gebhart/patrepeval huggingface dataset:
<title>AFM tip calibration using nanometer-sized structures induced by ion beam sputtering</title> (2001)

Atomic force microscopy (AFM) is usually the instrument of choice for the investigation of the surface roughness of thin films. Often a detailed image and roughness analysis is hindered by tip artifacts. Many of these artifacts arise from a spatial convolution or dilation of the actual tip and the shape of the surface features imaged. Therefore a careful tip evaluation and calibration is important for a reliable roughness evaluation. In this study about a process for the fabrication of self- assembled nanometer-sized surface structures using low- energy ion sputtering of semiconductor surfaces is reported. The dimension of these structures (typically between 10 and 100 nm), the distance between them and their shape can be tuned by the parameters of the sputter process. With the help of surfaces prepared by this way the influence of the actual AFM tip quality on the measured surface topography was evaluated. Furthermore, it is shown that the tip quality has a strong influence on the parameters extracted from first- and second-order statistics of the surface roughness. This applies particularly with regard to surfaces characterized by a low surface roughness (approximately 1 nm) as generally obtained by means of thin film technologies.
Ligand-Directed Surface Profiling of Human Cancer Cells with Combinatorial Peptide Libraries (2006)

A collection of 60 cell lines derived from human tumors (NCI-60) has been widely explored as a tool for anticancer drug discovery. Here, we profiled the cell surface of the NCI-60 by high-throughput screening of a phage-displayed random peptide library and classified the cell lines according to the binding selectivity of 26,031 recovered tripeptide motifs. By analyzing selected cell-homing peptide motifs and their NCI-60 recognition patterns, we established that some of these motifs (a) are similar to domains of human proteins known as ligands for tumor cell receptors and (b) segregate among the NCI-60 in a pattern correlating with expression profiles of the corresponding receptors. We biochemically validated some of the motifs as mimic peptides of native ligands for the epidermal growth factor receptor. Our results indicate that ligand-directed profiling of tumor cell lines can select functional peptides from combinatorial libraries based on the expression of tumor cell surface molecules, which in turn could be exploited as "druggable" receptors in specific types of cancer.
A supervised learning approach for diffusion MRI quality control with minimal training data (2018)

Quality control (QC) is a fundamental component of any study. Diffusion MRI has unique challenges that make manual QC particularly difficult, including a greater number of artefacts than other MR modalities and a greater volume of data. The gold standard is manual inspection of the data, but this process is time-consuming and subjective. Recently supervised learning approaches based on convolutional neural networks have been shown to be competitive with manual inspection. A drawback of these approaches is they still require a manually labelled dataset for training, which is itself time-consuming to produce and still introduces an element of subjectivity. In this work we demonstrate the need for manual labelling can be greatly reduced by training on simulated data, and using a small amount of labelled data for a final calibration step. We demonstrate its potential for the detection of severe movement artefacts, and compare performance to a classifier trained on manually-labelled real data.
Hands-on math (2010)

Students, scientists and engineers have to choose between the flexible, free-form input of pencil and paper and the computational power of Computer Algebra Systems (CAS) when solving mathematical problems. Hands-On Math is a multi-touch and pen-based system which attempts to unify these approaches by providing virtual paper that is enhanced to recognize mathematical notations as a means of providing in situ access to CAS functionality. Pages can be created and organized on a large pannable desktop, and mathematical expressions can be computed, graphed and manipulated using a set of uni- and bi-manual interactions which facilitate rapid exploration by eliminating tedious and error prone transcription tasks. Analysis of a qualitative pilot evaluation indicates the potential of our approach and highlights usability issues with the novel techniques used.
Alterations in mitosis and cell cycle progression caused by a mutant lamin A known to accelerate human aging (2007)

Mutations in the gene encoding nuclear lamin A (LA) cause the premature aging disease Hutchinson-Gilford Progeria Syndrome. The most common of these mutations results in the expression of a mutant LA, with a 50-aa deletion within its C terminus. In this study, we demonstrate that this deletion leads to a stable farnesylation and carboxymethylation of the mutant LA (LADelta50/progerin). These modifications cause an abnormal association of LADelta50/progerin with membranes during mitosis, which delays the onset and progression of cytokinesis. Furthermore, we demonstrate that the targeting of nuclear envelope/lamina components into daughter cell nuclei in early G(1) is impaired in cells expressing LADelta50/progerin. The mutant LA also appears to be responsible for defects in the retinoblastoma protein-mediated transition into S-phase, most likely by inhibiting the hyperphosphorylation of retinoblastoma protein by cyclin D1/cdk4. These results provide insights into the mechanisms responsible for premature aging and also shed light on the role of lamins in the normal process of human aging.
Phoneme classification using naive Bayes classifier in reconstructed phase space (2005)

A novel method for classifying speech phonemes is presented. Unlike traditional cepstral based methods, this approach uses histograms of reconstructed phase spaces. A naive Bayes classifier uses the probability mass estimates for classification. The approach is verified using isolated fricative, vowel, and nasal phonemes from the TIMIT corpus. The results show that a reconstructed phase space approach is a viable method for classification of phonemes, with the potential for use in a continuous speech recognition system.
New York Address (1985)

Alma in the DarkShe reaches over and puts a hand on his hipbone and presses.He turns softly away and she makes his shape against the back, her arm around the waist covering his unguarded stomach.
Structure-function analysis of the human interferon gamma. The COOH terminus is not essential for functional activity. (1990)

The structure-function relationships for the human interferon gamma (HuIFN-gamma) were studied using recombinant variants that had various deletions at the carboxyl terminus. Four COOH-terminal deletion variants were constructed that contained the amino-terminal 122, 117, 111, and 106 amino acid residues. These variants were constructed by specific DNA modifications and were expressed in Escherichia coli. The deletion of 21 amino acid residues resulted in only 2- and 3-fold reduction in the antiviral and antiproliferative specific activities, respectively. Thus, the carboxyl-terminal 21 residues are not directly involved in the function of the HuIFN-gamma. The level of intracellular accumulation was also decreased by 3-5-fold. Further deletions of 26, 32, and 37 residues from the COOH terminus resulted in the lack of detectable activity as well as in 50-100-fold reduction in the level of accumulation in the bacterial cell. However, each of the modified plasmids was found to have comparable efficiency in directing the production of the respective variant molecules relative to the full-length HuIFN-gamma molecule in an in vitro transcription-translation assay. Thus, the failure of some of the deletion variant molecules to accumulate in the E. coli cell is likely due to their instability in vitro. The loss of the COOH-terminal 21 amino acid residues of HuIFN-gamma also resulted in a substantial reduction in the ability of the molecule to be renatured in vitro from the treatment with chaotrophic agents, a method frequently used to extract and purify recombinant polypeptides from E. coli host. The latter result may account for some earlier reports which inferred the involvement of the COOH terminus in the functions of the HuIFN-gamma molecule due to their failure to detect activity upon deletions of only 11-18 residues.
Basic Fibroblast Growth Factor Modulates the Aminophospholipid Translocase Activity Present in the Plasma Membrane of Bovine Aortic Endothelial Cells (1995)

Vascular endothelial cells form the inner nonthrombogenic lining of the large blood vessel. Through back-exchange and fluorescence recovery after photobleaching experiments and using the two fluorescent lipids 1 -acyl-2–[6–[N -(7-nitrobenz-2–oxa-1,3–díazol-4-yl)amino]hexanoyl]glycerophosphocholine and 1–acyl-2[6-N -(7-nitrobenz-2–oxa-1,3–díazol-4–yl)amino]hexanoyl]glycerophosphoethanolamine, we have recently shown that an energy-dependent and protein-dependent aminophospholipid translocase activity is present in the plasma membrane of cultured bovine aortic endothelial cells, which specifically transports phosphatidylethanolamine from the outer leaflet toward the inner leaflet of the membrane lipid bilayer. In the present study, using the same approach and 1-acyl-2-[6–N -(7-nitrobenz-2–oxa-1,3-díazol-4-yl)ami-no]hexanoyl]glycerophosphoserine as the probe, it is shown that this conclusion is also valid for phosphatidylserine. Furthermore, evidence is presented indicating that this aminophospholipid translocase activity can be maintained, suppressed, and restored at will, depending on the conditions of cell incubation. Thus, the translocase activity is detected for cells maintained in their normal culture medium or in a serum-free incubation medium [Dulbecco's modified Eagle's medium (DMEM)] supplemented with the basic fibroblast growth factor, whereas inhibition is observed for cells exposed for at least 2 h to DMEM. The translocase activity is restored when these pretreated cells are further incubated at least for 1 h in the presence of serum or of basic fibroblast growth factor. In view of the importance of basic fibroblast growth factor as a mitogenic and differentiating agent for vascular endothelial cells, various growth factors were tested (acidic fibroblast growth factor, epidermal growth factor, platelet-derived growth factor, transforming growth factors α and β, vascular endothelial growth factor, interferon γ, tumor-necrosis factor, insulin, and interleukin 4). Only basic fibroblast growth factor was active in the maintenance and restoration of the translocase activity. With respect to the effects of serum, evidence is presented showing that high-density lipoproteins might play a role in the control of the translocase activity. However, the positive effects of basic fibroblast growth factor, serum and high-density lipoproteins on the translocase activity were suppressed when experiments were carried out in the presence of an anti-(basic fibroblast growth factor) IgG, thus indicating that in all cases, basic fibrobiast growth factor was directly involved in the modulation of the aminophospholipid translocase activity present in the plasma membrane of bovine aortic endothelial cells.
Safety of intravenous ferric carboxymaltose versus oral iron in patients with nondialysis-dependent CKD: an analysis of the 1-year FIND-CKD trial (2017)

These results further support the conclusion that correction of iron deficiency anemia with IV FCM is safe in patients with nondialysis-dependent CKD.
Increased Susceptibility of Vault Poly(ADP-Ribose) Polymerase–Deficient Mice to Carcinogen-Induced Tumorigenesis (2005)

Vault poly(ADP-ribose) polymerase (VPARP) and telomerase-associated protein 1 (TEP1) are components of the vault ribonucleoprotein complex. Vaults have been implicated in multidrug resistance of human tumors and are thought to be involved in macromolecular assembly and/or transport. Previous studies showed that VPARP-deficient mice were viable, fertile, and did not display any vault-related or telomerase-related phenotype, whereas disruption of telomerase-associated protein 1 in mice led to reduced stability of the vault RNA and affected its stable association with vaults, although there were no telomerase-related changes. In this study, we evaluated the susceptibility of Vparp-/- and Tep1-/- mice to dimethylhydrazine-induced colon tumorigenesis and urethane-induced lung tumorigenesis. Mice received i.p. injections of either 1 g/kg body weight of urethane twice a week for 2 weeks or 20 mg/kg body weight of dimethylhydrazine once a week for 10 weeks and were analyzed after 10 and 60 weeks, respectively. The colon tumor incidence and multiplicity were significantly higher and colon tumor latency was significantly shorter in Vparp-/- mice compared with wild-type mice. Increased colon tumor incidence, multiplicity, and reduced tumor latency were also seen in Tep1-/- mice, however, these results were statistically not significant. Lung tumor multiplicities were increased in both Vparp-/- and Tep1-/- mice but were not significant. The increase in carcinogen-induced tumors in VPARP-deficient mice is the only phenotype observed to date, and suggests a possible role for VPARP, directly or indirectly, in chemically induced neoplasia.
Role of Prostacyclin in the Cardiovascular Response to Thromboxane A 2 (2002)

Thromboxane (Tx) A2 is a vasoconstrictor and platelet agonist. Aspirin affords cardioprotection through inhibition of TxA2 formation by platelet cyclooxygenase (COX-1). Prostacyclin (PGI2) is a vasodilator that inhibits platelet function. Here we show that injury-induced vascular proliferation and platelet activation are enhanced in mice that are genetically deficient in the PGI2 receptor (IP) but are depressed in mice genetically deficient in the TxA2 receptor (TP) or treated with a TP antagonist. The augmented response to vascular injury was abolished in mice deficient in both receptors. Thus, PGI2 modulates platelet-vascular interactions in vivo and specifically limits the response to TxA2. This interplay may help explain the adverse cardiovascular effects associated with selective COX-2 inhibitors, which, unlike aspirin and nonsteroidal anti-inflammatory drugs (NSAIDs), inhibit PGI2 but not TxA2.
The Role of Markers of Inflammation in Traumatic Brain Injury (2013)

Within minutes of a traumatic impact, a robust inflammatory response is elicited in the injured brain. The complexity of this post-traumatic squeal involves a cellular component, comprising the activation of resident glial cells, microglia, and astrocytes, and the infiltration of blood leukocytes. The second component regards the secretion immune mediators, which can be divided into the following sub-groups: the archetypal pro-inflammatory cytokines (Interleukin-1, Tumor Necrosis Factor, Interleukin-6), the anti-inflammatory cytokines (IL-4, Interleukin-10, and TGF-beta), and the chemotactic cytokines or chemokines, which specifically drive the accumulation of parenchymal and peripheral immune cells in the injured brain region. Such mechanisms have been demonstrated in animal models, mostly in rodents, as well as in human brain. Whilst the humoral immune response is particularly pronounced in the acute phase following Traumatic brain injury (TBI), the activation of glial cells seems to be a rather prolonged effect lasting for several months. The complex interaction of cytokines and cell types installs a network of events, which subsequently intersect with adjacent pathological cascades including oxidative stress, excitotoxicity, or reparative events including angiogenesis, scarring, and neurogenesis. It is well accepted that neuroinflammation is responsible of beneficial and detrimental effects, contributing to secondary brain damage but also facilitating neurorepair. Although such mediators are clear markers of immune activation, to what extent cytokines can be defined as diagnostic factors reflecting brain injury or as predictors of long term outcome needs to be further substantiated. In clinical studies some groups reported a proportional cytokine production in either the cerebrospinal fluid or intraparenchymal tissue with initial brain damage, mortality, or poor outcome scores. However, the validity of cytokines as biomarkers is not broadly accepted. This review article will discuss the evidence from both clinical and laboratory studies exploring the validity of immune markers as a correlate to classification and outcome following TBI.
Myocardial perfusion acquisition without magnetization preparation or gating (2011)

Current myocardial perfusion MRI acquisitions are performed with a saturation recovery sequence, in large part to minimize sensitivity to arrhythmia. A new approach is proposed here where the images are acquired ungated at steady state without use of a saturation pulse. The data are acquired continuously and reach steady state after the first few images. A confluence of advances has made this new paradigm of an ungated steady-state acquisition possible-very rapid undersampled readouts with new reconstruction technologies permit enough measurements that continuous acquisition becomes a feasible approach. Gating can be applied retrospectively from a logged electrocardiogram (ECG) or with self-gating methods. In this work, simulations and measurements in a concentration phantom are used to demonstrate that similar contrast and signal can be obtained with the standard saturation recovery and the proposed spoiled gradient echo (SPGR) acquisition. Specifically, for a flip angle of 14° and a saturation recovery time of 80 ms, similar signals are acquired over a range of T(1) s that reflect realistic myocardial tissue concentrations. Preliminary results in one subject are presented to show the potential of this new approach. The method may allow for cine cardiac perfusion and more signal-to-noise ratio-efficient acquisitions.
The SWI/SNF ATPase Brm Is a Gatekeeper of Proliferative Control in Prostate Cancer (2008)

Factors that drive prostate cancer progression remain poorly defined, thus hindering the development of new therapeutic strategies. Disseminated tumors are treated through regimens that ablate androgen signaling, as prostate cancer cells require androgen for growth and survival. However, recurrent, incurable tumors that have bypassed the androgen requirement ultimately arise. This study reveals that the Brm ATPase, a component of selected SWI/SNF complexes, has significant antiproliferative functions in the prostate that protect against these transitions. First, we show that targeted ablation of Brm is causative for the development of prostatic hyperplasia in mice. Second, in vivo challenge revealed that Brm-/- epithelia acquire the capacity for lobe-specific, castration-resistant cellular proliferation. Third, investigation of human specimens revealed that Brm mRNA and protein levels are attenuated in prostate cancer. Fourth, Brm down-regulation was associated with an increased proliferative index, consistent with the mouse model. Lastly, gene expression profiling showed that Brm loss alters factors upstream of E2F1; this was confirmed in murine models, wherein Brm loss induced E2F1 deregulation in a tissue-specific manner. Combined, these data identify Brm as a major effector of serum androgen-induced proliferation in the prostate that is disrupted in human disease, and indicate that loss of Brm confers a proliferative advantage in prostate cancer.
A One Step Synthesis of Benzimidazo[2,1-c][1,2,4]triazole Derivatives Using Hydrazonoyl Halides (1993)

A synthesis of benzimidazo[2,1-cl[l,2,4]triazole derivatives ( 9 ) has been accomplished from t h e reaction of hydrazonoyl halides ( I ) with 2-methylmercaptohenzimidazole (6) in chloroform in t h e pres e n c e of triethylamine.Hydrazonoyl halides (1) represent a unique class of compounds which undergo base catalysed 1,3-elimination reaction t o give nittilimines (2).The latter a r e versatile synthetic intermediates R/Y/X a , 0C2H5/H/CI b, 0C2H51CH31CI c , CH3/H/CI d, C H 3 1 ~~3 1 ~~ e , C ~H ~/ H / B I f , C6H5/CH3/Br
Perpendicularly Arranged Ruthenium Porphyrin Dimers and Trimers (1997)

A series of ruthenium(II) porphyrin dimers and trimers (carbonyl dimers, 1-4; carbonyl trimers, 5-7, bis(pyridyl) trimers, 8-10), having axial or bridging porphyrin ligands, were synthesized and characterized by (1)H NMR and IR spectroscopy and mass spectrometry. An X-ray structural determination of Ru(II)(OEP)(CO)(H(2)PyP(3)P) (1) (OEP = octaethylporphyrinato dianion, H(2)PyP(3)P = 5-pyridyl-10,15,20-triphenylporphyrinato dianion) was carried out. The axial porphyrin ligand is coordinated to the ruthenium porphyrin subunit obliquely. The Ru-N(Py) bond length is 2.237(4) Å, and the angle between the ruthenium porphyrin macrocycle and the pyridyl ring is 63.23(35) degrees. Crystallographic data for 1 are as follows: chemical formula C(80)H(73)N(9)ORu.CH(2)Cl(2), triclinic, P&onemacr;, a = 14.954(5) Å, b = 25.792(5) Å, c = 10.124(3) Å, alpha = 90.21(2) degrees, beta = 108.43(2) degrees, gamma = 73.39(2) degrees, Z = 2, R(F) = 0.0674. (1)H NMR signals of 2,6- and 3,5-pyridyl protons of the axial ligand porphyrins of the oligomers 1-10 showed significant upfield shifts, indicating that the axial porphyrin subunits are coordinated to the ruthenium porphyrin subunits through the pyridyl group in solution. UV-vis spectra revealed the presence of excitonic interaction between two axial ligand porphyrin subunits in the trimers 8-10. The MLCT bands from the central ruthenium(II) ions to the octaethylporphyrin rings were observed around 450 nm in 8 and 9. Cyclic voltammograms of the carbonyl dimers and trimers showed no redox waves of the ruthenium(II) ions, because the ruthenium(II) oxidation state of these complexes was significantly stabilized by the coordination of the axial CO ligands. On the other hand, bis(pyridyl) trimers exhibit the Ru(III/II) waves in the region of -0.12 to +0.15 V vs Ag/Ag(+) reference electrode.
A Feedback Information-Theoretic Approach to the Design of Brain–Computer Interfaces (2010)

This article presents a new approach to designing brain–computer interfaces (BCIs) that explicitly accounts for both the uncertainty of neural signals and the important role of sensory feedback. This approach views a BCI as the means by which users communicate intent to an external device and models intent as a string in an ordered symbolic language. This abstraction allows the problem of designing a BCI to be reformulated as the problem of designing a reliable communication protocol using tools from feedback information theory. Here, this protocol is given by a posterior matching scheme. This scheme is not only provably optimal but also easily understood and implemented by a human user. Experimental validation is provided by an interface for text entry and an interface for tracing smooth planar curves, where input is taken in each case from an electroencephalograph during left- and right-hand motor imagery.
Safety and Pharmacokinetic Effects of TNP-470, an Angiogenesis Inhibitor, Combined With Paclitaxel in Patients With Solid Tumors: Evidence for Activity in Non–Small-Cell Lung Cancer (2002)

The combination of TNP-470 and paclitaxel, each at full single-agent dose, seems well tolerated, with minimal pharmacokinetic interaction between the two agents. Further studies of TNP-470 with chemotherapy regimens are warranted in NSCLC and other solid tumors.
Microfluidic Memory and Control Devices (2003)

We demonstrate microscopic fluidic control and memory elements through the use of an aqueous viscoelastic polymer solution as a working fluid. By exploiting the fluid's non-Newtonian rheological properties, we were able to demonstrate both a flux stabilizer and a bistable flip-flop memory. These circuit elements are analogous to their solid-state electronic counterparts and could be used as components of control systems for integrated microfluidic devices. Such miniaturized fluidic circuits are insensitive to electromagnetic interference and may also find medical applications for implanted drug-delivery devices.