gebhart/patrepeval huggingface dataset:
Evaluation of co-culture and alternative culture systems for promoting in-vitro development of mouse embryos. (1995)

The goal of this study was to compare mouse embryo development in a defined synthetic medium (human tubal fluid) against the same medium supplemented with a defined synthetic serum (SS), co-culture on human tubal epithelium (TECC), and culture on human fibronectin (FN) with and without SS. After 48 h, TECC, SS and FN + SS cultures demonstrated accelerated development with > 70% achieving > or = 8-cell stage. After 72 h, these culture conditions also significantly increased the proportion of embryos reaching the blastocyst stage but only TECC significantly increased the number of hatching blastocysts. Nuclei of the trophectoderm of unhatched and hatched blastocysts were stained with propidium iodide before fixing and labelling both the trophectoderm and inner cell mass with bisbenzimide. Blastocysts from the TECC contained a significantly higher total cell number (TCN) and trophectoderm and inner cell mass cell numbers than all other groups. These findings indicate equivalent improvements in mouse embryo development to the blastocyst stage in response to TECC, SS and FN and an enhanced number of cells and rate of hatching found only with TECC.
MODES IN SEQUENCES OF LENSES (1961)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Respiratory Tract Mucin Genes and Mucin Glycoproteins in Health and Disease (2005)

This review focuses on the role and regulation of mucin glycoproteins (mucins) in airway health and disease. Mucins are highly glycosylated macromolecules (> or =50% carbohydrate, wt/wt). MUC protein backbones are characterized by numerous tandem repeats that contain proline and are high in serine and/or threonine residues, the sites of O-glycosylation. Secretory and membrane-tethered mucins contribute to mucociliary defense, an innate immune defense system that protects the airways against pathogens and environmental toxins. Inflammatory/immune response mediators and the overproduction of mucus characterize chronic airway diseases: asthma, chronic obstructive pulmonary diseases (COPD), or cystic fibrosis (CF). Specific inflammatory/immune response mediators can activate mucin gene regulation and airway remodeling, including goblet cell hyperplasia (GCH). These processes sustain airway mucin overproduction and contribute to airway obstruction by mucus and therefore to the high morbidity and mortality associated with these diseases. Importantly, mucin overproduction and GCH, although linked, are not synonymous and may follow from different signaling and gene regulatory pathways. In section i, structure, expression, and localization of the 18 human MUC genes and MUC gene products having tandem repeat domains and the specificity and application of MUC-specific antibodies that identify mucin gene products in airway tissues, cells, and secretions are overviewed. Mucin overproduction in chronic airway diseases and secretory cell metaplasia in animal model systems are reviewed in section ii and addressed in disease-specific subsections on asthma, COPD, and CF. Information on regulation of mucin genes by inflammatory/immune response mediators is summarized in section iii. In section iv, deficiencies in understanding the functional roles of mucins at the molecular level are identified as areas for further investigations that will impact on airway health and disease. The underlying premise is that understanding the pathways and processes that lead to mucus overproduction in specific airway diseases will allow circumvention or amelioration of these processes.
Recovering Homography from Camera Captured Documents using Convolutional Neural Networks (2017)

Removing perspective distortion from hand held camera captured document images is one of the primitive tasks in document analysis, but unfortunately, no such method exists that can reliably remove the perspective distortion from document images automatically. In this paper, we propose a convolutional neural network based method for recovering homography from hand-held camera captured documents. Our proposed method works independent of document's underlying content and is trained end-to-end in a fully automatic way. Specifically, this paper makes following three contributions: Firstly, we introduce a large scale synthetic dataset for recovering homography from documents images captured under different geometric and photometric transformations; secondly, we show that a generic convolutional neural network based architecture can be successfully used for regressing the corners positions of documents captured under wild settings; thirdly, we show that L1 loss can be reliably used for corners regression. Our proposed method gives state-of-the-art performance on the tested datasets, and has potential to become an integral part of document analysis pipeline.
A viscoelastic-aware experimentally-derived model for analog RF MEMS varactors (2010)

In this paper we present, for the first time, an experimentally-extracted model for the spring constant and tuning range of an analog RF-MEMS varactor that includes viscoelastic effects in RF-MEMS devices. By utilizing a bi-state bias condition with one state lasting 60 minutes and the other 1 minute, this model focuses on capturing the true electromechanical behavior of the varactor. An experimental setup with very high long-term accuracy is created to measure capacitance of the varactor up to 1,370 hours. The impact of these effects and the effectiveness of the model are demonstrated on a tunable-resonator loaded with RF-MEMS varactors.
Rho-ROCK Inhibitors for the Treatment of CNS Injury (2007)

Injured axons in the adult central nervous system (CNS) exhibit almost no regeneration. Several myelin-associated proteins such as myelin-associated glycoprotein (MAG), Nogo, and oligodendrocyte-myelin glycoprotein (OMgp) have been identified as inhibitors of CNS axonal regeneration in the CNS. Recently, repulsive guidance molecule (RGM) was identified as a potential myelin-derived neurite outgrowth inhibitor in vitro and in vivo. These axonal growth inhibitors transmit inhibitory signals through common intracellular molecules such as RhoA and its effector Rho kinases (ROCK). The effects of these axonal growth inhibitors are blocked by inhibition of the Rho-ROCK pathway in vitro. Injuries to the adult CNS induce the activation of the Rho-ROCK pathway, and the inhibition of this pathway promotes axonal regeneration and functional recovery in the injured CNS. Therefore, the Rho-ROCK pathway is a promising target for drug development for the treatment of human CNS injuries such as spinal cord injuries. This review also discusses recent patents and future developments which are useful in the treatment of human CNS injuries.
B7-H1 Expression Is Required for Human Endometrial Regenerative Cells in the Prevention of Transplant Vasculopathy in Mice (2018)

Vasculopathy is one of the primary pathological changes in chronic rejection of vascularized allograft transplantation. Endometrial regenerative cells (ERCs) are mesenchymal-like stromal cells with immunosuppressive effect. B7-H1 is a negative costimulator that mediates active immune suppression. The aim of this study was to investigate the requirement of B7-H1 in the immunoregulation of ERCs in preventing transplant vasculopathy of aorta allografts. The results showed that B7-H1 expression on ERCs was upregulated by IFN-<i>γ</i> in a dose-dependent manner and it was required for ERCs to inhibit the proliferation of peripheral blood mononuclear cells (PBMCs) <i>in vitro</i>. ERCs could alleviate transplant vasculopathy, as the intimal growth of transplanted aorta was limited, and the preventive effects were correlated with an increase in the percentages of CD11c<sup>+</sup>MHC class II<sup>low</sup>CD86<sup>low</sup> dendritic cells, CD68<sup>+</sup>CD206<sup>+</sup> macrophages, and CD4<sup>+</sup>CD25<sup>+</sup>Foxp3<sup>+</sup> T cells, as well as a decrease in the percentages of CD68<sup>+</sup> macrophages, CD3<sup>+</sup>CD4<sup>+</sup> T cells, CD3<sup>+</sup>CD8<sup>+</sup> T cells, and donor-reactive IgM and IgG antibodies. Moreover, overexpression of B7-H1 by IFN-<i>γ</i> can promote the immunosuppressive effect of ERCs. These results suggest that overexpression of B7-H1 stimulated by IFN-<i>γ</i> is required for ERCs to prevent the transplant vasculopathy, and this study provides a theoretical basis for the future clinical use of human ERCs.
Development of an Immunochromatographic Kit for Rapid Diagnosis of H5 Avian Influenza Virus Infection (2007)

Highly pathogenic avian influenza (HPAI) caused by the H5N1 subtype has given rise to serious damage in poultry industries in Asia. The virus has expanded its geographical range to Europe and Africa, posing a great risk to human health as well. For the control of avian influenza, a rapid diagnosis by detecting the causative virus and identifying its subtype is essential. In the present study, a rapid diagnosis kit combining immunochromatography with enzyme immunoassay which detects the H5 HA antigen of influenza A virus was developed using newly established anti-H5 HA monoclonal antibodies. The present kit specifically detected all of the H5 influenza viruses tested, and did not react with the other HA subtypes. H5 HA antigens were detected from swabs and tissue homogenates of chickens infected with HPAI virus strain A/chicken/Yamaguchi/7/04 (H5N1) from 2 days post inoculation. The kit showed enough sensitivity and specificity for the rapid diagnosis of HPAI.
A simulated annealing algorithm for constrained Multi-Objective Optimization (2008)

In this paper, we introduce a simulated annealing algorithm for constrained Multi-Objective Optimization (MOO). When searching in the feasible region, the algorithm behaves like recently proposed Archived Multi-Objective Simulated Annealing (AMOSA) algorithm [1], whereas when operating in the infeasible region, it tries to minimize constraint violation by moving along Approximate Descent Direction (ADD) [2]. An Archive of non-dominated solutions found during the search is maintained. The acceptance probability of a new point is determined by its feasibility status, and its domination status as compared to the current point and the points in the Archive. We report the performance of the proposed algorithm on a set of seven constrained bi-objective test problems (CTP2 to CTP8), which have been known to pose difficulties to existing multi-objective algorithms. A comparative study of current algorithm with the widely used multi-objective evolutionary algorithm NSGA-II has been included.
Protection from Cytotoxic Effects Induced by the Nitrogen Mustard Mechlorethamine on Human Bronchial Epithelial Cells in Vitro (2000)

The present study was undertaken to find potent molecules against the toxicity of nitrogen mustard mechlorethamine (HN2) on respiratory epithelial cells, using a human bronchial epithelial cell line (16HBE14o-) as an in vitro model. The compounds examined included inhibitors of poly(ADP-ribose) polymerase (PARP), sulfhydryl-group donors as nucleophiles, and iron chelators and inhibitors of lipid peroxidation as antioxidants. Their effectiveness was determined upon observance of metabolic dysfunction induced by HN2 following a 4-h exposure, using (3-(4,5-dimethylthiazole-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) reduction and ATP-level assays as indicators. Moreover, the fluorescent probe, monobromobimane (mBBr), and 2',7'-dichlorofluorescin-diacetate (H2DCF-DA) were used to assess intracellular sulfhydryl and peroxide level modifications by flow cytometry, respectively, following a 3-h exposure. At last, cell death was assessed by flow cytometry using the propidium iodide (PI)-dye-exclusion assay following 24-h exposure. PARP inhibitors (niacinamide, 3-aminobenzamide, 6(5H)-phenanthridinone), and two sulfhydryl-group donors (N-acetylcysteine, WR-1065) were found to be effective in preventing HN2-induced metabolic dysfunction when added in immediate or delayed treatment with HN2. Only N-acetylcysteine, however, was found to prevent cell death induced by HN2, though it must be present at the time of the HN2 challenge. Flow cytometric measurements of intracellular sulfhydryl levels strongly suggested that N-acetylcysteine and WR-1065 are preventive in alkylation of cellular compounds, mainly by direct extracellular interaction with HN2. PARP inhibitors prevent secondary deleterious effects induced by HN2, considering metabolism dysfunction as the endpoint. Elsewhere, the oxidative stress appears to be a side effect in HN2 toxicity only upon considering the inefficiency of several antioxidants.
Efficient Adaptations of the Non-Blocking Buffer for Event Message Communication between Real-Time Threads (2007)

Enabling message communication among concurrent computing threads without relying on mutual exclusion (i.e., locking) is highly desirable in real-time computing systems. This paper presents a refined version of the Non-Blocking Buffer (NBB), which is a lock-free interaction mechanism that enables efficient event-message communication between a single producer thread and a single consumer thread. The NBB scheme presented here contains improvements over the previous version in two aspects. First, application designers now have the flexibility of choosing the consumer's retry strategy for the case when the buffer is empty but the producer is in the middle of inserting an item. Second, in the refined version the producer inserts pointers to data items into the buffer whereas the consumer obtains copies of the items. This design is consistent with the fact that shared heap management must be avoided to enable fully lock-free interaction between the producer and the consumer. This paper also discusses the approaches based on the NBB mechanism for supporting all conceivable producer-consumer scenarios.
Manipulating, Deforming and Animating Sampled Object Representations (2007)

Abstract A sampled object representation (SOR) defines a graphical model using data obtained from a sampling process, which takes a collection of samples at discrete positions in space in order to capture certain geometrical and physical properties of one or more objects of interest. Examples of SORs include images, videos, volume datasets and point datasets. Unlike many commonly used data representations in computer graphics, SORs lack in geometrical, topological and semantic information, which is much needed for controlling deformation and animation. Hence it poses a significant scientific and technical challenge to develop deformation and animation methods that operate upon SORs. Such methods can enable computer graphics and computer animation to benefit enormously from the advances of digital imaging technology. In this state of the art report, we survey a wide range of techniques that have been developed for manipulating, deforming and animating SORs. We consider a collection of elementary operations for manipulating SORs, which can serve as building blocks of deformation and animation techniques. We examine a collection of techniques that are designed to transform the geometry shape of deformable objects in sampled representations and pay particular attention to their deployment in surgical simulation. We review a collection of techniques for animating digital characters in SORs, focusing on recent developments in volume animation.
A JINI framework for distributed service flexibility (2003)

Existing distributed middleware technologies and Enterprise Application frameworks lack in support to service flexibility from both the developer's and user's point of view. In this paper we propose a JINI-based framework, namely PRINCEPS (Pluggable Reliable Infrastructure for Network Computing and Enhanced Properties of Service), which provides a distributed and dynamic environment for flexible service provision. We claim that the adoption of JINI makes it possible to dramatically improve service flexibility by federating services in a dynamic and self-healing networked community. The framework provides the clients with a (web-based) mechanism for selecting services according to functional requirements (i.e., the service interface) and non-functional requirements (the quality of service, i.e., reliability, performance). More implementations of the same service can coexist in the framework, each of one satisfying different non-functional requirements. PRINCEPS provides service substitutability at various levels. In fact, any kind of service can be plugged in PRINCEPS: CORBA-based services, socket-based services, and centralized services. PRINCEPS also supports service developers with its own mechanism to integrate existing services. Preliminary performance experiments and lessons learned from the PRINCEPS prototype are also discussed.
Suppression of <i>O</i>-Methyltransferase Gene by Homologous Sense Transgene in Quaking Aspen Causes Red-Brown Wood Phenotypes1 (1998)

Homologous sense suppression of a gene encoding lignin pathway caffeic acid O-methyltransferase (CAOMT) in the xylem of quaking aspen (Populus tremuloides Michx.) resulted in transgenic plants exhibiting novel phenotypes with either mottled or complete red-brown coloration in their woody stems. These phenotypes appeared in all independent transgenic lines regenerated with a sense CAOMT construct but were absent from all plants produced with antisense CAOMT. The CAOMT sense transgene expression was undetectable, and the endogenous CAOMT transcript levels and enzyme activity were reduced in the xylem of some transgenic lines. In contrast, the sense transgene conferred overexpression of CAOMT and significant CAOMT activity in all of the transgenic plants' leaves and sclerenchyma, where normally the expression of the endogenous CAOMT gene is negligible. Thus, our results support the notion that the occurrence of sense cosuppression depends on the degree of sequence homology and endogene expression. Furthermore, the suppression of CAOMT in the xylem resulted in the incorporation of a higher amount of coniferyl aldehyde residues into the lignin in the wood of the sense plants. Characterization of the lignins isolated from these transgenic plants revealed that a high amount of coniferyl aldehyde is the origin of the red-brown coloration-a phenotype correlated with CAOMT-deficient maize (Zea mays L.) brown-midrib mutants.
Growth in the Neonatal Intensive Care Unit Influences Neurodevelopmental and Growth Outcomes of Extremely Low Birth Weight Infants (2006)

These analyses suggest that growth velocity during an ELBW infant's NICU hospitalization exerts a significant, and possibly independent, effect on neurodevelopmental and growth outcomes at 18 to 22 months' corrected age.
Scheduling Concurrent Applications on a Cluster of CPU-GPU Nodes (2012)

Heterogeneous architectures comprising a multicore CPU and many-core GPU(s) are increasingly being used within cluster and cloud environments. In this paper, we study the problem of optimizing the overall throughput of a set of applications deployed on a cluster of such heterogeneous nodes. We consider two different scheduling formulations. In the first formulation, we consider jobs that can be executed on either the GPU or the CPU of a single node. In the second formulation, we consider jobs that can be executed on the CPU, GPU, or both, of any number of nodes in the system. We have developed scheduling schemes addressing both of the problems. In our evaluation, we first show that the schemes proposed for first formulation outperform a blind round-robin scheduler and approximate the performances of an ideal scheduler that involves an impractical exhaustive exploration of all possible schedules. Next, we show that the scheme proposed for the second formulation outperforms the best of existing schemes for heterogeneous clusters, TORQUE and MCT, by up to 42%.
Active-site mutations impairing the catalytic function of the catalytic subunit of human protein phosphatase 2A permit baculovirus-mediated overexpression in insect cells (2001)

Members of the phosphoprotein phosphatase (PPP) family of protein serine/threonine phosphatases, including protein phosphatase (PP)1, PP2A and PP2B, share invariant active-site residues that are critical for catalytic function [Zhuo, Clemens, Stone and Dixon (1994) J. Biol. Chem. 269, 26234–26238]. Mutation of the active-site residues Asp88 or His118 within the human PP2A catalytic subunit (PP2Ac)α impaired catalytic activity in vitro; the D88N and H118N substitutions caused a 9- and 23-fold reduction in specific activity respectively, when compared with wild-type recombinant PP2Ac, indicating an important role for these residues in catalysis. Consistent with this, the D88N and H118N substituted forms failed to provide PP2A function in vivo, because, unlike wild-type human PP2Acα, neither substituted for the endogenous PP2Ac enzyme of budding yeast. Relative to wild-type PP2Ac, the active-site mutants were dramatically overexpressed in High Five® insect cells using the baculovirus system. Milligram quantities of PP2Ac were purified from 1×109 High Five cells and the kinetic constants for dephosphorylation of the peptide RRA(pT)VA (single-letter amino-acid notation) by PP2Ac (Km = 337.5μM; kcat = 170s−1) and D88N (Km = 58.4μM; kcat = 2s−1) were determined. The results show that the substitution impairs catalysis severely without a significant effect on substrate binding, consistent with the PPP catalytic mechanism. Combination of the baculovirus and yeast systems provides a strategy whereby the structure–function of PP2Ac may be fully explored, a goal which has previously proven difficult, owing to the stringent auto-regulatory control of PP2Ac protein levels in vivo.
Two human trypsinogens. Purification, molecular properties, and N-terminal sequences (1978)

The two human trypsinogens have been isolated from human pancreatic juice in a sufficient amount to study molecular and structural properties. The purification procedure included filtration on Sephadex G-100 followed by ion-exchange chromatography on DEAE-cellulose. The two trypsinogens represent 19% of total proteins of pancreatic juice. Trypsinogen 1, the major form, is present in a quantity twice that of trypsinogen 2, which is the most anionic protein in human pancreatic juice. The two proteins have partial immunological identity, close molecular weights (23 438 and 25 006 for trypsinogens 1 and 2, respectively) and similar amino acid compositions. The N-terminal sequences are the same for the first 9 residues: Ala-Pro-Phe-Asp4-Lys-Ile. The two proteins differ in the activation peptides released during the transformation to trypsins. Trypsinogen 2 liberates one octapeptide Ala-Pro-Phe-Asp4-Lys while trypsinogen 1 liberates two peptides, the same octapeptide and the pentapeptide (Asp)4-Lys.
Extending OpenMP for heterogeneous chip multiprocessors (2003)

The emergence of system-on-chip (SOC) design shows the growing popularity of the integration of multiple-processors into one chip. We propose that high-level abstraction of parallel programming like OpenMP is suitable for chip multiprocessors. For SOCs, the heterogeneity exists within one chip such that it may have different types of multiprocessors, e.g. RISC-like processors or DSP-like processors. Incorporating different processors into OpenMP is challenging. We present our solutions to extend OpenMP directives to tackle this heterogeneity. Several optimization techniques are proposed to utilize advanced architecture features of our target SOC, the software scalable system on chip (3SoC). Preliminary performance evaluation shows scalable speedup using different types of processors and performance improvement through individual optimization.