gebhart/patrepeval huggingface dataset:
Biomechanical Diversity Despite Mechanobiological Stability in Tissue Engineered Vascular Grafts Two Years Post-Implantation (2015)

Recent advances in vascular tissue engineering have enabled a paradigm shift from ensuring short-term graft survival to focusing on long-term stability and growth potential. We present the first experimental-computational study of a tissue-engineered vascular graft (TEVG) effectively over the full lifespan of the recipient. We show that grafts implanted within the venous circulation of mice remained patent over 2 years without thrombus, stenosis, or aneurysmal dilatation. Moreover, the gross appearance and mechanical properties of the grafts evolved to be similar to the host vein within 24 weeks, with mean neovessel geometry and properties remaining unchanged thereafter despite a continued turnover of extracellular matrix. Biomechanical diversity manifested after 24 weeks, however, via two subsets of grafts despite all procedures being the same. Computational modeling and associated immunohistological analyses suggested that this diversity likely resulted from a differential ratio of collagen types I and III, with lower I to III ratios promoting grafts having a compliance similar to the native vein. We submit that TEVGs can exhibit the desired long-term mechanobiological stability; hence, we must now focus on evaluating growth potential and optimizing scaffold properties to achieve compliance matching throughout neovessel development.
Designing neutral metallophilic hydrogels from di- and tripeptides (2011)

Here we report the metallophilic attraction driven gel-forming capability of four cysteine-containing short peptides at neutral pH. Such peptides were designed to have an isoelectric point (pI) close to 7, aided by the introduction of an arginine unit with its highly basic guanidinium group.
Comparative evaluation of medicated and non-medicated IUDs of the same size and shape. (1980)

The size of non-medicated IUDs has a partial bearing on their contraceptive activity while the efficiency of copper-bearing IUDs depends mainly on the amount of copper added to the IUD. Non-medicated IUDs commonly used are larger and those with added copper are smaller. In comparing the expulsion rates and the number of bleeding/pain removals in the 2 types, the question persists whether the reduced frequency of these events, usually ascribed to copper-bearing IUDs, is the direct consequence of the copper ion activity or of the reduced size. A comparative analysis of IUD performance in age/parity adjusted users has shown that after 1-2 years, net cumulative pertinent event rates were not significantly different for plain and copper-bearing Spring Coil users. Both users of the 2 types of Spring Coil experienced increased amount and duration of menstrual flow. Preliminary data for Lippes Loop D with and without copper show similar results. Thus it was concluded that the addition of copper to the large devices failed to improve performance, and, therefore, its addition should be reserved only for small devices which do not offer efficient contraceptive protection in their inert form. Use of smaller devices which produce less endometrial trauma and consequently less bleeding is preferred as the association between copper activity and reduced bleeding is not upheld.
Urinary Proteomic Biomarkers for Diagnosis and Risk Stratification of Autosomal Dominant Polycystic Kidney Disease: A Multicentric Study (2013)

Treatment options for autosomal dominant polycystic kidney disease (ADPKD) will likely become available in the near future, hence reliable diagnostic and prognostic biomarkers for the disease are strongly needed. Here, we aimed to define urinary proteomic patterns in ADPKD patients, which aid diagnosis and risk stratification. By capillary electrophoresis online coupled to mass spectrometry (CE-MS), we compared the urinary peptidome of 41 ADPKD patients to 189 healthy controls and identified 657 peptides with significantly altered excretion, of which 209 could be sequenced using tandem mass spectrometry. A support-vector-machine based diagnostic biomarker model based on the 142 most consistent peptide markers achieved a diagnostic sensitivity of 84.5% and specificity of 94.2% in an independent validation cohort, consisting of 251 ADPKD patients from five different centers and 86 healthy controls. The proteomic alterations in ADPKD included, but were not limited to markers previously associated with acute kidney injury (AKI). The diagnostic biomarker model was highly specific for ADPKD when tested in a cohort consisting of 481 patients with a variety of renal and extrarenal diseases, including AKI. Similar to ultrasound, sensitivity and specificity of the diagnostic score depended on patient age and genotype. We were furthermore able to identify biomarkers for disease severity and progression. A proteomic severity score was developed to predict height adjusted total kidney volume (htTKV) based on proteomic analysis of 134 ADPKD patients and showed a correlation of r = 0.415 (p<0.0001) with htTKV in an independent validation cohort consisting of 158 ADPKD patients. In conclusion, the performance of peptidomic biomarker scores is superior to any other biochemical markers of ADPKD and the proteomic biomarker patterns are a promising tool for prognostic evaluation of ADPKD.
Immune Response to Postprimary Tuberculosis in Mice:<i>Mycobacterium tuberculosis</i>and<i>Miycobacterium bovis</i>bacille Calmette‐Guérin Induce Equal Protection (2004)

We addressed the question of whether protective immunity induced by natural infection with Mycobacterium tuberculosis and that induced by vaccination with Mycobacterium bovis bacille Calmette-Guerin (BCG) differ in the murine model. We infected mice with M. tuberculosis Erdman, cured them by chemotherapy, and subsequently reinfected them with a low dose of M. tuberculosis H37Rv. The course of tuberculosis was compared with that in mice previously vaccinated with BCG Danish 1331. Protection against postprimary M. tuberculosis infection did not differ significantly between the 2 groups. After challenge infection, numbers of interferon- gamma -positive splenocytes did not differ between mice with primary infection and vaccinated mice. Splenocytes from primary M. tuberculosis-infected mice conferred marginally higher protection than did those from BCG-vaccinated mice. Serum transfer did not protect against reinfection in either group. Our data emphasize that natural infection with M. tuberculosis and vaccination with BCG do not differ in their capacity to induce protective immunity against tuberculosis and support the notions that reinfection contributes to the development of active disease and that any novel vaccine against tuberculosis has to perform better than both vaccination with BCG and immunity evoked by natural infection.
Spatial Partitioning of Large Urban Road Networks (2014)

The rapid global migration of people towards urban areas is multiplying the traffic volume on urban road networks. As a result these networks are rapidly growing in size, in which different sub-networks exhibit distinctive traffic flow patterns. In this paper, we propose a scalable framework for traffic congestion-based spatial partitioning of large urban road networks. It aims to identify different sub-networks or partitions that exhibit homogeneous traffic congestion patterns internally, but heterogenous to others externally. To this end, we develop a two-stage procedure within our framework that first transforms the large road graph into a well-structured and condensed supergraph via clustering and link aggregation based on traffic density and adjacency connectivity, respectively. We then devise a spectral theory based novel graph cut (referred as α-Cut) to partition the supergraph and compare its performance with that of an existing method for partitioning urban networks. Our results show that the proposed method outperforms the normalized cut based existing method in all the performance evaluation metrics for small road networks and provides good results for much larger networks where other methods may face serious problems of time and space complexities.
Quantitative Superresolution Microscopy Reveals Differences in Nuclear DNA Organization of Multiple Myeloma and Monoclonal Gammopathy of Undetermined Significance (2014)

The mammalian nucleus has a distinct substructure that cannot be visualized directly by conventional microscopy. In this study, the organization of the DNA within the nucleus of multiple myeloma (MM) cells, their precursor cells (monoclonal gammopathy of undetermined significance; MGUS) and control lymphocytes of the representative patients is visualized and quantified by superresolution microscopy. Three-dimensional structured illumination microscopy (3D-SIM) increases the spatial resolution beyond the limits of conventional widefield fluorescence microscopy. 3D-SIM reveals new insights into the nuclear architecture of cancer as we show for the first time that it resolves organizational differences in intranuclear DNA organization of myeloma cells in MGUS and in MM patients. In addition, we report a significant increase in nuclear submicron DNA structure and structure of the DNA-free space in myeloma nuclei compared to normal lymphocyte nuclei. Our study provides previously unknown details of the nanoscopic DNA architecture of interphase nuclei of the normal lymphocytes, MGUS and MM cells. This study opens new avenues to understanding the disease progression from MGUS to MM.
Efficient Weight Vector Representation for Closed-Loop Transmit Diversity (2004)

For a closed-loop transmit (Tx) diversity, the Tx weights are calculated at a receiver, and fed back to a transmitter. As the number of Tx antennas increases, the potential gain of closed-loop Tx diversity may be significant. However, the amount of feedback information, which is the number of Tx weights that should be fed back, linearly increases, and the performance improvement of a closed-loop Tx diversity system may not be as significant as expected due to delay in the feedback process. Thus, an efficient Tx weight representation, which can reduce the amount of feedback information, is needed. In this letter, a Tx weight vector representation is presented, and its performance is analyzed. Analysis shows that this weight vector representation, referred to as basis selection, significantly reduces the amount of feedback information with little performance degradation.
Electronic energy levels in<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mrow><mml:mi mathvariant="normal">In</mml:mi></mml:mrow><mml:mrow><mml:mi mathvariant="normal">x</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math><mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mrow><mml:mi mathvariant="normal">Ga</mml:mi></mml:mrow><mml:mrow><mml:mn>1</mml:mn><mml:mi mathvariant="normal">−</mml:mi><mml:mi mathvariant="normal">x</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math>As/InP strained-layer superlattices (1987)

We use intentionally-lattice-mismatched superlattices of ${\mathrm{In}}_{\mathrm{x}}$${\mathrm{Ga}}_{1\mathrm{\ensuremath{-}}\mathrm{x}}$As/InP, where 0.3x0.8, to study the energy levels of confined-particle states characteristic of strained-layer superlattices. We demonstrate that the energy difference between the lowest heavy- and light-hole exciton levels of ${\mathrm{In}}_{\mathrm{x}}$${\mathrm{Ga}}_{1\mathrm{\ensuremath{-}}\mathrm{x}}$As quantum wells changes continuously with strain. For x0.44 the exciton levels switch positions so that the light hole becomes the lower-energy state. The experimental results can be modeled with very high accuracy over the entire range of In compositions studied with a phenomenological deformation-potential theory.
Electroluminescence of pure poly(<i>N</i>-vinylcarbazole) and its blends with a multiblock copolymer (1994)

Electroluminescence (EL) in pure poly(N-vinylcarbazole) (PVK) has been observed in a simple single active layer EL device with the structure of ITO/PVK/Al (or Ca). The emitted light is violet with a maximum intensity at 426 nm; a part of the spectrum lies within the UV region. Blends of PVK with a conjugated-nonconjugated multiblock copolymer (CNMBC) previously described are also electroluminescent. In these blends a new emission peak in the EL spectra appeared and can be attributed to the emission from an exciplex formed by the two polymers. As the composition of the aforementioned blend changes from a PVK-poor to a PVK-rich ratio, the emitted light changes from green to blue. Further, blends containing 97 wt. % PVK and 3 wt. % CNMBC yielded an EL spectrum with a single emission peak different in location from either that of pure PVK or the pure CNMBC; the latter is blue with a maximum intensity at 476 nm. The EL output of the blends can be clearly seen in a brightly lit room at ambient temperature. An electron transport layer consisting of butyl-2-(4-biphenyl)-5-(4-tert-butylphenyl-1,3,4-oxadiazole) (PBD) in PMMA on the cathodic side of the EL device greatly increased the brightness of the emitted light to 200 cd/m2 in the case of a PVK-rich blend, but it had less effect on a PVK-poor blend or in pure PVK and had little effect on the pure form of the CNMBC.
Endothelial dysfunction and inflammation—is there a link? (2001)

The endothelium is a functional barrier between vessel wall and blood stream that for a long time has been regarded as a relatively inert container for blood. However, the last 20 years, researchers have found an extraordinary variety of important endothelial functions, including control of coagulation, fibrinolysis, vascular tone, growth, and immune response. The endothelium modulates vascular tone by releasing a number of vasoactive substances including nitric oxide (NO). It is now clear that dysfunction of the endothelium disturbs the physiological protective regulatory balance, which is a critical factor in the atherosclerotic disease progression. Thus, endothelial dysfunction occurs in many diseasesudisorders associated with an increased cardiovascular risk, such as essential hypertension w1x, dyslipidaemia w2x, smoking w3x and mental stress w4x. The significant burden of atherosclerotic cardiovascular disease (CVD) in end-stage renal disease (ESRD) has been recognized since more than 25 years w5x. The increased incidence of CVD is probably the result of a high prevalence of both traditional risk factors (such as hypertension, dyslipidaemia, and smoking) and non-traditional risk factors (such as inflammation, oxidative stress, advanced glycation end products, and homocysteine). C-reactive protein (CRP), a sensitive and objective marker of one non-traditional risk factor, inflammation, has been shown to be associated to CVD in both predialysis w6x and dialysis w7x patients populations.
Mechanisms of secondary injury to spinal cord axons in vitro: role of Na+, Na(+)-K(+)-ATPase, the Na(+)-H+ exchanger, and the Na(+)-Ca2+ exchanger (1996)

There is evidence that intracellular Na+ entry potentiates hypoxic-ischemic cell death by causing cytotoxic cell edema, intracellular acidosis, and gating of Ca2+ entry by reverse activation of the Na(+)-Ca2+ exchanger. In this study, we examined the role of Na+ in mediating traumatic injury to spinal cord axons. Dorsal column segments from adult rats (n = 87) were isolated and maintained in an in vitro recording chamber while being superfused with oxygenated Ringer's solution (95% O2/5% CO2, 25 degrees C). Selected experiments (n = 10) also were done at 33 degrees C. Compound action potentials (CAP) were recorded from microelectrodes. Injury was performed by compression of the dorsal column segment for 15 sec with a modified aneurysm clip exerting a closing force of 2 gm. With injury, the CAP decreased to 72.1 +/- 9.6% of baseline values. Removal of extracellular Na+ and replacement with the impermeant cation N-methyl-D-glucamine enhanced recovery of the CAP to 98.3 +/- 18.3% (p < 0.05) of baseline. The Na+ channel blockers tetrodotoxin and procaine also improved recovery of the CAP to 96.3 +/- 23.7% (p < 0.05) and 82.8 +/- 4.6% (p < 0.05) of baseline values, respectively. In contrast, increasing Na+ permeability with veratridine resulted in greater attenuation of CAP amplitude after 1 hr of trauma (60.1 +/- 8.4%, p < 0.05). Similarly, prevention of extrusion of Na+ from the intracellular compartment by inhibiting the Na(+)-K(+)-ATPase pump with ouabain resulted in greater attenuation of CAP amplitude at 1 hr after trauma (56.7 +/- 3.6%, p < 0.05). The Na(+)-H+ exchange blockers amiloride (100 microM) and harmaline (100 microM) significantly improved recovery after injury to 89.6 +/- 17.0% (p < 0.05) and 85.7 +/- 7.2% (p < 0.05) of baseline, respectively. However, administration of the Na(+)-Ca2+ exchange blockers benzamil (100 or 500 microM) and bepridil (50 microM) was ineffective. In summary, reduction of extracellular Na+ confers neuroprotection after spinal cord injury in vitro. Intracellular sodium rises appear to be mediated by voltage-gated Na+ channels. Blockade of the Na(+)-H+ exchanger also is neuroprotective, possibly by reducing intracellular acidosis. Furthermore, prevention of extrusion of intracellular Na+ by the Na(+)-K(+)-ATPase pump exacerbates the effects of compression trauma. However, reverse operation of the Na(+)-Ca2+ exchanger does not explain the injurious effects of Na+ in traumatically injured CNS white matter.
Functional significance of phosphorylation to the human immunodeficiency virus Rev protein (1989)

The human immunodeficiency virus Rev protein is posttranslationally modified by a serine kinase activity present in the nucleus of the cell. Site-directed mutagenesis was used to identify the site of phosphorylation. Changing of serine residues 92 and 99 dramatically reduced Rev phosphorylation, suggesting that at least one, if not both, of these residues is the one recognized by the Rev-specific serine kinase. Similarly, a truncated Rev protein lacking the 25 carboxy-terminal amino acids was not phosphorylated. By using two independent assays, both the serine mutant proteins and the truncated form of Rev were found to be fully functional. Thus, phosphorylation and the 25 carboxy-terminal amino acids appear to be dispensable for protein function.
On some cryptographic solutions for access control in a tree hierarchy (1987)

We consider the access control problem in a system where users and information items are classified into security classes organized as a rooted tree, with the most privileged security class at the root. In practice we expect such a tree to be quite broad and shallow. It is also inevitable that new security classes will need to be added as the needs of the organization evolve. We compare some cryptographic techniques which have been proposed in the literature for solution of this problem.
Synthesis of p-Co3O4/n-TiO2 Nanoparticles for Overall Water Splitting under Visible Light Irradiation (2016)

p-Co₃O₄/n-TiO₂ nanoparticles (~400 nm) for photocatalysis were prepared via carbon assisted method and sol-gel method in this work. The paper also studied the application of visible light illuminated p-Co₃O₄/n-TiO₂ nanocomposites cocatalyst to the overall pure water splitting into H₂ and O₂. In addition, the H₂ evolution rate of the p-Co₃O₄/n-TiO₂ nanocomposites is 25% higher than that of the pure Co₃O₄ nanoparticles. Besides, according to the results of the characterizations, the scheme of visible light photocatalytic water splitting is proposed, the Co₃O₄ of the nanocomposites is excited by visible light, and the photo-generated electrons and holes existing on the conduction band of Co₃O₄ and valence band of TiO₂ have endowed the photocatalytic evolution of H₂ and O₂ with higher efficiency. The optimal evolution rate of H₂ and O₂ is 8.16 μmol/h·g and 4.0 μmol/h·g, respectively.
Optimal design of achromatic true zero-order waveplates using twisted nematic liquid crystal (2005)

Phase retarders usually show strong wavelength dependence. A novel and simple configuration with the combination of two twisted nematic liquid-crystal cells is proposed for the design of a true zero-order achromatic quarter-wave plate. The present optimization method considers the material dispersion. Simulation computations show a good achromatic behavior of the optimized waveplate. Compared with other types of broadband quarter-wave plates, the present device is compatible with classical liquid-crystal displays and can be expected to be used in precision polarimeters with low cost and enhanced light efficiency.
Absence of Ni on the outer surface of Sr doped La<sub>2</sub>NiO<sub>4</sub>single crystals (2013)

A combination of surface sensitive techniques was used to determine the surface structure and chemistry of La2−xSrxNiO4+δ. These measurements unequivocally showed that Ni is not present in the outermost atomic layer, suggesting that the accepted model with the B-site cations exposed to the environment is incorrect.
OLAP with UDFs in digital libraries (2009)

Queries on digital libraries generally involve the retrieval of specific documents, but most techniques lack the ability to efficiently explore these collections. The integration of OLAP techniques with digital libraries allows users to navigate throughout these collections on multiple levels. In order to accomplish this, we propose the creation of OLAP networks, a complex data structure that contains summarized representations of the original collection of metadata to enrich traditional retrievals and allow the users to quickly explore the collection. We developed a system that enables OLAP-based exploration on the metadata of digital libraries through the use of a combination of efficient UDFs and optimized SQL queries. In addition, we also incorporated visualization methods into our system to allow fast navigation and exploration.
Single-cell sequencing provides clues about the host interactions of segmented filamentous bacteria (SFB) (2012)

Segmented filamentous bacteria (SFB) are host-specific intestinal symbionts that comprise a distinct clade within the Clostridiaceae, designated Candidatus Arthromitus. SFB display a unique life cycle within the host, involving differentiation into multiple cell types. The latter include filaments that attach intimately to intestinal epithelial cells, and from which "holdfasts" and spores develop. SFB induce a multifaceted immune response, leading to host protection from intestinal pathogens. Cultivation resistance has hindered characterization of these enigmatic bacteria. In the present study, we isolated five SFB filaments from a mouse using a microfluidic device equipped with laser tweezers, generated genome sequences from each, and compared these sequences with each other, as well as to recently published SFB genome sequences. Based on the resulting analyses, SFB appear to be dependent on the host for a variety of essential nutrients. SFB have a relatively high abundance of predicted proteins devoted to cell cycle control and to envelope biogenesis, and have a group of SFB-specific autolysins and a dynamin-like protein. Among the five filament genomes, an average of 8.6% of predicted proteins were novel, including a family of secreted SFB-specific proteins. Four ADP-ribosyltransferase (ADPRT) sequence types, and a myosin-cross-reactive antigen (MCRA) protein were discovered; we hypothesize that they are involved in modulation of host responses. The presence of polymorphisms among mouse SFB genomes suggests the evolution of distinct SFB lineages. Overall, our results reveal several aspects of SFB adaptation to the mammalian intestinal tract.