gebhart/patrepeval huggingface dataset:
Integrated Genomic Profiling of Chronic Lymphocytic Leukemia Identifies Subtypes of Deletion 13q14 with Differential Expression of LATS2. (2007)

Abstract Chronic lymphocytic leukemia (CLL) is a biologically heterogeneous illness with a variable clinical course. Loss of chromosomal material on chromosome 13 at cytoband 13q14 is the most frequent genetic abnormality in CLL but the molecular aberrations underlying del13q14 in CLL remain incompletely characterized. We analyzed 171 CLL cases for LOH and sub-chromosomal copy loss on chromosome 13 in DNA from FACS-sorted CD19+ cells and paired buccal cells using the Affymetrix XbaI 50K SNP array platform. Comparative analysis of SNP-array-derived detection of del13q14 using copy number analysis compared with clinical FISH results for del13q14 demonstrated strong agreement between both methods: FISH detected 91/171=53% overall del13q14 incidence and 77/171=45% del13q14 cases with greater than 25% of cells involved. SNP-arrays detected 82/171=48% del13q14 incidence. SNP-arrays detected 74/77=96% of all CLL cases that were greater than 25% FISH positive and 82/91=90% of all CLL cases that were FISH positive (% positive range for FISH was 2–97%). Finally, SNP-arrays detected 2 CLL cases not previously known to be del13q14 by FISH. The resulting high-resolution genomic maps, together with array-based measurements of expression levels of RNA in CLL cases with and without del13q14 and Q-PCR-based expression analysis of selected genes, support the following conclusions: del13q14 is heterogeneous and composed of multiple subtypes (types Ia, Ib and II) with deletion of Rb or the miR15a/16 loci serving as anatomic landmarks, respectively; del13q14 type Ia deletions are relatively uniform in length and extend from breakpoints close to the miR15a/16 cluster to a newly identified telomeric breakpoint cluster at ∼50.2–50.5 Mb physical position; LATS2 RNA levels are ∼2.6–2.8 fold lower in cases with del13q14 type I that do not delete Rb, as opposed to del13q14 type II lesions or all other CLL cases; ∼15% of CLL cases display marked reductions in miR15a/16 expression that are often but not invariably associated with bi-allelic miR15a/16 loss; and Bcl-2 levels and miR16/15a locus loss or miR16/15a expression are not correlated. This data should aid future investigations into biological differences imparted on CLL by different del13q14 subtypes, including investigations into LATS2 as one of the genes found deregulated as part of del13q14 type I and investigations into additional miR16/15a targets.
An Information-Intensive Approach to the Molecular Pharmacology of Cancer (1997)

Since 1990, the National Cancer Institute (NCI) has screened more than 60,000 compounds against a panel of 60 human cancer cell lines. The 50-percent growth-inhibitory concentration (GI50) for any single cell line is simply an index of cytotoxicity or cytostasis, but the patterns of 60 such GI50 values encode unexpectedly rich, detailed information on mechanisms of drug action and drug resistance. Each compound's pattern is like a fingerprint, essentially unique among the many billions of distinguishable possibilities. These activity patterns are being used in conjunction with molecular structural features of the tested agents to explore the NCI's database of more than 460,000 compounds, and they are providing insight into potential target molecules and modulators of activity in the 60 cell lines. For example, the information is being used to search for candidate anticancer drugs that are not dependent on intact p53 suppressor gene function for their activity. It remains to be seen how effective this information-intensive strategy will be at generating new clinically active agents.
Preventing Cross Site Request Forgery Attacks (2006)

The Web has become an indispensable part of our lives. Unfortunately, as our dependency on the Web increases, so does the interest of attackers in exploiting Web applications and Web-based information systems. Previous work in the field of Web application security has mainly focused on the mitigation of cross site scripting (XSS) and SQL injection attacks. In contrast, cross site request forgery (XSRF) attacks have not received much attention. In an XSRF attack, the trust of a Web application in its authenticated users is exploited by letting the attacker make arbitrary HTTP requests on behalf of a victim user. The problem is that Web applications typically act upon such requests without verifying that the performed actions are indeed intentional. Because XSRF is a relatively new security problem, it is largely unknown by Web application developers. As a result, there exist many Web applications that are vulnerable to XSRF. Unfortunately, existing mitigation approaches are time-consuming and error-prone, as they require manual effort to integrate defense techniques into existing systems. In this paper, we present a solution that provides a completely automatic protection from XSRF attacks. More precisely, our approach is based on a server-side proxy that detects and prevents XSRF attacks in a way that is transparent to users as well as to the Web application itself. We provide experimental results that demonstrate that we can use our prototype to secure a number of popular open-source Web applications, without negatively affecting their behavior
Speckle variance detection of microvasculature using swept-source optical coherence tomography (2008)

We report on imaging of microcirculation by calculating the speckle variance of optical coherence tomography (OCT) structural images acquired using a Fourier domain mode-locked swept-wavelength laser. The algorithm calculates interframe speckle variance in two-dimensional and three-dimensional OCT data sets and shows little dependence to the Doppler angle ranging from 75 degrees to 90 degrees . We demonstrate in vivo detection of blood flow in vessels as small as 25 microm in diameter in a dorsal skinfold window chamber model with direct comparison with intravital fluorescence confocal microscopy. This technique can visualize vessel-size-dependent vascular shutdown and transient vascular occlusion during Visudyne photodynamic therapy and may provide opportunities for studying therapeutic effects of antivascular treatments without on exogenous contrast agent.
Full text document retrieval: Hebrew legal texts (1971)

A series of 60 cases of nephroblastoma treated at the Abidjan University Hospital from 1971 to 1981 were reported. Nephroblastoma is a frequent childhood tumour representing 26.40% of malignant childhood tumours. It is a tumour of the young child. There is no sex predominance and both sides are equally involved. The tumour is the only clinical manifestation and is always palapable. Factors of poor prognosis were often observed in our patients including: age less than 2 years with major tumour volume (56.6%), advanced stage (89.3%). Antimitotic treatment was used in all cases and in 16 surgery was required. The poor prognosis criteria observed in this series explain the poor outcome in most of the cases.
Hearing aids for mild to moderate hearing loss in adults (2017)

The available evidence concurs that hearing aids are effective at improving hearing-specific health-related quality of life, general health-related quality of life and listening ability in adults with mild to moderate hearing loss. The evidence is compatible with the widespread provision of hearing aids as the first-line clinical management in those who seek help for hearing difficulties. Greater consistency is needed in the choice of outcome measures used to assess benefits from hearing aids. Further placebo-controlled studies would increase our confidence in the estimates of these effects and ascertain whether they vary according to age, gender, degree of hearing loss and type of hearing aid.
Use of two enzyme-linked immunosorbent assays to monitor antibody responses in swine with experimentally induced infection with porcine epidemic diarrhea virus (1991)

A blocking ELISA was developed to detect antibodies directed against porcine epidemic diarrhea virus (PEDV). The PEDV antigen was first incubated with dilutions of test sera. Any antigen that was not blocked by antibodies in the serum was assayed in a double-antibody sandwich ELISA, using 2 monoclonal antibodies directed against different antigenic sites on PEDV as capture and detecting antibodies, respectively. The blocking ELISA was compared with a fixed-cell ELISA that used monolayers of Vero cells infected with PEDV prototype strain CV777 as a solid phase and a conjugate of an IgG-specific monoclonal antibody for antibody detection. Pigs were inoculated with PEDV strain CV777 or 1 of 2 field isolates, and antibody responses were measured by use of the 2 tests. Antibodies were detected by the blocking ELISA as early as postinoculation day 7 and, by the fixed-cell ELISA, as early as postinoculation day 14. From day 14 on, antibody titers for both tests correlated highly. Titers for the fixed-cell ELISA were 5.4 times higher than those for the blocking ELISA. The latter technique is easier to perform and discriminates well between infected and noninfected pigs, which makes this test useful for routine diagnosis and serologic surveys of porcine epidemic diarrhea.
The Linkage Between Oxygenation and Subunit Dissociation in Human Hemoglobin (1974)

The use of subunit dissociation as a means of probing intersubunit contact energy changes which accompany cooperative ligand binding has been studied for the case of human hemoglobin. An analysis is presented delineating the information that can be obtained from the linkage relationships between ligand binding and subunit dissociation of hemoglobin tetramers into dimers. The analysis defines ( a ) the variation of the saturation function, Ȳ , with total protein concentration, ( b ) the variation of the subunit dissociation constant x K 2 with ligand concentration ( X ) and ( c ) the correlations between changes in dimer-dimer contact energy and the sequential ligand binding steps. Sensitivity of the linkage function has been explored by numerical simulation. It is shown that subunit dissociation may appreciably affect oxygenation curves under usual conditions of measurement and that relying solely on either x K 2 or Ȳ may lead to incorrect picutres of the energetics, whereas the combination defines the system much more exactly.
Delivery of Telomerase Reverse Transcriptase Small Interfering RNA in Complex with Positively Charged Single-Walled Carbon Nanotubes Suppresses Tumor Growth (2006)

-CONH-(CH(2))(6)-NH(3)(+)Cl(-) functionalized SWNTs carry complexed siRNA into tumor cells, wherein they release the siRNA from the nanotube sidewalls to silence the targeted gene. The -CONH-(CH(2))(6)-NH(3)(+)Cl(-) functionalized SWNTs may represent a new class of molecular transporters applicable for siRNA therapeutics.
Modal field deformation and transition losses in UV side-written optical fibers (2000)

The asymmetry of the UV-induced refractive-index profile in photosensitive optical fibers causes a deformation of the modal fields, resulting in transition losses between UV-exposed and unexposed fiber sections up to 0.1 dB for UV-induced index changes of the order of <or=10(-2). A numerical analysis of the transition losses is developed. It is verified experimentally that the loss is caused by coupling of power of the fundamental mode to cladding modes at such a transition.
Synthesis of MIL-102, a Chromium Carboxylate Metal−Organic Framework, with Gas Sorption Analysis (2006)

A new three-dimensional chromium(III) naphthalene tetracarboxylate, CrIII3O(H2O)2F{C10H4(CO2)4}1.5.6H2O (MIL-102), has been synthesized under hydrothermal conditions from an aqueous mixture of Cr(NO3)3.9H2O, naphthalene-1,4,5,8-tetracarboxylic acid, and HF. Its structure, solved ab initio from X-ray powder diffraction data, is built up from the connection of trimers of trivalent chromium octahedra and tetracarboxylate moieties. This creates a three-dimensional structure with an array of small one-dimensional channels filled with free water molecules, which interact through hydrogen bonds with terminal water molecules and oxygen atoms from the carboxylates. Thermogravimetric analysis and X-ray thermodiffractometry indicate that MIL-102 is stable up to approximately 300 degrees C and shows zeolitic behavior. Due to topological frustration effects, MIL-102 remains paramagnetic down to 5 K. Finally, MIL-102 exhibits a hydrogen storage capacity of approximately 1.0 wt % at 77 K when loaded at 3.5 MPa (35 bar). The hydrogen uptake is discussed in relation with the structural characteristics and the molecular simulation results. The adsorption behavior of MIL-102 at 304 K resembles that of small-pore zeolites, such as silicalite. Indeed, the isotherms of CO2, CH4, and N2 show a maximum uptake at 0.5 MPa, with no further significant adsorption up to 3 MPa. Crystal data for MIL-102: hexagonal space group P(-)6 (No. 169), a = 12.632(1) A, c = 9.622(1) A.
Very late antigen-4 function of myeloblasts correlates with improved overall survival for patients with acute myeloid leukemia (2008)

Adhesion of acute myeloid leukemia (AML) blasts in the bone marrow microenvironment confers protection from chemotherapy-induced apoptosis. One mechanism for retention of blasts within the bone marrow is adhesion via very late antigen-4 (VLA-4), the alpha(4)beta(1) integrin heterodimer that binds to its main ligands, fibronectin, and vascular cell adhesion molecule-1 (VCAM-1). To examine the relationship of functional expression of VLA-4 to prognosis in AML, we studied marrow samples from 175 adult AML patients who underwent induction chemotherapy with anthracycline and cytarabine on Southwest Oncology Group trials. The studies included flow cytometry and functional in vitro assays for ligand binding and maximal beta(1) activation. VLA-4 expression varied widely, with mean expression 60.6% for alpha(4), and was not significantly associated with response to chemotherapy, relapse-free, or overall survival (OS). However, increased binding of soluble VCAM-1 via VLA-4 was significantly associated with longer OS, corrected for age (P = .033). Estimated 5-year OS was 31% (95% confidence interval, 14%-48%) in 30 patients with soluble VCAM-1 binding greater than or equal to 40%, compared with 10% (confidence interval, 3%-17%) in 72 patients with lower binding. Adhesion and migratory properties of AML blasts thus appear to influence chemosensitivity and therefore may be therapeutic targets.
Surface T‐cell antigen receptor expression and availability for long‐term antigenic signaling (2003)

It is important to understand how T-cell antigen receptor (TCR) engagement and signaling are regulated throughout an immune response. This review examines the dynamics of surface TCR expression and signaling capacity during thymic and effector T-cell development. Although the TCR can undergo vast changes in surface expression, T cells remain capable of sustaining TCR engagement for long periods of time. This may be achieved by a combination of mechanisms that involve (a) controlling the quantity of surface TCR available for ligand interaction and (b) controlling the quality of surface TCR expression during T-cell activation. TCR signaling itself appears to be one of the main quantitative modulators of surface TCR expression, and it can cause both downregulation and upregulation at different times of T-cell activation. Recent studies indicate that the degree of upregulation is tunable by the strength of antigenic stimulation. There is evidence that qualitatively distinct forms of the TCR exist, and their potential role in sustained antigenic signaling is also discussed. A goal of future studies will be to better characterize these modulations in surface TCR expression and to clarify their impact on the regulation of immune responses.
Hypophosphatasia (2000)

Hypophosphatasia (McKusick #146300, #241500, #241510) is a heritable metabolic bone disease that establishes a critical (but as yet unspecified) role for alkaline phosphatase (ALP) in skeletal mineralization (1,2). Subnormal activity of ALP in serum (hypophosphatasemia) is the biochemical hallmark of the disorder, and reflects a generalized deficiency of activity of the tissue-nonspecific (liver/bone/ kidney) ALP isoenzyme (TNSALP) (3). Catalysis by the tissue-specific ALP isoenzymes—intestinal, placental, and germ-cell (placental-like) ALP—is not diminished (3). The impaired skeletal mineralization caused by the deficient TNSALP activity manifests clinically as rickets in infants and children and as osteomalacia in adults. In fact, the severity of the disease among patients with this inborn error of metabolism is extraordinarily variable (1–3).
Natural sources of health-promoting starch (2006)

© 2006 VUP Food Research Institute, Bratislava 69 The idea that human health is affected by food is very old. Long ago Hippocrates (460–377 A.A.C.) wrote in his medical documents: “Each food component acts on the human body and changes it. Future human life depends upon these changes and there will be either health, disease or healing”. Another well known saying is: “Let food be the medicine”. Concepts regarding food function for human life, were modified in stages. In the past, the functions of hunger satiation and life sustenance were emphasized. Later, it was recognized that disease developed in the absence of nutrients. Currently, attention is being paid to foods that improve wellness. In effort to prevent the civilization diseases, increased attention has been given to functional foods. They fall somewhere between everyday foods and medicines. Over the past 20 years, functional foods have been preferred in Japan (FOSHU Foods for Specific Health Uses), as well as presently, in countries of the Europe Union (PARNUTS Foods for Particular Nutritional Uses). These foods also possess, in addition to their nutritional value, a beneficial effect on human health, mental alertness and physical performance. Functional foods are foods to which a component has been added for a resultant positive health effect or eliminated due to a deleterious effect on health. [1]. Consumption of functional foods is recommended for their preventative benefits. Functional foods must remain foods and at the same time the beneficial effects from their consumption must be evident after consumption of portions which are commonly consumed. Among the added components are: probiotics (bifidobacteries), prebiotics (resistant starch, β-glucan, oligosaccharides, pectins), vitamins (B6, B12, D, K, folic acid), minerals (Ca, Mg, Zn), antioxidants (vitamin E and C, carotenoids, flavonoids), fatty acids (ω-3 fatty acids, γ-linolenic acid, conjugated linoleic acid), proteins, peptides, aminoacids and phytochemicals (phytosterols, isoflavons, lignans). Among the components removed from functional food are: food allergens, patho genic microorganisms, mycotoxins, pesticide residuals, and heavy metals. One of components of functional foods is resistant starch (RS). The RS latter is defined as sum of starch and starch degradation products not absorbed in the small intestine of healthy man [2]. There are four types of RS: starch that is physically inaccessible for degradation by amylolytic enzymes of the digestive tract (RS1); starch with a primary structure and conformation that results in its natural resistance to degradation, such as the green Natural sources of health-promoting starch
Human papillomavirus 16 dna in cervical cancers and in lymph nodes of cervical cancer patients: A diagnostic marker for early metastases? (1989)

Human papillomavirus (HPV) 16 is most prevalent in cervical cancers and also persists in metastases. We examined HPV16-DNA-positive primary cancers and several lymph nodes from each of 14 patients to evaluate the use of HPV16 DNA as a diagnostic marker for the detection of early node involvement. The HPV16 DNA was exclusively integrated in 39% of the primary cancers, predominantly episomal in 36%, and integrated and extrachromosomal to a similar extent in 25%. Thirteen of 16 involved lymph nodes contained HPV16 sequences. Integrated viral DNA showed the same pattern in primary tumors and in metastases. The level of extrachromosomal HPV16 DNA, however, appeared to be considerably reduced in some nodes. HPV16 DNA was also detected in 18 out of 59 histologically negative lymph nodes. This result recommends nucleic acid hybridization as a sensitive method for the detection of HPV-DNA-positive cancer cells. The prognostic significance of viral sequences in histologically negative nodes remains to be established.
Nonlinear joint-transform correlation: an optimal solution for adaptive image discrimination and input noise robustness (1994)

We develop a processor for pattern recognition that is optimum in terms of discrimination and is tolerant to variations of the object to be recognized. This optimum processor is found to be adaptive nonlinear joint-transform correlator.
Differential and competitive activation of human immune cells by distinct classes of CpG oligodeoxynucleotide (2002)

Synthetic oligodeoxynucleotides (ODN) expressing "CpG motifs" show promise as immune adjuvants, antiallergens, anticancer, and immunoprotective agents. Two structurally distinct classes of CpG ODN have been identified that stimulate human PBMC. This work establishes that both types of ODN bind to and are internalized by the same individual B cells, NK cells, and monocytes. However, the intracellular localization of "D" and "K" ODN differs, as does their functional activity: "K" type ODN trigger monocytes and B cells to proliferate and secrete IL-6 and IgM, whereas "D" type ODN induce NK cells to produce IFN-gamma and monocytes to differentiate into CD83(+)/CD86(+) dendritic cells. In monocytes, these two types of ODN (which differ in backbone composition and CpG motif) cross-inhibit one another's activity. Thus, different types of CpG ODN have distinct and in some cases incompatible effects on the same cells, a finding with important implications for the therapeutic use of these agents.
Optical Metasurfaces and Prospect of Their Applications Including Fiber Optics (2015)

Metasurfaces have emerged in the recent years as a platform to design subwavelength-thick optical components (“flat optics”), which can be used to implement any optical function (beam deflection, focusing, waveplates, etc). These flat optical components can be fabricated using a single lithographic step. The approach is particularly suited for patterning nonconventional substrates, such as semiconductor laser facets and optical fiber facets. In this paper, we review recent applications of metasurfaces to flat optical devices, including their use in semiconductor lasers and fiber optics. Metasurfaces make it possible to design all properties of light (amplitude, phase, and polarization), which enable us to build a large variety of flat optical components, including planar lenses, quarter-wave plates, optical vortex plates, holograms for vector beam generation, and ultrathin perfect absorbers and color coatings. We also review flat collimating lenses integrated on the facets of mid-infrared and far-infrared (terahertz) quantum cascade lasers, and novel techniques to create large arrays of nanostructures on fiber facets.
Developing Embedded Networked Products using the Simics Full-System Simulator (2006)

This paper is an industrial case and tool study that describes the Simics full-system simulator and its network simulation facilities. It also gives a number of examples showing how full-system simulation of heterogeneous networked embedded systems is used in the development, debugging, and testing of networked embedded systems. Simics is a commercial product with many active customers in industry, and our experience from servicing these customers has had a great effect on the design of the tool.