gebhart/patrepeval huggingface dataset:
Infrared MALDI Mass Spectrometry of Large Nucleic Acids (1998)

Mass spectrometry has become an increasingly important tool of high accuracy, efficiency, and speed for the routine analysis of nucleic acids. To make it useful for large-scale sequencing of genomic material as required for example in genotyping and clinical diagnosis, it is necessary to find approaches that allow the analysis of sequences much larger than the 100 nucleotides currently possible. Matrix-assisted laser desorption/ionization (MALDI) mass spectra of synthetic DNA, restriction enzyme fragments of plasmid DNA, and RNA transcripts up to a size of 2180 nucleotides are reported. The demonstrated mass accuracy of 1 percent or better and the sample requirement of a few femtomoles or less surpass all currently available techniques for the analysis of large nucleic acids. DNA and RNA can be analyzed with only a limited investment in sample purification.
AntMonitor (2015)

Mobile devices play an essential role in the Internet today, and there is an increasing interest in using them as a vantage point for network measurement from the edge. At the same time, these devices store personal, sensitive information, and there is a growing number of applications that leak it. We propose AntMonitor -- the first system of its kind that supports (i) collection of large-scale, semantic-rich network traffic in a way that respects users' privacy preferences and (ii) detection and prevention of leakage of private information in real time. The first property makes AntMonitor a powerful tool for network researchers who want to collect and analyze large-scale yet fine-grained mobile measurements. The second property can work as an incentive for using AntMonitor and contributing data for analysis. As a proof-of-concept, we have developed a prototype of AntMonitor, deployed it to monitor 9 users for 2 months, and collected and analyzed 20 GB of mobile data from 151 applications. Preliminary results show that fine-grained data collected from AntMonitor could enable application classification with higher accuracy than state-of-the-art approaches. In addition, we demonstrated that AntMonitor could help prevent several apps from leaking private information over unencrypted traffic, including phone numbers, emails, and device identifiers.
Tracking people with twists and exponential maps (2002)

This paper demonstrates a new visual motion estimation technique that is able to recover high degree-of-freedom articulated human body configurations in complex video sequences. We introduce the use of a novel mathematical technique, the product of exponential maps and twist motions, and its integration into a differential motion estimation. This results in solving simple linear systems, and enables us to recover robustly the kinematic degrees-of-freedom in noise and complex self occluded configurations. We demonstrate this on several image sequences of people doing articulated full body movements, and visualize the results in re-animating an artificial 3D human model. We are also able to recover and re-animate the famous movements of Eadweard Muybridge's motion studies from the last century. To the best of our knowledge, this is the first computer vision based system that is able to process such challenging footage and recover complex motions with such high accuracy.
Cerebrospinal fluid control system (1988)

An implantable, therapeutic system for hydrocephalus, with an noninvasively adjustable flow valve and a telemetered intracranial pressure (ICP) and cerebrospinal fluid (CSF) flow is presented. The system contains an implant unit, a patient unit, and a physician's console. This system provides an improved shunt system for the better treatment of hydrocephalus, accommodates changing patient needs without revision, helps to wean patients from shunt dependency, and collects information the physiological behavior of CSF generation and absorption. The nearly constant-flow microvalve can adjust its flow rate by external command through a transceiver link. The patients unit as well as the physician's console have a communications head that can communicate with the implant unit. It will receive online data and send in commands to adjust the valve position to alter CSF flow. The system has been designed and is currently being prototyped.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Alpha-1-antitrypsin (AAT) anomalies are associated with lung disease due to rapidly growing mycobacteria and AAT inhibits Mycobacterium abscessus infection of macrophages (2007)

Rapidly growing mycobacteria (RGM) are ubiquitous in the environment but cause lung disease in only a fraction of exposed individuals. This variable susceptibility to disease implies vulnerability to RGM infection due to weakness in host defense. Since most persons who contract RGM lung disease have no known host defense defect, it is likely that uncharacterized host deficiencies exist that predispose to RGM infection. Alpha-1-antitrypsin (AAT) is a host factor that may protect individuals from respiratory infections. Therefore, we assessed AAT protein anomalies as a risk factor for RGM lung disease. In a cohort of 100 patients with RGM lung disease, Mycobacterium (M.) abscessus was the most prevalent organism, isolated in 64 (64%) subjects. Anomalous AAT proteins were present in 27% of the cohort, which is 1.6 times the estimated prevalence of anomalous AAT proteins in the United States population (p=0.008). In in vitro studies, both AAT and a synthetic inhibitor of serine proteases suppressed M. abscessus infection of monocyte-derived macrophages by up to 65% (p<0.01). AAT may be an anti-RGM host-defense factor, and anomalous AAT phenotypes or AAT deficiency may constitute risk factors for pulmonary disease due to RGM.
Worldwide communications and information systems (1992)

The challenges facing providers of global communication and information systems are discussed. Globe-girdling systems are compared to more confined systems. Unique facets of global systems are illustrated using IBM's worldwide information system as an example of an integrated enterprise network. Progress is sketched in other uses, including travel reservation, banking and finance, military, research and education. It is concluded that global systems' evolution can be predicted, in large measure, from prior progress in shorter-reach applications.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Therapeutic Target Metabolism Observed Using Hyperpolarized 15N Choline (2008)

Choline is a precursor of cellular phospholipid metabolism that provides Magnetic Resonance (MR) and Positron Emission Tomography (PET) biomarkers for cancer detection and response assessment. Employing Dynamic Nuclear Polarization we show that the MR signal of 15N in choline can be enhanced by at least 4 orders of magnitude with a relaxation time of ca. 4 min, providing a method to observe the action of choline kinase, an important target for novel cancer therapeutics.
von Willebrand factor binds to platelets and induces aggregation in platelet-type but not type IIB von Willebrand disease. (1983)

Platelet-type von Willebrand disease (vWD) and pseudo-vWD are two recently described intrinsic platelet defects characterized by enhanced ristocetin-induced agglutination in platelet-rich plasma. A similar finding is also typical of type IIB vWD, where it has been related to a von Willebrand factor (vWF) rather than a platelet abnormality. Platelet aggregation induced by unmodified human vWF in the absence of other stimuli has been reported in pseudo-vWD. In this study we demonstrate that vWF induces aggregation in platelet-type but not type IIB vWD. Aggregation is observed when normal plasma cryoprecipitate or purified vWF are added to platelet-rich plasma. Cryoprecipitate also aggregates washed platelets, although at higher concentrations than required for platelet-rich plasma. Purified vWF, however, induces significant aggregation of washed platelets only when plasma is added. EDTA inhibits vWF-induced aggregation. Its effect can be overcome by calcium but much less effectively by magnesium ions. Unstimulated platelets in platelet-rich plasma from patients with platelet-type but not type IIB vWD bind 125I-vWF in a specific and saturable manner. All different sized multimers of vWF become associated with platelets. Both aggregation and binding exhibit a similar vWF concentration dependence, suggesting that a correlation exists between these two events. Removal of ADP by appropriate consuming systems is without effect upon such binding or upon vWF-induced aggregation. Thrombin-induced 125I-vWF binding to washed platelets is normal in platelet-type as well as type IIB vWD. These results demonstrate that a specific binding site for unmodified human vWF is exposed on unstimulated platelets in platelet-type vWD. The relatively high vWF concentrations required for aggregation and binding may explain the lack of significant in vivo aggregation and thrombocytopenia in these patients. Moreover, these studies provide additional evidence that platelet-type and type IIB vWD are different diseases with distinct pathogeneses.
Integrin α9 gene promoter is hypermethylated and downregulated in nasopharyngeal carcinoma (2015)

Epigenetic silencing of tumor suppressor genes (TSGs) by promoter methylation can be an early event in the multi-step process of carcinogenesis. Human chromosome 3 contains clusters of TSGs involved in many cancer types including nasopharyngeal carcinoma (NPC), the most common cancer in Southern China. Among ten candidate TSGs identified in chromosome 3 using NotI microarray, ITGA9 and WNT7A could be validated. 5'-aza-2' deoxycytidine treatment restored the expression of ITGA9 and WNT7A in two NPC cell lines. Immunostaining showed strong expression of these genes in the membrane and cytoplasm of adjacent control nasopharyngeal epithelium cells, while they were weakly expressed in NPC tumor cells. The ITGA9 promoter showed marked differentially methylation between tumor and control tissue, whereas no differentially methylation could be detected for the WNT7A promoter. The expression level of ITGA9 in NPC tumors was downregulated 4.9-fold, compared to the expression in control. ITGA9 methylation was detected by methylation specific PCR (MSP) in 56% of EBV positive NPC-cases with 100% specificity. Taken together, this suggests that ITGA9 might be a TSG in NPC that is involved in tumor cell biology. The possibility of using ITGA9 methylation as a marker for early detection of NPC should further be explored.
Electrothermal Bonding of Carbon Nanotubes to Glass (2008)

Applications that exploit the exceptional properties of carbon nanotubes CNTs[1] at practical length scales almost invariably involve the fundamental issues of nanotube-to-surface contacts; indeed, interface properties often dominate mechanical, electrical, and thermal performance in devices and materials based on CNTs. In this paper we present a method to attach CNTs to glass surfaces and investigate the mechanism of bonding at the interface. An electric field which induces migration of alkali ions from glass into CNTs, with a reversed polarity as compared to an analogous anodic bonding configuration, is employed to form a chemical bond between nanotubes and glass. We report a pull-off force of 4.35 N/cm2 averaged over the bonded area, with the possibility of localized areas of higher bonding strength.
Reversal of Chemoresistance of Lymphoma Cells by Antisense-Mediated Reduction of bcl -2 Gene Expression (1994)

The bcl-2 gene is expressed in many types of human tumours and becomes transcriptionally deregulated in the majority of non-Hodgkin's lymphomas as the result of t(14;18) chromosomal translocations. The 26-kDa Bcl-2 protein has been shown to block programmed cell death (apoptosis) induced by many types of stimuli, including a wide variety of chemotherapeutic drugs and radiation. The presence of bcl-2 in tumor cells has been correlated with poor responses to therapy in patients with some types of cancer. To explore further the relevance of bcl-2 to drug resistance, we used antisense (As) approaches to achieve reductions in the levels of steady state Bcl-2 protein levels in t(14;18)-containing human lymphoma cell lines. Both synthetic bcl-2-As oligonucleotides and inducible expression plasmids that produce bcl-2-As transcripts induced reductions in bcl-2 expression, resulting in a marked enhancement in the sensitivity of neoplastic cells to conventional chemotherapeutic drugs such as cytosine arabinoside (ara-C) and methotrexate (MTX). These results suggest that novel therapeutics targeted against bcl-2 could provide the means for improved treatment of cancer by affecting physiological pathways distal to the targets of cytotoxic drugs.
Absolute length calibration of gauge blocks using optical comb of a femtosecond pulse laser (2006)

We report an exploitation of the optical comb of a femtosecond pulse laser as the wavelength ruler for the task of absolute length calibration of gauge blocks. To that end, the optical comb was stabilized to the Rb clock of frequency standard and an optical frequency synthesizer was constructed by tuning an external single-frequency laser to the optical comb. The absolute height of gauge blocks was measured by means of multi-wavelength interferometry using multiple beams of different wavelengths consecutively provided by the optical frequency synthesizer. The wavelength uncertainty was measured 1.9 x 10(-10) that leads to an overall calibration uncertainty of 15 nm (k=1) in determining the absolute length of gauge blocks.
Peripheral vestibular disorders (2012)

Although progress has been made in the diagnosis and treatment of most peripheral vestibular disorders, more state-of-the-art trials are needed on the treatment of bilateral vestibulopathy to prove the efficacy of balance training, of vestibular neuritis (in terms of recovery of peripheral vestibular function and central compensation), of vestibular paroxysmia to prove the effects of carbamazepine, and of Menière's disease to find the optimal dosage of betahistine.
Quantitative determination of 13C‐labeled and endogenous β‐carotene, lutein, and vitamin A in human plasma (2001)

Quantitative procedures employing liquid-chromatography/particle beam-mass spectrometry (LC/PB-MS) and gas chromatography-mass spectrometry (GC-MS) were applied to the determination of the endogenous and 13C-labeled beta-carotene, lutein, and retinol in plasma of a subject who consumed kale (Brassica oleracea) that had been grown in a 13CO2-enriched atmosphere. All compounds were analyzed in the negative chemical ionization (NCI) mode using methane as the moderating reagent gas. Beta-carotene and lutein were analyzed using LC/PB-MS applying reversed-phase high-performance liquid chromatography (HPLC) separation procedures to resolve the analytes. The concentrations of the beta-carotene isotopomers in the plasma over a several-week period were determined using 2H8-beta-carotene as an internal standard. The total plasma concentrations of all trans-lutein were quantified by HPLC analysis with a photodiode array detector using beta-apo-8'-carotenal as an internal standard, and the ratio of the 13C:12C isotopomers of lutein was determined by PB-MS. The retinol isotopomers were collected from individual HPLC fractions of the plasma extract and then analyzed as the trimethylsilyl ethers by GC-MS in the NCI mode. The 13C- and 12C-retinol isotopomers were quantified using 2H4-retinol as an internal standard. These methods demonstrate the application of highly sensitive procedures employing NCI MS for the quantitative determination of carotenoids and vitamin A for the purpose of conducting metabolism studies of phytonutrients.
Neonatal Neural Progenitor Cells and Their Neuronal and Glial Cell Derivatives Are Fully Permissive for Human Cytomegalovirus Infection (2008)

Congenital human cytomegalovirus (HCMV) infection causes central nervous system structural abnormalities and functional disorders, affecting both astroglia and neurons with a pathogenesis that is only marginally understood. To better understand HCMV's interactions with such clinically important cell types, we utilized neural progenitor cells (NPCs) derived from neonatal autopsy tissue, which can be differentiated down either glial or neuronal pathways. Studies were performed using two viral isolates, Towne (laboratory adapted) and TR (a clinical strain), at a multiplicity of infection of 3. NPCs were fully permissive for both strains, expressing the full range of viral antigens (Ags) and producing relatively large numbers of infectious virions. NPCs infected with TR showed delayed development of cytopathic effects (CPE) and replication centers and shed less virus. This pattern of delay for TR infections held true for all cell types tested. Differentiation of NPCs was carried out for 21 days to obtain either astroglia (>95% GFAP(+)) or a 1:5 mixed neuron/astroglia population (beta-tubulin III(+)/GFAP(+)). We found that both of these differentiated populations were fully permissive for HCMV infection and produced substantial numbers of infectious virions. Utilizing a difference in plating efficiencies, we were able to enrich the neuron population to approximately 80% beta-tubulin III(+) cells. These beta-tubulin III(+)-enriched populations remained fully permissive for infection but were very slow to develop CPE. These infected enriched neurons survived longer than either NPCs or astroglia, and a small proportion were alive until at least 14 days postinfection. These surviving cells were all beta-tubulin III(+) and showed viral Ag expression. Surprisingly, some cells still exhibited extended processes, similar to mock-infected neurons. Our findings strongly suggest neurons as reservoirs for HCMV within the developing brain.
Hematopoietic Stem Cell in Acute Myeloid Leukemia Development (2012)

the process maintains the same number of stem cells. This is accomplished by the so-called asymmetric cell division, so that each dividing stem cell originates one new stem cell and one differentiated cell (Gordon, 2005) (Figure In the symmetric division, the stem cells originate 100% of identical stem cells.
Thermal, Chemical, and Enzymatic Stability of the Cyclotide Kalata B1:  The Importance of the Cyclic Cystine Knot (2004)

The cyclotides constitute a recently discovered family of plant-derived peptides that have the unusual features of a head-to-tail cyclized backbone and a cystine knot core. These features are thought to contribute to their exceptional stability, as qualitatively observed during experiments aimed at sequencing and characterizing early members of the family. However, to date there has been no quantitative study of the thermal, chemical, or enzymatic stability of the cyclotides. In this study, we demonstrate the stability of the prototypic cyclotide kalata B1 to the chaotropic agents 6 M guanidine hydrochloride (GdHCl) and 8 M urea, to temperatures approaching boiling, to acid, and following incubation with a range of proteases, conditions under which most proteins readily unfold. NMR spectroscopy was used to demonstrate the thermal stability, while fluorescence and circular dichroism were used to monitor the chemical stability. Several variants of kalata B1 were also examined, including kalata B2, which has five amino acid substitutions from B1, two acyclic permutants in which the backbone was broken but the cystine knot was retained, and a two-disulfide bond mutant. Together, these allowed determinations of the relative roles of the cystine knot and the circular backbone on the stability of the cyclotides. Addition of a denaturant to kalata B1 or an acyclic permutant did not cause unfolding, but the two-disulfide derivative was less stable, despite having a similar three-dimensional structure. It appears that the cystine knot is more important than the circular backbone in the chemical stability of the cyclotides. Furthermore, the cystine knot of the cyclotides is more stable than those in similar-sized molecules, judging by a comparison with the conotoxin PVIIA. There was no evidence for enzymatic digestion of native kalata B1 as monitored by LC-MS, but the reduced form was susceptible to proteolysis by trypsin, endoproteinase Glu-C, and thermolysin. Fluorescence spectra of kalata B1 in the presence of dithiothreitol, a reducing agent, showed a marked increase in intensity thought to be due to removal of the quenching effect on the Trp residue by the neighboring Cys5-Cys17 disulfide bond. In general, the reduced peptides were significantly more susceptible to chemical or enzymatic breakdown than the oxidized species.
Enzymatic and extraenzymatic role of ecto‐adenosine deaminase in lymphocytes (1998)

Adenosine deaminase (ADA, EC 3.5.4.4) is an enzyme of the purine metabolism which has been the object of considerable interest mainly because the congenital defect causes severe combined immunodeficiency (SCID). In the last 10 years, ADA, which was considered to be cytosolic, has been found on the cell surface of many cells and, therefore, it can be considered an ecto-enzyme. There is recent evidence about a specific role of ecto-ADA, which is different from that of intracellular ADA. Apart from degrading extracellular adenosine (Ado) or 2'-deoxyadenosine (dAdo), which are toxic for lymphocytes, ecto-ADA has an extraenzymatic function via its interaction with CD26. ADA/CD26 interaction results in co-stimulatory signals in T cells. This co-stimulation is blocked by HIV-1, thus evidencing a role for ecto-ADA in the pathophysiology of AIDS. The fact that, besides CD26, ADA can interact with different cell-surface proteins opens new perspectives in the research for a role of ecto-ADA in the function of the immune system and in the interactions that take place between different cells in the development of the immune system. The most interesting aspect is the possible participation of the ecto-enzyme in cell-to-cell contacts during ontogenesis and maturation of immunocompetent cells.
Cigarette Smoke Exposure and Hypercholesterolemia Increase Mitochondrial Damage in Cardiovascular Tissues (2002)

These data are consistent with the hypothesis that cardiovascular disease risk factors cause mitochondrial damage and dysfunction.
Getting the inside out: the transporter associated with antigen processing (TAP) and the presentation of viral antigen. (1995)

Micro-nano plastics originating from the prevalent usage of plastics have raised increasingly alarming concerns worldwide. However, there remains a fundamental knowledge gap in nanoplastics because of the lack of effective analytical ...Plastics are now omnipresent in our daily lives. The existence of microplastics (1 µm to 5 mm in length) and possibly even nanoplastics (<1 μm) has recently raised health concerns. In particular, nanoplastics are believed to be more toxic since their ...
Computing the aspect graph for line drawings of polyhedral objects (1990)

An algorithm for computing the aspect graph for polyhedral objects is described. The aspects graph is a representation of three-dimensional objects by a set of two-dimensional views. The set of viewpoints on the Gaussian sphere is partitioned into regions such that in each region the qualitative structure of the line drawing remains the same. At the boundaries between adjacent regions are the accidental viewpoints where the structure for the line drawing changes. It is shown that for polyhedral objects there are two fundamental visual events: (1) the projections of an edge and a vertex coincide; and (2) the projections of three nonadjacent edges intersect at a point. The geometry of the object is reflected in the locus of the accidental viewpoints. The algorithm computes the partition together with a representative view for each region of the partition.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>