gebhart/patrepeval huggingface dataset:
<title>Scanning apertureless fluorescence microscope</title> (1999)

We describe a near-field apertureless fluorescence microscope, capable of imaging fluorescent latex beads with subwavelength precision. The instrument is based on a home- built tapping-mode atomic-force microscope, to which an inverted optical microscope was added. The fact that the wavelength of the fluorescence that we observe is different from the wavelength of the illumination allows for a relatively straightforward detection mechanism. Sample images are presented, along with evidence that the observe effect is of optical origin.
The Immune Factors Involved in the Pathogenesis, Diagnosis, and Treatment of Sjogren's Syndrome (2013)

Sjogren's syndrome (SS) is a systemic, autoimmune disorder characterized by salivary insufficiency and lymphocytic infiltration of the exocrine glands. Even though the mechanism of its pathology and progression has been researched ever since its discovery, the roles of different parts of immune system remain inconclusive. There is no straightforward and simple theory for the pathogenesis and diagnosis of Sjogren's syndrome because of the multiple kinds and functions of autoantibodies, changing proportion of different T-lymphocyte subsets with the progression of disease, unsuspected abilities of B lymphocytes discovered recently, crosstalk between cytokines connecting the factors mentioned previously, and genetic predisposition that contributes to the initiation of this disease. On the other hand, the number of significant reports and open-label studies of B-cell depletion therapy showing clinical efficacy in sjogren's syndrome has continued to accumulate, which provides a promising future for the patients. In a word, further elucidation of the role of different components of the immune system will open avenues for better diagnosis and treatment of SS, whose current management is still mainly supportive.
Predictive Sensitivity of Human Cancer Cells in vivo Using Semipermeable Polysulfone Fibers (1998)

An in vivo experimental model was developed to predict efficiently and accurately chemosensitivity of human tumors. Human cancer cells either from cultured cell lines or from patients' tumors were injected directly into semipermeable polysulfone fibers subsequently implanted into immunocompetent rats. Results suggest utility of this novel model system for predicting tumor sensitivity to a wide range of anticancer agents and for potentially guiding the treatment of cancer patients in the clinical setting.
Stability, specificity and fluorescence brightness of multiply-labeled fluorescent DNA probes (1997)

In this work, we studied the fluorescence and hybridization of multiply-labeled DNA probes which have the hydrophilic fluorophore 1-(straightepsilon-carboxypentynyl)-1'-ethyl- 3,3,3', 3'-tetramethylindocarbocyanine-5,5'-disulfonate (Cy3) attached via either a short or long linker at the C-5 position of deoxyuridine. We describe the effects of labeling density, fluorophore charge and linker length upon five properties of the probe: fluorescence intensity, the change in fluorescence upon duplex formation, the quantum yield of fluorescence (Phif), probe-target stability and specificity. For the hydrophilic dye Cy3, we have demonstrated that the fluorescence intensity andPhifare maximized when labeling every 6th base using the long linker. With a less hydrophilic dye, a labeling density this high could not be achieved without serious quenching of the fluorescence. The target specificity of multiply-labeled DNA probes was just as high as compared to the unmodified control probe, however, a less stable probe-target duplex is formed that exhibits a lower melting temperature. A mechanism that accounts for this destabilization is proposed which is consistent with our data. It involves dye-dye and dye-nucleotide interactions which appear to stabilize a single-stranded conformation of the probe.
Two-laboratory collaborative study on identification of mycobacteria: molecular versus phenotypic methods (1996)

Previous studies have indicated that the conventional tests used for the identification of mycobacteria may (i) frequently result in erroneous identification and (ii) underestimate the diversity within the genus Mycobacterium. To address this issue in a more systematic fashion, a study comparing phenotypic and molecular methods for the identification of mycobacteria was initiated. Focus was given to isolates which were difficult to identify to species level and which yielded inconclusive results by conventional tests performed under day-to-day routine laboratory conditions. Traditional methods included growth rate, colonial morphology, pigmentation, biochemical profiles, and gas-liquid chromatography of short-chain fatty acids. Molecular identification was done by PCR-mediated partial sequence analysis of the gene encoding the 16S rRNA. A total of 34 isolates was included in this study; 13 of the isolates corresponded to established species, and 21 isolates corresponded to previously uncharacterized taxa. For five isolates, phenotypic and molecular analyses gave identical results. For five isolates, minor discrepancies were present; four isolates remained unidentified after biochemical testing. For 20 isolates, major discrepancies between traditional and molecular typing methods were observed. Retrospective analysis of the data revealed that the discrepant results were without exception due to erroneous biochemical test results or interpretations. In particular, phenotypic identification schemes were compromised with regard to the recognition of previously undescribed taxa. We conclude that molecular typing by 16S rRNA sequence determination is not only more rapid (12 to 36 h versus 4 to 8 weeks) but also more accurate than traditional typing.
Illumination and detection systems for quantitative fluorescence microscopy (1987)

Systems are described for the illumination and detection of light microscope images of fluorescence in living cells at low levels of excitation. The illumination system is based on the use of an acousto-optic modulator to control the wavelength and power of the excitation beam. The detection system utilizes an image intensifier coupled with a television camera to acquire images at extremely low intensities. Both the illumination and detection systems have superior performance compared to existing devices.
FTIR spectroscopy: A tool for quantitative analysis of ciprofloxacin in tablets (2012)

A simple, accurate and sensitive spectroscopic method has been proposed for the assay of ciprofloxacin in tablet by least square treatment of fourier transform infrared spectrometric data obtained at the wavenumber corresponding to the carbonyl group centered at 1707 cm(-1). The method involves the extraction of the active ingredient with methanol followed by phosphate buffer pH 6.0. The excipients in the commercial tablet preparation did not interfere with the assay. The specifity, linearity, detection limits, precision and accuracy of the calibration curve, drug extraction, infrared analysis and data manipulation were determined in order to validate the method. Moreover, the statistical results were compared with other methods for quantification of ciprofloxacin.
Immunotherapeutic strategies in neuroblastoma: Antitumoral activity of deglycosylated ricin A conjugated anti-GD2 antibodies and anti-CD3xanti-GD2 bispecific antibodies (2001)

We envisage a combined immunotherapeutic regimen consisting of BW704dgA mediated stem cell purging, followed by a systemic treatment with anti-CD3xanti-GD2 bispecific antibodies in neuroblastoma.
Satellite-DMB applied to the 8PSK hierarchical modulation (2007)

Satellite digital multimedia broadcasting (S-DMB) system is a service for private users with characteristics of personal concept that broadcasting service is taken by the mobile phone or terminals of vehicle anytime and anywhere. We need to modify the modulation scheme in order to increase more transmission capacity and maintain the channel bandwidth. In this paper we present the primary S-DMB system and the transmission schemes for backward compatibility (BC) mode that exploits the hierarchical modulation to improve the channel capacity and maintain performance of the currently deployed system. And we propose the new total S-DMB system block diagram and channel coding for efficient performance of BC mode and analyze the log likelihood ratio (LLR) algorithm for demapping of the hierarchical modulation of BC-8PSK.
Isolation and culture of human endometrial cells in a three-dimensional culture system (1994)

A cell culture system was established in which endometrial stromal cells were embedded in a collagen matrix and separated from the endometrial epithelium by basement membrane material (Matrigel). The epithelium, seeded on top of the collagen matrix, grew in a monolayer. The cultures were evaluated by light microscopy and transmission and scanning electron microscopy. Light and transmission electron microscopy indicated a polarized columnar epithelium in monolayer with basally positioned nuclei. Scanning electron microscopy revealed a confluent epithelium with an abundance of microvilli and cilia, as well as pinopodes on the apical surface. Immunohistochemical staining for cytokeratin confirmed the epithelial origin of the surface cells, and staining for human collagen IV demonstrated its presence underneath the epithelial cells. This culture system represents a three-dimensional system that imitates the normal endometrium.
Flipping of cloned d(pCpG)n.d(pCpG)n DNA sequences from right- to left-handed helical structure by salt, Co(III), or negative supercoiling. (1982)

Negative supercoiling of plasmid DNAs containing 24--42 base pairs of alternating d(pCpG) inserts is shown to cause the flipping of the helical hand of the inserts from right to left under physiological conditions. For a negatively supercoiled DNA with a fixed linking number, this flipping reduces its superhelicity and, therefore, is accompanied by a shift of its electrophoretic mobility in agarose gel. Quantitation of the mobility shifts indicates that essentially the whole stretch of contiguous alternating d(pCpG) flips to the left-handed helical form when the negative superhelical density (specific linking difference) is greatest than or equal to 0.03.
Molecular evolution of breast cancer (2005)

Molecular analysis of invasive breast cancer and its precursors has furthered our understanding of breast cancer progression. In the past few years, new multi-step pathways of breast cancer progression have been delineated through genotypic-phenotypic correlations. Nuclear grade, more than any other pathological feature, is strongly associated with the number and pattern of molecular genetic abnormalities in breast cancer cells. Thus, there are two distinct major pathways to the evolution of low- and high-grade invasive carcinomas: whilst the former consistently show oestrogen receptor (ER) and progesterone receptor (PgR) positivity and 16q loss, the latter are usually ER/PgR-negative and show Her-2 overexpression/amplification and complex karyotypes. The boundaries between the evolutionary pathways of well-differentiated/low-grade ductal and lobular carcinomas have been blurred, with changes in E-cadherin expression being one of the few distinguishing features between the two. In addition, lesions long thought to be precursors of breast carcinomas, such as hyperplasia of usual type, are currently considered mere risk indicators, whilst columnar cell lesions are now implicated as non-obligate precursors of atypical ductal hyperplasia (ADH) and well-differentiated ductal carcinoma in situ (DCIS). However, only through the combination of comprehensive morphological analysis and cutting-edge molecular tools can this knowledge be translated into clinical practice and patient management.
Enhancement of retrovirus production by anti-interferon serum. (1979)

In order to investigate the role of endogenous interferon in retrovirus production by infected or induced cells, the effect of two sera raised against mouse interferon has been tested on various C-type murine viruses. Addition of a highly potent anti-interferon serum to 3T3/IC cells chronically infected by the Moloney strain of MLV results in a considerable increase of virus production, as tested by reverse transcriptase assay. This effect is neutralized by an excess of exogenous interferon. The greatest effect of anti-interferon sera was obtained in the derepression of endogenous retroviruses: in K. BALB/c cells treated by IUDR, anti-interferon serum increases up to 50-fold the expression of the endogenous virus. The extinction of virus production which secondarily occurs after its induction by IUdR is likely to be caused by cellular endogenous interferon. The biological parameters of the viral agent produced in the presence of anti-interferon serum are those of the xenotropic endogenous virus.
DySER: Unifying Functionality and Parallelism Specialization for Energy-Efficient Computing (2012)

The DySER (Dynamically Specializing Execution Resources) architecture supports both functionality specialization and parallelism specialization. By dynamically specializing frequently executing regions and applying parallelism mechanisms, DySER provides efficient functionality and parallelism specialization. It outperforms an out-of-order CPU, Streaming SIMD Extensions (SSE) acceleration, and GPU acceleration while consuming less energy. The full-system field-programmable gate array (FPGA) prototype of DySER integrated into OpenSparc demonstrates a practical implementation.
Idiotypic protein-pulsed adherent peripheral blood mononuclear cell-derived dendritic cells prime immune system in multiple myeloma. (1998)

Adherent peripheral blood mononuclear cell-derived dendritic cells pulsed with autologous idiotypic protein (Id) were given to a patient with advanced-stage refractory myeloma. Potentially beneficial antimyeloma Id-specific immune responses were produced, characterized by MHC-dependent T-cell-proliferative responses with cytokine release and the production of anti-Id antibodies. A T-cell line generated after vaccination was also able to lyse autologous Id-pulsed targets and recognize fresh autologous myeloma cells. The immune responses were associated with a transient minor fall in the serum Id level and were not ablated by high-dose myeloablative chemotherapy. This report therefore demonstrates the clinical use of adherent peripheral blood mononuclear cell-derived dendritic cells for vaccination in cancer and the persistence of immune responses after high-dose chemotherapy. Such a therapeutic approach may be useful in reducing the relapse rate in patients who have minimal residual disease after chemotherapy.
Pigment epithelium-derived factor suppresses ischemia-induced retinal neovascularization and VEGF-induced migration and growth. (2002)

These data indicate that elevated concentrations of PEDF inhibit VEGF-induced retinal endothelial cell growth and migration and retinal neovascularization. These findings suggest that localized administration of PEDF may be an effective approach for the treatment of ischemia-induced retinal neovascular disorders.
FD, a bZIP Protein Mediating Signals from the Floral Pathway Integrator FT at the Shoot Apex (2005)

FLOWERING LOCUS T (FT) is a conserved promoter of flowering that acts downstream of various regulatory pathways, including one that mediates photoperiodic induction through CONSTANS (CO), and is expressed in the vasculature of cotyledons and leaves. A bZIP transcription factor, FD, preferentially expressed in the shoot apex is required for FT to promote flowering. FD and FT are interdependent partners through protein interaction and act at the shoot apex to promote floral transition and to initiate floral development through transcriptional activation of a floral meristem identity gene, APETALA1 (AP1). FT may represent a long-distance signal in flowering.
Significance of serum amyloid a on the prognosis in patients with renal cell carcinoma (2001)

Evaluation of serum SM level in RCC patients may be a useful prognostic indicator.
M13 bacteriophage vectors for the expression of foreign proteins in Escherichia coli: the rabies glycoprotein. (1984)

The expression of a protein-coding DNA fragment in a microorganism such as Escherichia coli requires that the exogenous DNA segment be inserted precisely in phase with bacterial translation initiation signals. We report the construction of derivatives of the M13 vectors M13mp7 and M13mp701 in which a HindIII site has been inserted, within the N-terminal section of the beta-galactosidase gene, in all three phases of translation. These vectors may thus be used for the expression, under the control of the lac promoter and translation initiation signals, of protein coding DNA segments flanked by a HindIII site. In all cases the insertion of a DNA fragment can be recognized by the abolition of beta-galactosidase activity. These vectors have been used to direct the expression, in E. coli, of a cDNA segment coding for the rabies virus surface glycoprotein. The proteins produced have been shown to react with antisera raised against authentic rabies glycoprotein.
A novel cell ablation strategy blocks tobacco anther dehiscence. (1997)

We utilized a new cell ablation strategy to ablate specific anther cell types involved in the dehiscence process. The tobacco TA56 gene promoter is active within the circular cell cluster, stomium, and connective regions of the anther at different developmental stages. We introduced a cytotoxic TA56/barnase gene into tobacco plants together with three different anticytotoxic barstar genes. The anticytotoxic barstar genes were used to protect subsets of anther cell types from the cytotoxic effects of the TA56/barnase gene. The chimeric barstar genes were fused with (1) the tobacco TP12 gene promoter that is active at high levels in most anther cell types; (2) the soybean lectin gene promoter that is active earlier in the connective, and at lower levels in the circular cell cluster and stomium, than is the TA56 promoter; and (3) the tobacco TA20 gene promoter that is active at high levels in most anther cell types but has a different developmental profile than does the TP12 promoter. Normal anther development and dehiscence occurred in plants containing the TA56/barnase and TP12/barstar genes, indicating that barstar protects diverse anther cell types from the cytotoxic effects of barnase. Anthers containing the TA56/barnase and lectin/barstar genes also developed normally but failed to dehisce because of extensive ablation of the circular cell cluster, stomium, and contiguous connective regions. Anthers containing the TA56/barnase and TA20/barstar genes failed to dehisce as well. However, only the stomium region was ablated in these anthers. The connective, circular cell cluster, and adjacent wall regions were protected from ablation by the formation of barnase/barstar complexes. We conclude that anther dehiscence at flower opening depends on the presence of a functional stomium region and that chimeric barnase and barstar genes containing promoters that are active in several overlapping cell types can be used for targeted cell ablation experiments.
Biology of Immune Responses to Vaccines in Elderly Persons (2008)

With increasing age, the human immune system undergoes characteristic changes, termed immunosenescence, which lead to increased incidence and severity of infectious diseases and to insufficient protection following vaccination. Functional defects and altered frequencies of innate and adaptive immune cells impair local responses at the site of vaccine injection, hamper the generation of primary responses to neoantigens, prevent the effective induction of memory lymphocytes, and decrease the effect of booster vaccination. As a result, antibody responses of elderly vaccinees are weaker and decline faster, and long-term protective effects of vaccination cannot be taken for granted in elderly persons. Improved vaccination strategies, new adjuvants, and new vaccines that specifically target the aged immune system will help to overcome the limitations of immunosenescence and ensure a better protection of the vulnerable elderly population.
Plasma Levels of Tumor Necrosis Factor in the Adult Respiratory Distress Syndrome (1991)

The purpose of the study was to evaluate the role of tumor necrosis factor alpha (TNF alpha) in the pathogenesis of acute lung injury in critically ill patients. An immunoradiometric assay with an upper normal limit of 9 pg/ml was used to measure plasma TNF alpha levels (pl-TNF alpha) in 34 patients with adult respiratory distress syndrome (ARDS) and in 16 patients in whom, despite the presence of risk factors, ARDS did not develop. Pl-TNF alpha was elevated in 76% of the patients with ARDS (71 +/- 104 pg/ml) and in 48% of the at-risk patients (47 +/- 73 pg/ml); the difference between the two groups was not statistically significant. In 13 patients studied serially from the onset (Day 0) to the fifth day of ARDS, the peak pl-TNF alpha occurred later than Day 0 in seven subjects. Although the highest pl-TNF alpha levels were found in septic patients, moderately elevated values were also observed in 56% of nonseptic subjects. We conclude that plasma TNF alpha level is not a marker of ARDS but rather of shock and sepsis. These results do not exclude a pathogenic role of TNF alpha in acute lung injury since this cytokine could be produced and exert its effects within the lungs. The large incidence of abnormally high could be produced and exert its effects within the lungs. The large incidence of abnormally high plasma TNF alpha levels raises important questions on the role of this toxic cytokine in other disorders occurring in critically ill patients.
Effect of stage of disease and drug dose on zidovudine susceptibilities of isolates of human immunodeficiency virus. (1990)

Ninety-seven isolates of human immunodeficiency virus (HIV) from 73 individuals were assayed for susceptibility to zidovudine (AZT). All isolates from 41 individuals with no known therapy with zidovudine were uniformly susceptible to the drug in vitro. In contrast to isolates from subjects with AIDS or AIDS-related complex, isolates from subjects with fewer signs and symptoms or high CD4 lymphocyte counts developed reduced susceptibility at slower rates and lower levels of resistance. Patients receiving lower doses of zidovudine at both early and late stages of disease did not develop resistance more readily than patients receiving higher doses of drug.
Etiology of Ibrutinib Therapy Discontinuation and Outcomes in Patients With Chronic Lymphocytic Leukemia (2015)

clinicaltrials.gov Identifiers:NCT01105247, NCT01217749, NCT01589302, and NCT01578707.
Practical image registration concerns overcome by the weighted and filtered mutual information metric (2012)

Contemporary research in automated panorama creation utilizes camera calibration or extensive knowledge of camera locations and relations to each other to achieve successful results. Research in image registration attempts to restrict these same camera parameters or apply complex point-matching schemes to overcome the complications found in real-world scenarios. This paper presents a novel automated panorama creation algorithm by developing an affine transformation search based on maximized mutual information (MMI) for region-based registration. Standard MMI techniques have been limited to applications with airborne/satellite imagery or medical images. We show that a novel MMI algorithm can approximate an accurate registration between views of realistic scenes of varying depth distortion. The proposed algorithm has been developed using stationary, color, surveillance video data for a scenario with no a priori camera-to-camera parameters. This algorithm is robust for strict- and nearly-affine-related scenes, while providing a useful approximation for the overlap regions in scenes related by a projective homography or a more complex transformation, allowing for a set of efficient and accurate initial conditions for pixel-based registration.