gebhart/patrepeval huggingface dataset:
Fast, on-line failure recovery in redundant disk arrays (2002)

The authors describe and evaluate two algorithms for performing online failure recovery (data reconstruction) in redundant disk arrays. An implementation of disk-oriented reconstruction, a data recovery algorithm that allows the reconstruction process to absorb essentially all the disk bandwidth not consumed by the user processes, is presented, and this algorithm is compared to a previous-proposed parallel stripe-oriented approach. The disk-oriented approach yields better overall failure-recovery performance. Performance is evaluated via detailed simulation on two different disk array architectures: the RAID level five organization and the declustered parity organization. The benefits of the disk-oriented algorithm can be achieved using controller or host buffer memory no larger than the size of three disk tracks per disk in the array. The tradeoffs involved in selecting the size of the disk accesses used by the failure recovery process are also investigated.
Efficacy of type-specific and cross-reactive murine monoclonal antibodies directed against endotoxin during experimental sepsis. (1985)

To study the role of antibodies in promoting survival during gram-negative bacterial sepsis, we have developed several murine monoclonal antibodies (MAbs). One MAb (5B10) reacted in an enzyme-linked immunosorbent assay with only a single organism (Escherichia coli 0111:B4), while the other (8A1) reacted to all gram-negative whole-cell and lipopolysaccharide (LPS) antigens examined. Either 5B10 MAb, 8A1 MAb, or sterile saline solution was administered intravenously to outbred male Swiss-Webster mice immediately before one of three challenges: (1) viable bacteria intravenously, (2) viable bacteria with hemoglobin intraperitoneally, or (3) intravenous actinomycin D plus LPS. 5B10 MAb provided significant protection against either an E. coli 0111:B4 bacterial or LPS challenge but not against any other organism or type of LPS. 8A1 MAb provided protection against several challenge bacteria (intravenously or intraperitoneally) and against all types of LPS studied except Pseudomonas aeruginosa LPS. A higher dose (2 mg) of cross-reactive antibody (8A1 MAb) was required to produce protection when compared with the type-specific protection produced with 5B10 MAb (0.1 mg). Although ideal antibody therapy would consist of directing a specific MAb against a single microorganism, the acute nature of the disease process and time required to prepare reagents may preclude the use of type-specific MAbs. We believe that the cross-reactive and cross-protective capacity of 8A1 MAb or a similar MAb may be useful in averting the lethal effects of clinical gram-negative bacterial sepsis and warrants testing in the clinical setting.
Dissociation between steroid receptor expression and cell proliferation in the human breast. (1997)

We have shown previously that estradiol stimulates cell proliferation and progesterone receptor (PgR) synthesis in luminal epithelial cells of the normal human breast. Approximately 10-15% of luminal epithelial cells within the normal breast express immunodetectable estrogen receptor (ER), but little is known about their distribution within lobules and their organization in relation to the smaller population of proliferating cells. Using normal human breast tissue, we show that ER-positive cells are distributed evenly throughout the mammary epithelium. Using double antibody immunofluorescence, we show that 96% of steroid receptor-positive cells synthesize both ER and PgR (n = 25). Double labeling with antibodies to either ER or PgR coupled with either [3H]thymidine histoautoradiography or with antibodies to the Ki67 proliferation antigen indicates that dividing cells are separate from those expressing the receptors (although they are often in close proximity). However, in contrast to the normal human breast, two-thirds of ER-positive human mammary tumors examined (n = 19) have a high proportion of dividing cells that are ER positive. These data are consistent with the hypothesis that cells in normal human breast epithelium are hierarchical in organization and support a model in which proliferation of ER-negative cells is controlled by paracrine factors released from ER-positive cells under the influence of estradiol. This organization may be disrupted in some tumors.
Modular and rapid testing of SOCs with unwrapped logic blocks (2005)

Extensive research has been carried out for test planning of core-based system-on-a-chip devices. Most of the prior work assumes that all of the embedded cores are wrapped for test purpose. However, some designs may contain user-defined logic or cores that cannot be wrapped due to area constraints or timing violations. This paper discusses how these unwrapped logic blocks can be tested rapidly by adapting the TestRail architecture, which uses only the test control mechanism and the test instructions available through the IEEE 1500 standard for embedded core test. A new test scheduling algorithm, which facilitates a concurrent test of both unwrapped logic blocks and IEEE 1500-wrapped cores, is proposed, and experiments show that it outperforms a previous approach when the available number of tester channels and/or the number of unwrapped logic blocks are small.
Applications of microbial cytochrome P450 enzymes in biotechnology and synthetic biology (2016)

Cytochrome P450 enzymes (P450s) are a superfamily of monooxygenase enzymes with enormous potential for synthetic biology applications. Across Nature, their substrate range is vast and exceeds that of other enzymes. The range of different chemical transformations performed by P450s is also substantial, and continues to expand through interrogation of the properties of novel P450s and by protein engineering studies. The ability of P450s to introduce oxygen atoms at specific positions on complex molecules makes these enzymes particularly valuable for applications in synthetic biology. This review focuses on the enzymatic properties and reaction mechanisms of P450 enzymes, and on recent studies that highlight their broad applications in the production of oxychemicals. For selected soluble bacterial P450s (notably the high-activity P450-cytochrome P450 reductase enzyme P450 BM3), variants with a multitude of diverse substrate selectivities have been generated both rationally and by random mutagenesis/directed evolution approaches. This highlights the robustness and malleability of the P450 fold, and the capacity of these biocatalysts to oxidise a wide range of chemical scaffolds. This article reviews recent research on the application of wild-type and engineered P450s in the production of important chemicals, including pharmaceuticals and drug metabolites, steroids and antibiotics. In addition, the properties of unusual members of the P450 superfamily that do not follow the canonical P450 catalytic pathway are described.
Review—Superconcentrated Electrolytes for Lithium Batteries (2015)

Ever-increasing demand for better batteries has set extraordinarily high standards for electrolyte materials, which are far beyond the realm of a conventional nonaqueous electrolyte design. Superconcentrated (or highly concentrated) solutions are emerging as a new class of liquid electrolytes with various unusual functionalities beneficial for advanced lithium (Li) battery applications. This article reviews unique features, as well as basic physicochemical properties, of highly concentrated electrolytes from the viewpoint of their peculiar solution structure, and discusses their future contributions to advanced battery technologies.
Performance assessment of a visual attention system entirely based on a human vision modeling (2005)

It is now commonly assumed that the human visual attention, which is a selecting process of the most relevant locations in a scene according to a particular behavior, is driven by both top-down (task-dependent) and bottom-up (signal-dependent) control. A new model attempting to simulate the bottom-up process has been designed Le Meur, O et al., (2004). This model is purely based on visual system properties that provides noticeable advantages compared to the classical published approaches. This paper focuses on the performance assessment of this model by achieving a comparison with real fixation points stemming from eye-tracking apparatus both subjectively and objectively.
Movement imitation with nonlinear dynamical systems in humanoid robots (2003)

Presents an approach to movement planning, on-line trajectory modification, and imitation learning by representing movement plans based on a set of nonlinear differential equations with well-defined attractor dynamics. The resultant movement plan remains an autonomous set of nonlinear differential equations that forms a control policy (CP) which is robust to strong external perturbations and that can be modified on-line by additional perceptual variables. We evaluate the system with a humanoid robot simulation and an actual humanoid robot. Experiments are presented for the imitation of three types of movements: reaching movements with one arm, drawing movements of 2-D patterns, and tennis swings. Our results demonstrate (a) that multi-joint human movements can be encoded successfully by the CPs, (b) that a learned movement policy can readily be reused to produce robust trajectories towards different targets, (c) that a policy fitted for one particular target provides a good predictor of human reaching movements towards neighboring targets, and (d) that the parameter space which encodes a policy is suitable for measuring to which extent two trajectories are qualitatively similar.
Elevated Th1- or Th0-like cytokine mRNA in peripheral circulation of patients with rheumatoid arthritis. Modulation by treatment with anti-ICAM-1 correlates with clinical benefit (1995)

The current studies examined whether cytokine patterns indicative of an imbalance in Th1 and Th2 cells could be identified in PBMC of patients with active rheumatoid arthritis (RA). To investigate this possibility, a reproducible PCR technique to assess cytokine mRNA levels in PBMC was employed that minimized in vitro manipulation of the cells. Seven of 14 RA patients had increased mRNA levels for IL-2, 5/14 for IFN-gamma, 3/14 for IL-4, and 4/14 for the IL-2R alpha-chain, compared with normal donors. Whereas 4 patients had elevated mRNA for IL-2 and IFN-gamma, indicative of an increase in activated Th1 or Th0 cells, 1 of 14 patients expressed low levels of IL-2 and IFN-gamma and high levels of IL-4 mRNA. Seven RA patients were treated with a mAb to ICAM-1 (CD54). To determine whether changes in cytokine mRNA levels might be associated with and/or account for the anti-inflammatory effect of anti-ICAM-1 mAb therapy, changes in cytokine mRNA levels were assessed and correlated with clinical improvement. Anti-ICAM-1 mAb administration was followed by a prompt and transient increase of IFN-gamma mRNA. Elevation of IFN-gamma mRNA expression throughout the treatment period reflected a temporary increase in the number of circulating CD3+CD4+ T cells, suggestive of altered circulatory patterns of activated Th1-like cells and was related to clinical efficacy. The results indicate that elevated cytokine mRNA levels characteristic for Th1 cells can be detected in the PBMC in active RA and, furthermore, that anti-ICAM-1 mAb may be beneficial in RA by altering the recruitment of activated Th1-like cells into the synovium. This assumption further strengthens the hypothesis of a significant contribution of Th1-like cells to the pathogenesis of RA.
Catalytic Antibodies with Lipase Activity and R or S Substrate Selectivity (1989)

The specific hydrolysis of unactivated esters bearing an R or S enantiomeric alcohol has been achieved by two separate classes of catalytic antibodies induced to bind either the R or S substrates. The antibodies exhibit rate accelerations (10(3) to 10(5] above background hydrolysis that, coupled with their antipodal specificity, provide a novel set of reagents for use in synthesis.
Characterization of a Novel Human Respiratory Syncytial Virus Chimeric FG Glycoprotein Expressed Using a Baculovirus Vector (1989)

Human respiratory syncytial virus (RSV) codes for two glycoproteins (F and G) which have been shown to the major targets for the host antibody response. We have expressed a novel chimeric glycoprotein (FG) in insect cells using a baculovirus vector. The chimeric glycoprotein contains the signal and extracellular regions of the RSV F glycoprotein linked to the extracellular region of the RSV G glycoprotein. Beginning at the amino terminus, the chimeric glycoprotein consists of amino acids 1 to 489 from RSV F followed by amino acids 97 to 279 from RSV G. The chimeric FG glycoprotein did not contain an anchor region and was efficiently secreted into the medium of recombinant baculovirus-infected insect cells. The FG glycoprotein ranged in size from 69K to 91K and was heterogeneous with respect to isoelectric point. The cleavage site present on the F glycoprotein was recognized on the chimeric FG, and the glycoprotein appeared to be antigenically similar to the native RSV F and G glycoproteins.
Release of RANTES, MIP-1 α, and MCP-1 into Asthmatic Airways Following Endobronchial Allergen Challenge (1997)

We have investigated the presence of regulated on activation, normal T-cell expressed and probably secreted (RANTES), macrophage inflammatory peptide-1 alpha (MIP-1 alpha), and macrophage chemotactic peptide (MCP-1) in the bronchoalveolar lavage fluid (BALF) obtained from normal (n = 7) and stable asthmatic subjects (n = 8), and studied their kinetic release into asthmatic airways following endobronchial allergen challenge (n = 18). Measurements of RANTES, MIP-1 alpha, and MCP-1 in 10 times (10x) concentrated BALF showed that these three chemokines were present in both normal controls and stable asthmatic patients, but no significant difference between the two groups was found in the levels of the three chemokines. However, at 4 h after allergen challenge, BALF levels of RANTES, MIP-1 alpha, and MCP-1 were significantly increased in fluid obtained from the allergen-challenge site when compared with the saline-challenge control site (median: 175 pg/ml versus 11.5 pg/ml, 258 pg/ml versus 88 pg/ml, and 900 pg/ml versus 450 pg/ml, respectively). At 24 h, levels of the three chemokines returned to baseline values. To investigate whether cells in BALF obtained 4 h after allergen exposure release chemokines, they were cultured for 24 h. BALF cells from the allergen site released more RANTES and MCP-1 than those from the saline site, but released similar amounts of MIP-1 alpha. These findings suggest that RANTES, MIP-1 alpha, and MCP-1 may regulate cell trafficking in asthma in response to allergen exposure.
Dachshund inhibits oncogene-induced breast cancer cellular migration and invasion through suppression of interleukin-8 (2008)

Oncogene-mediated signaling to the host environment induces a subset of cytokines and chemokines. The Drosophila Dac gene promotes migration of the morphogenetic furrow during eye development. Expression of the cell-fate determination factor Dachshund (DACH1) was lost in poor prognosis invasive breast cancer. Mouse embryo fibroblasts derived from Dach1(-/-) mice demonstrated endogenous Dach1 constitutively represses cellular migration. DACH1 inhibited cellular migration and invasion of oncogene (Ras, Myc, ErbB2, c-Raf)-transformed human breast epithelial cells. An unbiased proteomic analysis identified and immunoneutralizing antibody and reconstitution experiments demonstrated IL-8 is a critical target of DACH1 mediating breast cancer cellular migration and metastasis in vivo. DACH1 bound the endogenous IL-8 promoter in ChIP assays and repressed the IL-8 promoter through the AP-1 and NF-kappaB binding sites. Collectively, our data identify a pathway by which an endogenous cell-fate determination factor blocks oncogene-dependent tumor metastasis via a key heterotypic mediator.
Deep Trench Isolation for Crosstalk Suppression in Active Pixel Sensors with 1.7 µm Pixel Pitch (2007)

A deep trench isolation (DTI) process with a 4 µm deep trench has been developed and successfully applied to 5-megapixel complementary metal oxide silicon (CMOS) image sensors with a 1.7 µm pixel pitch. It was found that from the results of simulations and experiments, DTI is very effective for reducing electrical crosstalk without degrading other pixel characteristics, such as full well capacity, sensitivity, and white spot density. Therefore, DTI could be a solution for obtaining a high performance for CMOS image sensors with a small pixel size of sub-2.0 µm.
A server's perspective of Internet streaming delivery to mobile devices (2012)

Receiving Internet streaming services on various mobile devices is getting more and more popular. To understand and better support Internet streaming delivery to mobile devices, a number of studies have been conducted. However, existing studies have mainly focused on the client side resource consumption and streaming quality. So far, little is known about the server side, which is the key for providing successful mobile streaming services. In this work, we set to investigate the Internet mobile streaming service at the server side. For this purpose, we have collected a one-month server log (with 212 TB delivered video traffic) from a top Internet mobile streaming service provider serving worldwide mobile users. Through trace analysis, we find that (1) a major challenge for providing Internet mobile streaming services is rooted from the mobile device hardware and software heterogeneity. In this workload, we find over 2800 different hardware models with about 100 different screen resolutions running 14 different mobile OS and 3 audio codecs and 4 video codecs. (2) To deal with the device heterogeneity, transcoding is used to customize the video to the appropriate versions at runtime for different devices. A video clip could be transcoded into more than 40 different versions in order to serve requests from different devices. (3) Compared to videos in traditional Internet streaming, mobile streaming videos are typically of much smaller size (a median of 1.68 MBytes) and shorter duration (a median of 2.7 minutes). Furthermore, the daily mobile user accesses are more skewed following a Zipf-like distribution but users' interests also quickly shift. Considering the huge demand of CPU cycles for online transcoding, we further examine server-side caching in order to reduce CPU cycle demand. We show that a policy considering different versions of a video altogether outperforms other intuitive ones when the cache size is limited.
Human Embryonic Stem Cell-Derived Dopaminergic Neurons Reverse Functional Deficit in Parkinsonian Rats (2007)

We show that human embryonic stem cell-derived dopaminergic neurons survived transplantation to the neurotoxin 6-hydroxydopamine-lesioned rat striatum and, in combination with the cells newly differentiated from their progenitors, contributed to locomotive function recovery at 5 months. The animal behavioral improvement was correlated with the dopamine neurons present in the graft. Although the donor cells contained forebrain and midbrain dopamine neurons, the dopamine neurons present in the graft mainly exhibited a midbrain, or nigra, phenotype, suggesting the importance of midbrain dopamine neurons in functional repair. Furthermore, progenies of grafted cells were neurons and glia with greatly diminished mitotic activity by 5 months. Thus, the in vitro-produced human dopamine neurons can functionally engraft in the brain.
Application of robotics and image processing to automated colony picking and arraying. (1991)

We describe a system that applies image processing and robotic techniques to automatically pick individual colonies from square petri dishes and array them in 96-well microtiter plates. Digital images of the colony distribution in the dishes are acquired using a video camera and frame buffer. Commercial image processing software is used to identify individual colonies and determine their locations. A Hewlett-Packard Microassay System robot reads the resulting coordinate file for each dish, picks cells from each identified colony and transfers the cells into a microtiter plate well. A disposable pipet tip is used as the sterile implement for colony picking. Custom holders position the dishes accurately and provide common coordinate systems for imaging and picking. The system is calibrated to account for the depth of agar in the dishes. The robot can process up to 10 dishes and 20 plates (1920 colonies) in a single run. It has successfully arrayed a cosmid library of the S. pombe genome consisting of approximately 6000 colonies in 30 petri dishes in about 40 hours of robot time. Future enhancements to the system are discussed.
Recent progress and future options in the development of GLP-1 receptor agonists for the treatment of diabesity (2013)

The dramatic rise of the twin epidemics, type 2 diabetes and obesity is associated with increased mortality and morbidity worldwide. Based on this global development there is clinical need for anti-diabetic therapies with accompanied weight reduction. From the approved therapies, the injectable glucagon-like peptide-1 receptor agonists (GLP-1 RAs) are the only class of agents which are associated with a modest weight reduction. Physiological effects of the gastro-intestinal hormone GLP-1 are improvement of glycemic control as well as a reduction in appetite and food intake. Different approaches are currently under clinical evaluation to optimize the therapeutic potential of GLP-1 RAs directed to once-weekly up to once-monthly administration. The next generation of peptidic co-agonists comprises the activity of GLP-1 plus additional gastro-intestinal hormones with the potential for increased therapeutic benefits compared to GLP-1 RAs.
Analysis of a method of phase measurement of ultrashort pulses in the frequency domain (1991)

A detailed analysis of a method of phase measurement of ultrashort light pulses is performed. It is shown that the output pulse of a zero dispersion compressor with a mask consisting of a narrow slit is a wide pulse delayed an amount equal to the phase derivative of the field spectrum with respect to frequency. State criteria to determine whether the approximations are valid are presented. The method is not affected by artifacts coming from diffraction effects in the slit or by the fact that only correlations are measured. The effects of the errors in positioning the elements are considered and minimized in the construction of the experimental apparatus. A novel technique for measurement of the derivative of the cross correlation is described, and it is used to locate the delayed output pulse.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>