functional programming languages exist that can be efficiently executed on disparate architectures. The use of the Bird-Meertens formalism as the basis for a programming language is discussed, and it is shown that it is expressive enough to be used for general programming. Other models and programming languages with architecture-independent properties are reviewed. >
The Volumetric Efficiency of Direct and Port Injection Gasoline Engines with Different Fuels (2002)

&lt;div class="htmlview paragraph"&gt;A study has been undertaken with a single-cylinder engine, based on the Mitsubishi GDi combustion system, that has the option of either port injection or direct injection. Tests have been undertaken with pure fuel components (methane, iso-octane, toluene and methanol), and a representative gasoline that has also been tested with the addition of 10% methanol and 10% ethanol. The volumetric efficiency depends both on the fuel and its time and place of injection. For stoichiometric operation with unleaded gasoline, changing from port injection to direct injection led to a 9% increase in volumetric efficiency, which was improved by a further 3% when 10% methanol was blended with the gasoline.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;The improvements in volumetric efficiency will be used to quantify the extent of charge cooling by fuel evaporation, and these will be compared with predictions assuming the maximum possible level of fuel evaporation.&lt;/div&gt;
Gene expression signature associated with BRAF mutations in human primary cutaneous melanomas (2008)

With the aim to correlate BRAF mutation status with gene expression in human primary cutaneous melanomas, and thus to get more insight on the consequences of BRAF mutation on cell biology, we analyzed all expression data obtained in melanomas from which DNA was extracted from the same tissue slides that were used for the expression study. A cohort of 69 frozen primary melanoma whose oligonucleotide micro-array expression data were available, were genotyped for BRAF and NRAS genes. The expression data from these melanomas were re-analyzed according to BRAF mutational status. A set of 250 probes representing 209 genes that were significantly (raw P< or =0.001) associated with BRAF mutation status was identified and 17 of these were previously shown to be implicated in cutaneous melanoma progression or pigmentation pathway-associated genes driven by the microphthalmia transcription factor (MITF). The list of 34 top probes contained no more than 1% of false discoveries with a probability of 0.95. Among the genes that differentiated most strongly between BRAF mutated and non-mutated melanomas, there were those involved in melanoma immune response such as MAGE-D2, CD63, and HSP70. These findings support the immunogenicity of BRAF(V600E), eliciting patients T-cell responses in various in vitro assays. The genes whose expression is associated with BRAF mutations are not simply restricted to the MAPK/ERK signaling but also converge to enhanced immune responsiveness, cell motility and melanosomes processing involved in the adaptative UV response.
Small Intestinal Submucosa (1995)

Prosthetic graft material is often used for the repair of abdominal wall defects that result from trauma, infection, neoplastic, or congenital deformities. A new material, porcine small intestinal submucosa, has been successfully used as an arterial and venous graft material in both canine and primate animal models with graft patency and infection rates equal to autologous vein. On the basis of these studies, small intestinal submucosa was used as a graft material for the repair of a 2 x 2-cm full-thickness defect of the muscle and fascia in the rodent abdominal wall (N = 11). Two animals were euthanized at 1 week, 2 weeks, 4 weeks, 2 months, and 3 months. At the time of euthanization, no abdominal hernias were noted and only minimal intra-abdominal adhesions were observed. One animal died on postoperative day 5 as a result of a wound dehiscence. Histological analysis of the excised abdominal wall hernia repairs revealed moderate initial inflammation but with incorporation of small intestinal submucosa with minimal inflammation at 2 months. No evidence of graft-versus-host rejection was noted with hematoxylin and eosin stains and light microscopy. Porcine small intestinal submucosa merits further study as a graft material for abdominal wall replacement.
First peptide vaccine providing protection against viral infection in the target animal: studies of canine parvovirus in dogs (1994)

A synthetic peptide vaccine which protects dogs against challenge with virulent canine parvovirus is described. The amino acid sequence used was discovered in previous studies on the immunogenic properties of previously mapped antigenic sites and represents the amino-terminal region of viral protein VP2. As with marker vaccines, it is possible to discriminate between vaccinated dogs that have not been exposed to the virus and dogs that have been infected with the virus. The protective mechanism can be explained by a humoral response against the peptide aided by T-cell epitopes contained in the carrier protein used for peptide coupling. This is the first example of a synthetic peptide vaccine that induces protection in target animals.
Genomic Editing of the HIV-1 Coreceptor CCR5 in Adult Hematopoietic Stem and Progenitor Cells Using Zinc Finger Nucleases (2013)

The HIV-1 coreceptor CCR5 is a validated target for HIV/AIDS therapy. The apparent elimination of HIV-1 in a patient treated with an allogeneic stem cell transplant homozygous for a naturally occurring CCR5 deletion mutation (CCR5(Δ32/Δ32)) supports the concept that a single dose of HIV-resistant hematopoietic stem cells can provide disease protection. Given the low frequency of naturally occurring CCR5(Δ32/Δ32) donors, we reasoned that engineered autologous CD34(+) hematopoietic stem/progenitor cells (HSPCs) could be used for AIDS therapy. We evaluated disruption of CCR5 gene expression in HSPCs isolated from granulocyte colony-stimulating factor (CSF)-mobilized adult blood using a recombinant adenoviral vector encoding a CCR5-specific pair of zinc finger nucleases (CCR5-ZFN). Our results demonstrate that CCR5-ZFN RNA and protein expression from the adenoviral vector is enhanced by pretreatment of HSPC with protein kinase C (PKC) activators resulting in >25% CCR5 gene disruption and that activation of the mitogen-activated protein kinase kinase (MEK)/extracellular signal-regulated kinase (ERK) signaling pathway is responsible for this activity. Importantly, using an optimized dose of PKC activator and adenoviral vector we could generate CCR5-modified HSPCs which engraft in a humanized mouse model (albeit at a reduced level) and support multilineage differentiation in vitro and in vivo. Together, these data establish the basis for improved approaches exploiting adenoviral vector delivery in the modification of HSPCs.
American Society of Clinical Oncology/College of American Pathologists Guideline Recommendations for Human Epidermal Growth Factor Receptor 2 Testing in Breast Cancer (2007)

The panel recommends that HER2 status should be determined for all invasive breast cancer. A testing algorithm that relies on accurate, reproducible assay performance, including newly available types of brightfield ISH, is proposed. Elements to reliably reduce assay variation (for example, specimen handling, assay exclusion, and reporting criteria) are specified. An algorithm defining positive, equivocal, and negative values for both HER2 protein expression and gene amplification is recommended: a positive HER2 result is IHC staining of 3 + (uniform, intense membrane staining of 30% of invasive tumor cells), a fluorescent in situ hybridization (FISH) result of more than six HER2 gene copies per nucleus or a FISH ratio (HER2 gene signals to chromosome 17 signals) of more than 2.2; a negative result is an IHC staining of 0 or 1 +, a FISH result of less than 4.0 HER2 gene copies per nucleus, or FISH ratio of less than 1.8. Equivocal results require additional action for final determination. It is recommended that to perform HER2 testing, laboratories show 95% concordance with another validated test for positive and negative assay values. The panel strongly recommends validation of laboratory assay or modifications, use of standardized operating procedures, and compliance with new testing criteria to be monitored with the use of stringent laboratory accreditation standards, proficiency testing, and competency assessment. The panel recommends that HER2 testing be done in a CAP-accredited laboratory or in a laboratory that meets the accreditation and proficiency testing requirements set out by this document.
A New Software Platform to Improve Multidisciplinary Tumor Board Workflows and User Satisfaction: A Pilot Study (2018)

The study supported the hypothesis that the new software platform can improve Tumor Board preparation. Further study is needed to assess the impact of this platform in different hospitals, different data storage systems, with different observers, and different types of Tumor board cases as well as its impact on the quality of the tumor board discussion.