gebhart/patrepeval huggingface dataset:
Angiogenesis Factors. (2001)

Angiogenesis is a recent highlight in the medical field; the developmental process and pathological conditions for various diseases can be understood from the novel aspect of "angiogenesis". Many angiogenesis-related factors are involved in the development of vessels during embryogenesis (vasculogenesis), as well as the induction of new vessels in response to physiological or pathological stimuli. In particular, the appearance of hemangioblasts, precursor cells for vascular endothelial cells and blood cells, and blood islands are expected to play a "prelude" role in tubulogenesis. Gene knock out mice of vascular endothelial growth factor (VEGF)/VEGF receptor, ephrin-B2, and angiopoietin-1 results in a failure of normal vessels production. Dormant factors derived from proteolytic cleavage of various physiological substrates are expected to balance a homeostasis of "angiogenic states" in the host. Furthermore, angiogenesis under various pathological conditions of malignant tumors, ocular diseases, psoriasis, rheumatoid arthritis, atherosclerosis and other diseases is associated with complex angiogenesis networks, suggesting pleiotropic mechanisms for angiogenesis.
Pathogenic role of matrix metalloproteases and their inhibitors in asthma and chronic obstructive pulmonary disease and therapeutic relevance of matrix metalloproteases inhibitors. (2003)

Matrix metalloproteinases (MMPs) are an at least 23 member family of calcium and zinc dependent enzymes implicated in many physiological and pathological processes. Asthma, chronic obstructive pulmonary disease (COPD) and emphysema are diseases associated with an inflammation of the airways and lung parenchyma. In this review, we focus on the role played by MMPs in the pathogenesis of inflammation, airway remodelling and alveolar destruction, depicting the observational studies in humans and the experimental studies in animal models. During the course of asthma, MMP-2,-8,-9 and TIMP-1 are expressed at baseline and the allergen exposure or exacerbations of the disease lead to an increase of MMP-9 secretion being at this time much higher than that of TIMP-1, allowing temporarily a matrix damage, possibly followed by abnormal repair. Animal models suggest a predominant role for MMP-9 and MMP-12 in the pathogenesis of pulmonary inflammation and link an absence of MMP-2 to an increased parenchymal inflammation. In COPD and emphysema, human studies indicate an over-secretion of MMP-2,-8,-9 and animal models pointout MMP-1 and MMP-12 as being key players in the pathogenesis of emphysema. Taken together, these data identify specific MMP inhibition as appropriate target for therapeutic intervention in asthma or COPD/emphysema They also strongly argue against the widespread use of large spectrum non specific inhibitors that could be detrimental.
A Prospective Randomized Trial of an Antibiotic-and Antiseptic-Coated Central Venous Catheter in the Prevention of Catheter-Related Infections (1997)

Despite a marked decrease in catheter site colonization and catheter-related infection rates, the A-CVC did not significantly reduce the incidence of catheter-related septicemia. This may be due to a greater pathogenic dependence on catheter hub contamination rather than catheter site colonization or local catheter-related infection, or the relatively short (5.2 days) duration of catheterization in this study.
Tangible progress (1999)

We developed four widely different interfaces for users of Somewire, a prototype audio-only media space. We informally studied users experiences with the two screen- based interfaces. We prototyped a non-screen-based interface as an example of a novel tangible interface for a communication system. We explored the conflict between privacy and simplicity of representation, and identified two unresolved topics: the role of audio quality and the prospects for scsiling audio spaces beyond a single Workgroup. Finally, we formulated a set of design guidelines for control and representation in audio spaces, as follows: GUIs are not well-suited to audio spaces, users do not require control over localization or other audio attributes, and awareness of other users presence is desirable.
Dystrophin-glycoprotein complex and laminin colocalize to the sarcolemma and transverse tubules of cardiac muscle. (1993)

The expression and subcellular distribution of the dystrophin-glycoprotein complex and laminin were examined in cardiac muscle by immunoblot and immunofluorescence analysis of rabbit and sheep papillary muscle. The five dystrophin-associated proteins (DAPs), 156-DAG, 59-DAP, 50-DAG, 43-DAG, and 35-DAG, were identified in rabbit ventricular muscle and found to codistribute with dystrophin in both papillary myofibers and Purkinje fibers. The DAPs and dystrophin codistributed not only in the free surface sarcolemma but also in interior regions of the myofibers where T tubules are present. Neither the DAPs nor dystrophin were detected in intercalated discs, a specialized region of cardiac sarcolemma where neighboring myocardial cells are physically joined by cell-cell junctions. Similarly, in bundles of Purkinje fibers, which lack T tubules, DAPs and dystrophin were also found to codistribute at the free surface sarcolemma but were not detected either in the region of surface sarcolemma closely apposed to a neighboring Purkinje fiber or in interior regions of these myofibers. Comparison between the distribution of the dystrophin-glycoprotein complex and laminin showed that laminin codistributes with the components of this complex in both papillary myofibers and Purkinje fibers. These results are consistent with previous findings demonstrating that the extracellularly exposed 156-DAG (dystroglycan) of the skeletal muscle dystrophin-glycoprotein complex binds laminin, a component of the basement membrane. Although we demonstrate that DAPs, dystrophin, and laminin colocalize to the sarcolemma in rabbit and sheep papillary myofibers as they do in skeletal myofibers, the most striking difference between the subcellular distribution of these proteins in cardiac and skeletal muscle is that the dystrophin-glycoprotein complex and laminin also localize to regions of the fibers where T tubules are distributed in cardiac but not in skeletal muscle. These results imply that the protein composition and thus possibly some functions of T tubules in cardiac muscle are distinct from those of skeletal muscle.
The inclusion of the type III repeat ED-B in the fibronectin molecule generates conformational modifications that unmask a cryptic sequence. (1992)

We have previously reported an anti-fibronectin monoclonal antibody (mAb) (BC-1) which reacts with an ED-B-containing beta-galactosidase-fibronectin fusion protein but not with an identical beta-galactosidase-fibronectin fusion protein in which the ED-B sequence is omitted. In further experiments aimed at localizing more precisely the epitope recognized by this mAb, we demonstrate that 1) the mAb BC-1 is indeed specific for ED-B-containing fibronectin (FN) molecules even though the epitope recognized by this mAb is localized on the type III homology repeat 7 (the one which precedes the ED-B sequence) and 2) in fibronectin molecules lacking the ED-B sequence, this epitope is masked. We further demonstrate that, to mask the epitope recognized by the mAb BC-1, the presence of at least half of the FN type III homology repeat 9 is necessary. We also report the production of the mAb IST-6 which recognizes only FN molecules in which the ED-B sequence is lacking. These data clearly demonstrate that the presence of the ED-B sequence within FN molecules generates conformational modification in the central part of the molecules that unmasks previously cryptic sequences and masks others.
Optical sensing for robot perception and localization (2006)

Optical sensing, e.g., computer vision, provides a very compelling approach to solving a number of technological challenges for developing affordable, useful, and reliable robotic products. We describe key advancements in the field consisting of three core technologies for visual pattern recognition (ViPR), visual simultaneous localization and mapping (vSLAM), and a low-cost solution for localization using optical beacons (NorthStar). ViPR is an algorithm for visual pattern recognition based on scale invariant features (SIFT features) which provides a robust and computationally effective solution to fundamental vision problems including the correspondence problem; object recognition; structure; and pose estimation. vSLAM is an algorithm for visual simultaneous localization and mapping using one camera sensor in conjunction with dead-reckoning information, e.g., odometry. vSLAM provides a cost-effective solution to localization and mapping for cluttered environments and is reliable to dynamic changes in the environment Finally, NorthStar uses IR projections onto a surface to estimate the robot's pose based on triangulation. We give examples of concept prototypes as well as commercial products such as Sony's Aibo, which have incorporated these technologies in order to improve product utility and value.
On the implementation of perfectly matched layers in a three‐dimensional fourth‐order velocity‐stress finite difference scheme (2003)

Robust absorbing boundary conditions are central to the utility and advancement of 3‐D numerical wave propagation methods. It is in general preferred that an absorbing boundary method be capable of broadband absorption, be efficient in terms of memory and computation time, and be widely stable in connection with sophisticated numerical schemes. Here we discuss these issues for a promising absorbing boundary method, perfectly matched layers (PML), as implemented in the widely used fourth‐order accurate three‐dimensional (3‐D) staggered‐grid velocity‐stress finite difference (FD) scheme. Numerical results for point (explosive and double couple) and extended sources, velocity structures (homogeneous, 1‐D and 3‐D), and different thickness PML zones are excellent, in general, leaving no observable reflections in PML seismograms compared to the amplitudes of the primary phases. For both homogeneous half‐space and 1‐D models, typical amplitude reduction factors (with respect to the maximum trace amplitude) range between 1/100 and 1/625 for PML thicknesses of 5–20 nodes. A PML region of thickness 5 outperforms a simple exponential damping region of thickness 20 in a homogeneous half‐space model by a factor of 3. We find that PML is effective across the simulation bandwidth. For example, permanent offset artifacts due to particularly poor absorption of long‐period energy by the simple exponential damping are effectively absent when PML is used. The computational efficiency and storage requirements of PML, compared to the simple exponential damping, are reduced due to the need for only narrow absorbing regions. We also discuss stability and present the complete PML model for the 3‐D velocity‐stress system.
Model-Based Expectation-Maximization Source Separation and Localization (2009)

This paper describes a system, referred to as model-based expectation-maximization source separation and localization (MESSL), for separating and localizing multiple sound sources from an underdetermined reverberant two-channel recording. By clustering individual spectrogram points based on their interaural phase and level differences, MESSL generates masks that can be used to isolate individual sound sources. We first describe a probabilistic model of interaural parameters that can be evaluated at individual spectrogram points. By creating a mixture of these models over sources and delays, the multi-source localization problem is reduced to a collection of single source problems. We derive an expectation-maximization algorithm for computing the maximum-likelihood parameters of this mixture model, and show that these parameters correspond well with interaural parameters measured in isolation. As a byproduct of fitting this mixture model, the algorithm creates probabilistic spectrogram masks that can be used for source separation. In simulated anechoic and reverberant environments, separations using MESSL produced on average a signal-to-distortion ratio 1.6 dB greater and perceptual evaluation of speech quality (PESQ) results 0.27 mean opinion score units greater than four comparable algorithms.
Thermally Reversible Hydrogels via Intramolecular Folding and Consequent Self-Assembly of a de Novo Designed Peptide (2003)

A small de novo designed peptide (MAX3) is described that exhibits complete thermoreversible self-assembly into a hydrogel network. Importantly, a prerequisite to hydrogelation is that the peptide must first fold into a conformation conducive to self-assembly. At ambient temperature, MAX3 is unfolded, resulting in a low viscosity aqueous solution. On increasing the temperature, the peptide undergoes a unimolecular folding event, affording an amphiphilic beta-hairpin that consequently self-assembles into a hydrogel network. Increasing the temperature serves to dehydrate the nonpolar residues of the unfolded peptide and trigger folding via hydrophobic collapse. Cooling the resultant hydrogel results in beta-hairpin unfolding and consequent complete dissolution of the hydrogel. The temperature at which folding and consequent self-assembly into a rigid hydrogel occur can be tuned by altering the hydrophobicity of the peptides.
Effects of Cryopreservation on Histology and Viability of Cultured Corneal Epithelial Cell Sheets in Rabbit (2005)

The cell survival rates obtained after freezing storage were reasonable; however, the cryopreserved sheets could not maintain their original layered structure. More work needs to be done to better preserve the corneal epithelial cell sheets.
Electroporation by nucleofector is the best nonviral transfection technique in human endothelial and smooth muscle cells (2005)

BACKGROUND: The aim of this study was to determine the optimal non-viral transfection method for use in human smooth muscle cells (SMC) and endothelial cells (EC). METHODS: Coronary Artery (CoA) and Aortic (Ao) SMC and EC were transfected with a reporter plasmid, encoding chloramphenicol acetyltransferase type 1 (CAT), with seven different transfection reagents, two electroporation methods and a photochemical internalization (PCI) method. CAT determination provided information regarding transfection efficiency and total protein measurement was used to reflect the toxicity of each method. RESULTS: Electroporation via the nucleofector machine was the most effective method tested. It exhibited a 10 to 20 fold (for SMC and EC, respectively) increase in transfection efficiency in comparison to the lipofection method combined with acceptable toxicity. FuGene 6 and Lipofectamine PLUS were the preferred transfection reagents tested and resulted in 2 to 60 fold higher transfection efficiency in comparison to the PCI which was the least effective method. CONCLUSION: This study indicates that electroporation via the nucleofector machine is the preferred non-viral method for in vitro transfection of both human aortic and coronary artery SMC and EC. It may be very useful in gene expression studies in the field of vascular biology. Through improved gene transfer, non-viral transfer techniques may also play an increasingly important role in delivering genes to SMC and EC in relevant disease states.
Antiviral activity of dolutegravir in subjects with failure on an integrase inhibitor‐based regimen: week 24 phase 3 results from VIKING‐3 (2012)

Background VIKING‐3 aimed to examine efficacy and safety of dolutegravir (DTG) 50 mg twice daily in patients with resistance to multiple ARV classes, including integrase inhibitors (INI). Methods RAL and/or EVG‐resistant (current or historical) adult subjects with screening plasma HIV‐1 RNA ≥500 c/mL and resistance to ≥2 other ART classes received open‐label DTG 50 mg BID while continuing their failing regimen (without RAL/EVG). At Day 8 the background regimen was optimised and DTG continued. Activity of the optimized background regimen (OBR) was determined by Monogram Net Assessment. Primary endpoints were antiviral efficacy at Day 8 and Week 24. Results 183 subjects enrolled, 124 with INI‐resistance at screening and 59 with historical (but no screening) resistance. Population was advanced: at BL, median CD4 140, prior ART 13 yrs, 56% CDC Class C; 79% had &gt;2 NRTI, 75% &gt;1 NNRTI, and 70% &gt;2 PI resistance‐associated mutations, and 61% had non‐R5 HIV detected. Of the 114 subjects who had the opportunity to complete 24 weeks on study before data cutoff, 72 (63%) had &lt;50 c/mL RNA at Week 24 (SNAPSHOT algorithm). Mean HIV RNA declined by 1.4 log 10 c/mL (95% CI: 1.3, 1.5; p &lt; 0.001) at Day 8; response differed by genotype pathway (Table). Primary INI mutations at BL N Mean HIV RNA (log 10 ) Change from BL (SD) at Day 8 %&gt;1 log HIV RNA decline of &lt;50 c/mL at Day 8 TOTAL 183 −1.4 (0.61) 82% T66 1 −1.9 100% Y143 28 −1.7 (0.42) 96% N155 33 −1.4 (0.51) 82% Q148 + ≤1 secondary mutation # 32 −1.1 (0.51) 69% Q148 + ≥2 secondary mutations # 20 −1.0 (0.81) 48% ≥2 primary mutations 8 −1.4 (0.76) 75% No primary mutations 60 −1.6 (0.55) 95% Key secondary mutations comprised G140_ACS, L741, E138_AKT. In subjects with Q148 pathway mutations, virologic response decreased with increasing number of secondary mutations. Background overall susceptibility score (OSS) was not associated with Wk 24 response: % &lt;50 c/mL were 83%, 63%, 59% and 69% for OSS 0, 1, 2 and &gt;2, respectively. Discontinuations due to adverse events were uncommon (6/183, 3%); the most common drug‐related AEs were diarrhoea, nausea and headache, each reported in only 5% of subjects. Conclusion A majority of the highly treatment‐experienced subjects in VIKING‐3 achieved suppression with DTG‐based therapy. Responses were associated with Baseline IN genotype but not OSS, highlighting the importance and independence of DTG antiviral activity. DTG had a low rate of discontinuation due to adverse events at 50 mg BID in this advanced patient population.
Real-time imaging of single nerve cell apoptosis in retinal neurodegeneration (2004)

Apoptotic nerve cell death is implicated in the pathogenesis of several devastating neurodegenerative conditions, including glaucoma and Alzheimer's and Parkinson's diseases. We have devised a noninvasive real-time imaging technique using confocal laser-scanning ophthalmoscopy to visualize single nerve cell apoptosis in vivo, which allows longitudinal study of disease processes that has not previously been possible. Our method utilizes the unique optical properties of the eye, which allow direct microscopic observation of nerve cells in the retina. We have been able to image changes occurring in nerve cell apoptosis over hours, days, and months and show that effects depend on the magnitude of the initial apoptotic inducer in several models of neurodegenerative disease in rat and primate. This technology enables the direct observation of single nerve cell apoptosis in experimental neurodegeneration, providing the opportunity for detailed investigation of fundamental disease mechanisms and the evaluation of interventions with potential clinical applications, together with the possibility of taking this method through to patients.
Aluminum in Pediatric Parenteral Nutrition Products: Measured Versus Labeled Content (2011)

The actual aluminum concentrations of all the parenteral nutrition solutions were significantly less than the aluminum content based on manufacturers' labels. These findings indicate that 1) the manufacturers should label their products with actual aluminum content at the time of product release rather than at the time of expiry, 2) that there are manufacturers whose products provide significantly less aluminum contamination than others, and 3) pharmacists can select products with the lowest amounts of aluminum contamination and reduce the aluminum exposure in their patients.
Massive and parallel expression profiling using microarrayed single-cell sequencing (2016)

Single-cell transcriptome analysis overcomes problems inherently associated with averaging gene expression measurements in bulk analysis. However, single-cell analysis is currently challenging in terms of cost, throughput and robustness. Here, we present a method enabling massive microarray-based barcoding of expression patterns in single cells, termed MASC-seq. This technology enables both imaging and high-throughput single-cell analysis, characterizing thousands of single-cell transcriptomes per day at a low cost (0.13 USD/cell), which is two orders of magnitude less than commercially available systems. Our novel approach provides data in a rapid and simple way. Therefore, MASC-seq has the potential to accelerate the study of subtle clonal dynamics and help provide critical insights into disease development and other biological processes.
Osteoblast-specific overexpression of human interleukin-7 rescues the bone mass phenotype of interleukin-7–deficient female mice (2012)

Interleukin-7 is a critical cytokine for lymphoid development and a direct inhibitor of in vitro osteoclastogenesis in murine bone marrow cultures. To explore the role of IL-7 in bone, we generated transgenic mouse lines bearing the 2.3-kb rat collagen 1α1 promoter driving the expression of human IL-7 specifically in osteoblasts. In addition, we crossed these mice with IL-7-deficient mice to determine if the alterations in lymphopoiesis, bone mass, and osteoclast formation observed in the IL-7 knockout (KO) mice could be rescued by osteoblast-specific overexpression of IL-7. Here, we show that mice overexpressing human IL-7 in the osteoblast lineage showed increased trabecular bone volume in vivo by µCT and decreased osteoclast formation in vitro. Furthermore, targeted overexpression of IL-7 in osteoblasts rescued the osteopenic bone phenotype and B-cell development of IL-7 KO mice but did not have an effect on T lymphopoiesis, which occurs in the periphery. The bone phenotypes in IL-7 KO mice and targeted IL-7-overexpressing mouse models were observed only in females. These results likely reflect both direct inhibitory effects of IL-7 on osteoclastogenesis in vivo and sex-specific differences in responses to IL-7.
Intelligent Medical Diagnostics via Molecular Logic (2009)

In this communication, we describe the integration of microarray sensor technology with logic capability for screening combinations of proteins and DNA in a biological sample. In this system, we have demonstrated the use of a single platform amenable to both protein detection and protein-DNA detection using molecular logic gates. The pattern of protein and DNA inputs results in fluorescence outputs according to a truth table for AND and INHIBIT gates, thereby demonstrating the feasibility of performing medical diagnostics using a logic gate design. One possible application of this technique would be direct screening of various medical conditions that are dependent on combinations of diagnostic markers.
Excretion of alkaline phosphatase by Escherichia coli K-12 pho constitutive mutants transformed with plasmids carrying the alkaline phosphatase structural gene (1985)

Escherichia coli alkaline phosphatase constitutive mutants carrying a pst or a phoS mutation and a plasmid-bearing gene phoA+ excreted into the growth medium up to 50% of the total alkaline phosphatase production. This excretion was pH dependent and did not involve drastic modifications of the cell envelope. Alkaline phosphatase accounted for 80% of total released proteins. Amplification of gene phoA+ was a necessary condition for excretion to occur. When the beta-lactamase structural gene bla+ was coamplified with gene phoA+, both enzymes were excreted. pst-transformed excretory strains did not show the pleiotrophic phenotype previously described for lky mutants.