gebhart/patrepeval huggingface dataset:
Telomerase Expression in Noncancerous Bronchial Epithelia Is a Possible Marker of Early Development of Lung Cancer (2005)

Abstract Centrally located lung cancers in smokers frequently associated with subsequent primary tumors. We evaluated the telomerase expression chronologically in noncancerous epithelia as a risk factor of susceptibility to lung cancer development. Telomerase protein expression was examined in situ by immunohistochemistry in 26 noncancerous bronchial epithelia adjacent to centrally located early-stage lung cancers in sequential 23 patients treated by photodynamic therapy or surgery among 206 patients who underwent autofluorescence bronchoscopy from 1997 to 2003. Among the 15 lesions in 12 patients treated by photodynamic therapy alone, 11 lesions achieved complete remission after photodynamic therapy, and none of their noncancerous bronchial epithelia was telomerase positive. On the contrary, in the remaining four lesions, either recurrence or secondary lung cancer developed adjacent to the successfully treated primary cancer within 26 months, and the telomerase protein expression in noncancerous epithelia was detected before the secondary cancer development (P &amp;lt; 0.001). The overall relationship of human telomerase reverse transcriptase positivity in noncancerous epithelia and subsequent lung cancer development, including patients treated by radiation or surgery, showed higher significance (P &amp;lt; 0.0001). Histologically “normal” bronchial epithelia in smokers may unphysiologically express telomerase as a field, and such epithelia are likely susceptible to develop lung cancer. We propose that ectopic expression of telomerase in bronchial epithelia may precede transformation in human lung cancer development and that detection of telomerase protein in noncancerous bronchial epithelia will become a useful marker detecting high-risk patients for lung cancer development.
Cloning, sequence, and expression of bovine interleukin 2. (1986)

Interleukin 2 (IL-2) cDNA clones have been isolated from both human and murine sources. We report here the isolation of a cDNA clone encoding bovine IL-2. This was accomplished by screening a cDNA library constructed from lectin-stimulated bovine lymph node cells, using a human IL-2 probe. Bovine IL-2 is composed of 155 amino acids and has a predicted molecular weight of 19,555. Alignment of the amino acid sequence with human IL-2 indicates that mature bovine IL-2 is composed of 135 amino acids and has a predicted molecular weight of 15,452. It has an amino acid homology of 65% with human IL-2 and 50% with murine IL-2. Bovine IL-2 is unique among IL-2 homologs in that it has a single N-linked glycosylation site. Biologically active bovine IL-2 was synthesized in an Escherichia coli expression system.
Advances in the virology of HIV infections and implications for clinical management. (1998)

Recent advances have been made in basic science that have led to a better understanding of the mechanisms of HIV infection, particularly the dynamics and kinetics of in vivo viral replication and the emergence of drug resistance. Advances pertaining to HIV eradication, the virologic response to antiretroviral therapy, and resistance to antiretroviral drugs are reviewed. Clinical implications from these advances indicate that while the optimum time to initiate antiretroviral therapy is still uncertain, once begun, the therapy should be maximally suppressive to limit the potential of resistant variants. Also, a change to a salvage regimen should be considered when virus levels rise to values approaching 500 copies/ml. Strategies for long-term control of viral replication are currently being tested.
Purification and Properties of L-Citramalate Hydrolyase (1969)

Citramalate(3) was prepared by the enzymic method of Barker and Blair (4), D-(-)-citramalate
The entanglement fidelity and quantum error correction (1996)

Two new expressions for the entanglement fidelity recently introduced by Schumacher (LANL e-print quant-ph/9604023, to appear in Phys. Rev. A) are derived. These expressions show that it is the entanglement fidelity which must be maximized when performing error correction on qubits for quantum computers, not the fidelity, which is the most-often used generalization of the probability for storing a qubit correctly.
Silicon-on-Insulator microring resonator for sensitive and label-free biosensing (2007)

Label-free biosensors attempt to overcome the stability and reliability problems of biosensors relying on the detection of labeled molecules. We propose a label-free biosensor based on microring cavities in Silicon-on-Insulator (SOI) that fits in an area below 10x10mum(2). The resonance wavelength shift that occurs when the surroundings of a cavity is changed, is used for sensing. While theoretically the performance for bulk refractive index changes is moderate (10(-5)), this device performs outstanding in terms of absolute molecular mass sensing (theoretical sensitivity of 1fg molecular mass) thanks to its extremely small dimensions. We use the avidin/biotin high affinity couple to demonstrate good repeatability and detection of protein concentrations down to 10ng/ml. Fabrication with Deep UV lithography allows for cheap mass production and integration with electronic functions for complete lab-on-chip devices.
Paint by numbers: abstract image representations (1990)

Computer graphics research has concentrated on creating photo-realistic images of synthetic objects. These images communicate surface shading and curvature, as well as the depth relationships of objects in a scene. These renderings are traditionally represented by a rectangular array of pixels that tile the image plane.As an alternative to photo-realism, it is possible to create abstract images using an ordered collection of brush strokes. These abstract images filter and refine visual information before it is presented to the viewer. By controlling the color, shape, size, and orientation of individual brush strokes, impressionistic paintings of computer generated or photographic images can easily be created.
Gene Therapy for B-cell Lymphoma in a SCID Mouse Model using an Immunoglobulin-Regulated Diphtheria Toxin Gene Delivered by a Novel Adenovirus-Polylysine Conjugate (1994)

Despite advances in conventional therapy, many lives continue to be lost to common forms of B-cell cancers, including leukemias, lymphomas and multiple myeloma. We propose a novel approach to therapy of such cancers using controlled expression of a diphtheria toxin gene (DT-A) to kill malignant cells. We have previously demonstrated selective killing of various cell types, in vitro and in vivo, by cell-specific, transcriptionally controlled expression of this gene. Organ-specific ablation in otherwise healthy transgenic mice has convincingly demonstrated the exquisite specificity achievable by this technique. In the studies now described, DT-A was delivered in vitro and in vivo using a novel gene delivery system employing DNA physically attached to the exterior of adenovirus. After demonstrating the efficacy of gene delivery to Epstein-Barr virus transformed human B-cells in vitro, in vivo work was performed using a SCID mouse model for B-cell lymphoma, in which protection against tumor was observed. The concepts of tissue-regulated toxin gene therapy, and this novel adenovirus gene delivery system are discussed.
Central Anticholinergic Syndrome with the Antimalarial Drug Mefloquine (1994)

To the Editor: The neuropsychiatric side effects of the antimalarial drug mefloquine are well documented1,2. They include anxiety, depression, hallucinations, acute psychosis, and seizures. The incidence of these side effects is 1 in 13,000 with prophylactic use and 1 in 250 with therapeutic use2. The mechanism of action is unknown1. A 47-year-old, previously healthy Japanese tourist was admitted to our hospital because of severe falciparum malaria with parasitemia of 24 percent after a trip to Zaire without any antimalarial chemoprophylaxis. Treatment consisted of 750 mg of quinine per day and 450 mg of clindamycin three times . . .
Bromodomain brake on AML (2011)

A Cold Spring Harbor–led team has used a bromodomain inhibitor to treat acute myeloid leukemia in mice, greatly expanding the therapeutic potential for this emerging drug class. Tensha Therapeutics has licensed the findings and hopes to bring a compound into Phase I trials within two years.
FIX-Triple, a gain-of-function factor IX variant, improves haemostasis in mouse models without increased risk of thrombosis (2010)

Engineered recombinant factor IX (FIX) with augmented clotting activity may prove useful for replacement therapy, but it has not been studied for risk of thrombosis. We used three mouse models to evaluate thrombosis risk associated with the FIX variant FIX-Triple, which has a 13-fold higher specific activity than wild-type FIX (FIX-WT). Protein infusion of FIX-Triple into haemophilia B mice was not thrombogenic, even at a dose of 13-fold higher than FIX-WT. Gene knock-in to generate mice that constitutively produce FIX-WT or FIX-Triple protein revealed that all mice expressed equal antigen levels. FIX-Triple knock-in mice that exhibited 10-fold higher FIX clotting activity did not show hypercoagulation. Adeno-associated viral (AAV) delivery of the FIX gene into mice was used to mimic gene therapy. Haemophilia B and inbred C57Bl/6 mice injected with different doses of virus particles carrying FIX-WT or FIX-Triple and expressing up to a nearly 13-fold excess (1289% of normal) of FIX clotting activity did not show increased risk of thrombosis compared with untreated wild-type mice in a normal haemostatic state. When challenged with ferric chloride (FeCl3), the mesenteric venules of AAV-treated C57Bl/6 mice that gave a nearly five-fold excess (474%) of FIX clotting activity were not thrombotic; however, thrombosis became obvious in FeCl3-challenged mice expressing extremely high FIX clotting activities (976-1289%) achieved by AAV delivery of FIX-Triple. These studies suggest that FIX-Triple is not thrombogenic at therapeutic levels and is a potential therapeutic substitute for FIX-WT.
Epithelial-Mesenchymal Transition: NF-&kappa;B Takes Center Stage (2004)

Activation of the transcription factor NF-kappaB occurs in many human tumors, and studies have shown that NF-kappaB can promote cell proliferation and oncogenesis, possibly by protecting cells from apoptosis. Little is known, however, about whether NF-kappaB is involved in tumor progression including epithelial-mesenchymal transition (EMT), a central process governing both morphogenesis and carcinoma progression in multicellular organisms. In a combined in vitro/in vivo model of mammary carcinogenesis, NF-kappaB was essential both for the induction and maintenance of EMT and for in vivo metastasis. NF-kappaB and the signaling pathways that are involved in its activation should therefore receive attention as potential targets for the development of novel anti-metastatic cancer treatments.
Multilocus Sequence Typing and Phylogenetic Analysis of Propionibacterium acnes (2012)

Propionibacterium acnes is a commensal of human skin but is also implicated in the pathogenesis of acne vulgaris, in biofilm-associated infections of medical devices and endophthalmitis, and in infections of bone and dental root canals. Recent studies associate P. acnes with prostate cancer. As the species includes evolutionary lineages with distinct association with health and disease, there is a need for a high-resolution typing scheme. Recently, two multilocus sequence typing (MLST) schemes were reported, one based on nine and one based on seven housekeeping genes. In the present study, the two schemes were compared with reference to a phylogenetic tree based on 78 P. acnes genomes and their gene contents. Further support for a basically clonal population structure of P. acnes and a scenario of the global spread of epidemic clones of P. acnes was obtained. Compared to the Belfast scheme, the Aarhus MLST scheme (http://pacnes.mlst.net/), which is based on nine genes, offers significantly enhanced resolution and phylogenetic inferences more concordant with analyses based on a comprehensive sampling of the entire genomes, their gene contents, and their putative pathogenic potential.
Benchmarking of commercially available CHO cell culture media for antibody production (2013)

Publikationsserver. Reinhart, David; Kaisermayer, Christian; Damjanovic, Lukas; Kunert, Renate: Benchmarking of commercially available CHO cell culture media for antibody production. In: BMC Proceedings. BioMed Central (BMC), 2013
Motion-aware temporal coherence for video resizing (2009)

Temporal coherence is crucial in content-aware video retargeting. To date, this problem has been addressed by constraining temporally adjacent pixels to be transformed coherently. However, due to the motion-oblivious nature of this simple constraint, the retargeted videos often exhibit flickering or waving artifacts, especially when significant camera or object motions are involved. Since the feature correspondence across frames varies spatially with both camera and object motion, motion-aware treatment of features is required for video resizing. This motivated us to align consecutive frames by estimating interframe camera motion and to constrain relative positions in the aligned frames. To preserve object motion, we detect distinct moving areas of objects across multiple frames and constrain each of them to be resized consistently. We build a complete video resizing framework by incorporating our motion-aware constraints with an adaptation of the scale-and-stretch optimization recently proposed by Wang and colleagues. Our streaming implementation of the framework allows efficient resizing of long video sequences with low memory cost. Experiments demonstrate that our method produces spatiotemporally coherent retargeting results even for challenging examples with complex camera and object motion, which are difficult to handle with previous techniques.
Static Leakage Reduction through Simulteneous VTT/TOX and State Assignment (2005)

Standby leakage current minimization is a pressing concern for mobile applications that rely on standby modes to extend battery life. In this paper, we propose new leakage current reduction methods in standby mode. First, we propose a combined approach of sleep-state assignment and threshold voltage (V t ) assignment in a dual-V t process for subthreshold leakage (I sub ) reduction. Second, for the minimization of gate oxide leakage current (I gate ) which has become comparable to I sub in 90nm technologies, we extend the above method to a combined sleep-state, V t and gate oxide thickness (T ox ) assignments approach in a dual-V t and dual-T ox process to minimize both I sub and I gate . By combining V t or V t /T ox assignment with sleep-state assignment, leakage current can be dramatically reduced since the circuit is in a known state in standby mode and only certain transistors are responsible for leakage current and need to be considered for high-V t or thick-T ox assignment. A significant improvement in the leakage/performance trade-off is therefore achievable using such combined methods. We formulate the optimization problem for simultaneous state/V t and state/V t /T ox assignments under delay constraints and propose both an exact method for its optimal solution as well as two practical heuristics with reasonable run time. We implemented and tested the proposed methods on a set of synthesized benchmark circuits and show substantial leakage current reduction compared to the previous approaches using only state assignment or V t assignment alone.
Highly avid magnetic bead capture: An efficient selection method for de novo protein engineering utilizing yeast surface display (2009)

Protein engineering relies on the selective capture of members of a protein library with desired properties. Yeast surface display technology routinely enables as much as million-fold improvements in binding affinity by alternating rounds of diversification and flow cytometry-based selection. However, flow cytometry is not well suited for isolating de novo binding clones from naïve libraries due to limitations in the size of the population that can be analyzed, the minimum binding affinity of clones that can be reliably captured, the amount of target antigen required, and the likelihood of capturing artifactual binders to the reagents. Here, we demonstrate a method for capturing rare clones that maintains the advantages of yeast as the expression host, while avoiding the disadvantages of FACS in isolating de novo binders from naïve libraries. The multivalency of yeast surface display is intentionally coupled with multivalent target presentation on magnetic beads-allowing isolation of extremely weak binders from billions of non-binding clones, and requiring far less target antigen for each selection, while minimizing the likelihood of isolating undesirable alternative solutions to the selective pressure. Multivalent surface selection allows 30,000-fold enrichment and almost quantitative capture of micromolar binders in a single pass using less than one microgram of target antigen. We further validate the robust nature of this selection method by isolation of de novo binders against lysozyme as well as its utility in negative selections by isolating binders to streptavidin-biotin that do not cross-react to streptavidin alone.
Characterization of a complementary deoxyribonucleic acid coding for the .gamma. chain of human fibrinogen (1983)

A number of cDNAs coding for the gamma chain of human fibrinogen have been isolated from a liver cDNA library by employing a synthetic nucleotide mixture as a probe. One of the positive clones was then employed to screen the entire cDNA library of 18000 recombinants, yielding 320 positive clones for the gamma chain. The largest cDNA was 1638 base pairs in length and contained 10 base pairs of poly(G) at the 5'-end followed by 71 base pairs of noncoding nucleotides. The next 78 base pairs coded for a leader sequence that was 26 amino acids in length and included a methionine start signal and a typical hydrophobic core. The following 1233 base pairs coded for 411 amino acids that are present in the mature protein followed by a stop codon of TAA, 207 base pairs of noncoding nucleotides, a poly(A) track of 15 base pairs, and 22 base pairs of poly(C). Specific regions of the cDNA of the gamma chain were then compared with the cDNAs for the alpha and beta chains of human fibrinogen.
Exon amplification from complete libraries of genomic DNA using a novel phage vector with automatic plasmid excision facility: application to the mouse neurofibromatosis-1 locus. (1994)

The identification of transcription units in the vicinity of chromosomal lesions found in tumours is an essential step in the identification of new oncogenes. Here, we describe a lambda phage vector system for genomic exon-trapping (lambda GET), which dramatically simplifies the task of exon amplification from genomic DNA. The vector accommodates about 6.5 to 19 kb of DNA and allows inserts to be automatically subcloned as multi-copy plasmids containing splice donor and acceptor sites positioned flanking the inserted genomic DNA. RNA transcripts derived from such plasmids are processed in vivo and exons contained within the inserted genomic fragments become flanked by known sequences in the resulting mRNAs. RNA-based PCR can then be used for subsequent cloning and sequence analysis of trapped exons. We have exploited the large cloning capacity of lambda GET to construct highly redundant complete genomic libraries from Sau3AI partially digested vertebrae DNAs. Using this system, we have analysed a region of about 1 MB around the mouse neurofibromatosis-1 locus and have identified novel transcription units flanking the Nf-1 gene.
In vivo activation of naive T cells by antigen-presenting B cells. (1994)

In vivo experiments were performed to determine if the cross-linking of mlg on antigen-presenting B cells could induce them to present Ag to naive T cells in a stimulatory rather than a tolerogenic fashion. Mice were injected with a foreign mAb to a B cell Ag (Fc epsilon RII or CR1), and/or a self-anti-IgD mAb. Injection of either mAb alone failed to induce an Ab response; however, simultaneous injection of the foreign anti-B cell mAb plus the self-anti-IgD mAb stimulated a large response. Inasmuch as injection of the anti-IgD mAb should not have facilitated transfer of the foreign mAb to dendritic cells, this observation suggests that cross-linking of B cell mlg can induce B cells to acquire the ability to present Ag to naive T cells in an activating manner. Furthermore, when injected with anti-IgD mAb, both foreign anti-B cell mAbs were more potent in inducing Ab responses in this system than were isotype-matched control mAbs, consistent with the hypothesis that T cells were activated by Ag-presenting B cells. Results of dose-response and cell transfer studies, however, suggested that stringent cross-linking of B cell mlg on large numbers of B cells is required for B cell Ag presentation to induce T cell activation rather than tolerance. Therefore, these observations suggest that professional APCs usually are required to activate naive T cells, and that B cell Ag presentation can only activate naive T cells under unusual circumstances.
Razor: a low-power pipeline based on circuit-level timing speculation (2003)

With increasing clock frequencies and silicon integration, power aware computing has become a critical concern in the design of embedded processors and systems-on-chip. One of the more effective and widely used methods for power-aware computing is dynamic voltage scaling (DVS). In order to obtain the maximum power savings from DVS, it is essential to scale the supply voltage as low as possible while ensuring correct operation of the processor. The critical voltage is chosen such that under a worst-case scenario of process and environmental variations, the processor always operates correctly. However, this approach leads to a very conservative supply voltage since such a worst-case combination of different variabilities is very rare. In this paper, we propose a new approach to DVS, called Razor, based on dynamic detection and correction of circuit timing errors. The key idea of Razor is to tune the supply voltage by monitoring the error rate during circuit operation, thereby eliminating the need for voltage margins and exploiting the data dependence of circuit delay. A Razor flip-flop is introduced that double-samples pipeline stage values, once with a fast clock and again with a time-borrowing delayed clock. A metastability-tolerant comparator then validates latch values sampled with the fast clock. In the event of timing error, a modified pipeline mispeculation recovery mechanism restores correct program state. A prototype Razor pipeline was designed in a 0.18 /spl mu/m technology and was analyzed. Razor energy overhead during normal operation is limited to 3.1%. Analyses of a full-custom multiplier and a SPICE-level Kogge-Stone adder model reveal that substantial energy savings are possible for these devices (up to 64.2%) with little impact on performance due to error recovery (less than 3%).