gebhart/patrepeval huggingface dataset:
Automated Isotope Identification Algorithm Using Artificial Neural Networks (2017)

There is a need to develop an algorithm that can determine the relative activities of radioisotopes in a large data set of low-resolution gamma-ray spectra that contain a mixture of many radioisotopes. Low-resolution gamma-ray spectra that contain mixtures of radioisotopes often exhibit feature overlap, requiring algorithms that can analyze these features when overlap occurs. While machine learning and pattern recognition algorithms have shown promise for the problem of radioisotope identification, their ability to identify and quantify mixtures of radioisotopes has not been studied. Because machine-learning algorithms use abstract features of the spectrum, such as the shape of overlapping peaks and Compton continuum, they are a natural choice for analyzing radioisotope mixtures. An artificial neural network (ANN) has been trained to calculate the relative activities of 32 radioisotopes in a spectrum. The ANN is trained with simulated gamma-ray spectra, allowing easy expansion of the library of target radioisotopes. In this paper, we present our initial algorithms based on an ANN and evaluate them against a series of measured and simulated spectra.
Analysis of a tunable multichannel two-mode-interference wavelength-division-multiplexer/demultiplexer (1989)

An integrated optical multichannel wavelength-division multiplexer/demultiplexer for a single-mode fiber system is investigated by the beam propagation method (BPM). Important wavelength characteristics of dual-channel two-mode-interference (TMI) multiplexer/demultiplexer waveguide with and without electrode are studied and general design guidelines for realizing multichannel multiplexer/demultiplexer are given. Design and simulation of four-channel TMI multiplexer/demultiplexer are discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Erectile Function Following External Beam Radiotherapy for Clinically Organ-confined or Locally Advanced Prostate Cancer (2004)

XRT significantly reduced the maintenance rate of erectile function during the follow-up period, with the rate being 19% at 3 years in patients who received 3-dimensional conformal radiation. The XRT modality was involved in the reduction of erectile function. These results suggest that erectile dysfunction is a possible adverse event following XRT.
In Vivo Synthesis of the Periplasmic Domain of TonB Inhibits Transport through the FecA and FhuA Iron Siderophore Transporters of <i>Escherichia coli</i> (2001)

ABSTRACT The siderophore transport activities of the two outer membrane proteins FhuA and FecA of Escherichia coli require the proton motive force of the cytoplasmic membrane. The energy of the proton motive force is postulated to be transduced to the transport proteins by a protein complex that consists of the TonB, ExbB, and ExbD proteins. In the present study, TonB fragments lacking the cytoplasmic membrane anchor were exported to the periplasm by fusing them to the cleavable signal sequence of FecA. Overexpressed TonB(33-239), TonB(103-239), and TonB(122-239) fragments inhibited transport of ferrichrome by FhuA and of ferric citrate by FecA, transcriptional induction of the fecABCDE transport genes by FecA, infection by phage φ80, and killing of cells by colicin M via FhuA. Transport of ferrichrome by FhuAΔ5-160 was also inhibited by TonB(33-239), although FhuAΔ5-160 lacks the TonB box which is involved in TonB binding. The results show that TonB fragments as small as the last 118 amino acids of the protein interfere with the function of wild-type TonB, presumably by competing for binding sites at the transporters or by forming mixed dimers with TonB that are nonfunctional. In addition, the interactions that are inhibited by the TonB fragments must include more than the TonB box, since transport through corkless FhuA was also inhibited. Since the periplasmic TonB fragments cannot assume an energized conformation, these in vivo studies also agree with previous cross-linking and in vitro results, suggesting that neither recognition nor binding to loaded siderophore receptors is the energy-requiring step in the TonB-receptor interactions.
The use of steroids in the management of inoperable intestinal obstruction in terminal cancer patients: do they remove the obstruction? (2000)

This multicentre, randomized double-blind study was undertaken to assess the efficacy of corticosteroids as a palliative treatment of intestinal obstruction due to advanced and incurable cancer. Thirty-one French palliative care units agreed to participate in the study and 12 actually recruited at least one patient. To be included, patients had to have an advanced cancer with a surgically inoperable bowel obstruction and to have received no specific anticancer therapy within the preceding 28 days. They had to fulfil at least three of the following criteria: vomiting at least twice a day; colicky abdominal pain; no flatus for 12 h or more; no stool for at least 4 days, faecal impaction being excluded; intestinal distension; air-fluid levels or absence of gas in the colon on an abdominal radiograph. Patients were randomized in three groups to receive either a placebo for 3 days (group A), or methylprednisolone 240 mg daily for 3 days (group B) or methylprednisolone 40 mg daily for 3 days (group C). Symptoms were assessed daily but success or failure of the treatment was assessed on day 4, according to the disappearance or persistence of symptoms. Fifty-eight patients were randomized, of whom 52 were able to be evaluated. Details of symptoms and associated treatments are described below. Of 40 patients without a nasogastric tube, symptoms were relieved in 68% of cases versus 33% among placebo-treated patients (P = 0.047). In 12 patients who had a nasogastric tube already in place, the results are less significant (60% versus 33% with P = 0.080). Because of the small sample size, no conclusions can be reached about the relative efficacy of low versus high-dose treatment regimes.
Wound Healing Studies in Transgenic and Knockout Mice: A Review (2003)

Wound healing is a highly ordered and well coordinated process that involves inflammation, cell proliferation, matrix deposition, and tissue remodeling (1). During the past few years, a series of candidate key players in the wound-healing scenario have been identified. These include not only a variety of different growth factors and cytokines, but also molecules that are involved in cell-cell and cell-matrix interactions, and proteins responsible for cell stability and cell migration. In most cases, the suggested function of these molecules is based on descriptive expression studies and/or functional in vitro studies. By contrast, their in vivo function in wound repair has been poorly defined.
Review of "Software Security by J. Palare. Datamation Vol. 20 No. 1, January 1974" (1974)

No abstract available.
Foam Processing and Cellular Structure of Polycarbonate‐Based Nanocomposites (2006)

Abstract Summary: Via a batch process in an autoclave, foam processing of intercalated PC/clay nanocomposites, having different amounts of clay, has been conducted using supercritical CO 2 as a foaming agent. The cellular structures obtained from various foaming temperature‐CO 2 pressure ranges were investigated by SEM. The incorporation with nanoclay‐induced heterogeneous nucleation occurs because of a lower activation energy barrier compared with homogeneous nucleation as revealed by the characterization of the interfacial tension between bubble and matrix. The controlled structure of the PCCN foams changed from microcellular ( d ≅ 20 µm and N c ≅ 1.0 × 10 9 cells · cm −3 ) to nanocellular ( d ≅ 600 nm and N c ≅ 3.0 × 10 13 cells · cm −3 ). The mechanical properties of PCCN foams under compression test were discussed. TEM micrograph for the structure of the cell wall foamed at 160 °C. magnified image TEM micrograph for the structure of the cell wall foamed at 160 °C.
Transterm--extended search facilities and improved integration with other databases (2005)

Transterm has now been publicly available for >10 years. Major changes have been made since its last description in this database issue in 2002. The current database provides data for key regions of mRNA sequences, a curated database of mRNA motifs and tools to allow users to investigate their own motifs or mRNA sequences. The key mRNA regions database is derived computationally from Genbank. It contains 3' and 5' flanking regions, the initiation and termination signal context and coding sequence for annotated CDS features from Genbank and RefSeq. The database is non-redundant, enabling summary files and statistics to be prepared for each species. Advances include providing extended search facilities, the database may now be searched by BLAST in addition to regular expressions (patterns) allowing users to search for motifs such as known miRNA sequences, and the inclusion of RefSeq data. The database contains >40 motifs or structural patterns important for translational control. In this release, patterns from UTRsite and Rfam are also incorporated with cross-referencing. Users may search their sequence data with Transterm or user-defined patterns. The system is accessible at http://uther.otago.ac.nz/Transterm.html.
Single-beat estimation of end-diastolic pressure-volume relationship: a novel method with potential for noninvasive application (2006)

Whereas end-systolic and end-diastolic pressure-volume relations (ESPVR, EDPVR) characterize left ventricular (LV) pump properties, clinical utility of these relations has been hampered by the need for invasive measurements over a range of pressure and volumes. We propose a single-beat approach to estimate the whole EDPVR from one measured volume-pressure (Vm and Pm) point. Ex vivo EDPVRs were measured from 80 human hearts of different etiologies (normal, congestive heart failure, left ventricular assist device support). Independent of etiology, when EDPVRs were normalized (EDPVRn) by appropriate scaling of LV volumes, EDPVRns were nearly identical and were optimally described by the relation EDP = An.EDV (Bn), with An = 28.2 mmHg and Bn = 2.79. V0 (the volume at the pressure of approximately 0 mmHg) was predicted by using the relation V0 = Vm.(0.6 - 0.006.Pm) and V30 by V30 = V0 + (Vm,n - V0)/(Pm/An) (1/Bn). The entire EDPVR of an individual heart was then predicted by forcing the curve through Vm, Pm, and the predicted V0 and V30. This technique was applied prospectively to the ex vivo human EDPVRs not used in determining optimal An and Bn values and to 36 in vivo human, 12 acute and 14 chronic canine, and 80 in vivo and ex vivo rat studies. The root-mean-square error (RMSE) in pressure between measured and predicted EDPVRs over the range of 0-40 mmHg was < 3 mmHg of measured EDPVR in all settings, indicating a good predictive value of this approach. Volume-normalized EDPVRs have a common shape, despite different etiology and species. This allows the entire curve to be predicted by a new method with a potential for noninvasive application. The results are most accurate when applied to groups of hearts rather than to individual hearts.
Interleukin-1 Blockade in Acute Myocardial Infarction and Heart Failure: Ready for Clinical Translation? (2013)

The synthesis and release of Interleukin-1 (IL-1) are finely regulated processes necessary for the initiation of an inflammatory response to injury. Release of IL-1α from injured cells and of mature IL-1β from circulating monocytes initiates the local and systemic inflammatory response, respectively. An intense IL-1-dependent response occurs during Acute Myocardial Infarction (AMI) and promotes Heart Failure (HF). In advanced HF, a chronic IL-1β-dependent process alters cardiovascular function leading to impaired performance, poor quality of life and increased morbidity and mortality. Here in reviewing the evidence in preclinical studies; we discuss potential strategies to disrupt IL-1 signaling in AMI and HF, and review the results of the initial pilot clinical trials.
FGFR2 and WDR11 are neighboring oncogene and tumor suppressor gene on human chromosome 10q26 (2003)

Oncogenes and tumor suppressor genes are clustered around recombination hot spots or fragile sites in the genome, because double-strand break is the common initial step in translocation, deletion and gene amplification. FGFR2 gene on human chromosome 10q26 is amplified in diffuse-type gastric cancer, while WDR11 gene on human chromosome 10q26 is disrupted in glial tumors. Here, we investigated genomic structure around FGFR2 and WDR11 loci. The FGFR2 gene, consisting of 21 exons, was located within nucleotide position 485637-605687 of NT_030764.5 (reverse orientation), and WDR11 gene was located within nucleotide position 6515786-6574126 of NT_008902.12 (forward orientation). Because nucleotide position 1-91397 of NT_030764.5 corresponded to nucleotide position 6639437-6748623 of NT_008902.12, FGFR2 and WDR11 genes were found to be closely linked in tail-to-tail manner with an interval of ca. 570 kb. Due to the deletion of exon 21 within FGFR2 amplicons, exon 21 is substituted by exon 20 or other aberrant exons in aberrant FGFR2 transcripts previously isolated from KATO-III, OCUM-2M and HSC43 cells. Mapping of aberrant exons and deletion junctions around the WDR11-FGFR2 locus in KATO-III and OCUM-2M cells revealed that inverted-type recombination occurred through end joining of the FGFR2 locus on one allele and that on the other allele. Amplification of FGFR2 gene with such recombination around exon 21 results in exclusion of WDR11 gene from the FGFR2 amplicon. Tumor suppressor genes closely linked to oncogenes might be excluded from amplicon through a breakage-fusion-bridge process during oncogene amplification.
Exhaled breath profiling for diagnosing acute respiratory distress syndrome (2014)

NTR2750, registered 11 February 2011.
Design and applications of a secure and decentralized distributed hash table (2011)

Distributed Hash Tables (DHTs) are a powerful building block for highly scalable decentralized systems. They route requests over a structured overlay network to the node responsible for a given key. DHTs are subject to the well-known Sybil attack, in which an adversary creates many false identities in order to increase its influence and deny service to honest participants. Defending against this is challenging because (1) in an open network, creating many fake identities is cheap; (2) an attacker can subvert periodic routing table maintenance to increase its influence over time; and (3) specific keys can be targeted by clustering attacks. As a result, without centralized admission control, previously existing DHTs could not provide strong availability guarantees.
This dissertation describes Whanau, a novel DHT routing protocol which is both efficient and strongly resistant to the Sybil attack. Whanau solves this long-standing problem by using the social connections between users to build routing tables that enable Sybil-resistant one-hop lookups. The number of Sybils in the social network does not affect the protocol's performance, but links between honest users and Sybils do. With a social network of n well-connected honest nodes. Whanau provably tolerates up to O (n/log n) such attack edges. This means that an attacker must convince a large fraction of the honest users to make a social connection with the adversary's Sybils before any lookups will fail.
Whanau uses techniques from structured DHTs to build routing tables that contain Opn log n) entries per node. It introduces the idea of layered identifiers to counter clustering attacks, which have proven particularly challenging for previous DHTs to handle. Using the constructed tables, lookups provably take constant time.
Simulation results, using large-scale social network graphs from LiveJournal, Flickr, YouTube, and DBLP, confirm the analytic prediction that Whanau provides high availability in the face of powerful Sybil attacks. Experimental results using PlanetLab demonstrate that an implementation of the Whanau protocol can handle reasonable levels of churn. (Copies available exclusively from MIT Libraries, Rm. 14-0551, Cambridge, MA 02139-4307. Ph. 617-253-5668; Fax 617-253-1690.)
Prox-Method with Rate of Convergence <i>O</i>(1/<i>t</i>) for Variational Inequalities with Lipschitz Continuous Monotone Operators and Smooth Convex-Concave Saddle Point Problems (2004)

We propose a prox-type method with efficiency estimate $O(\epsilon^{-1})$ for approximating saddle points of convex-concave C$^{1,1}$ functions and solutions of variational inequalities with monotone Lipschitz continuous operators. Application examples include matrix games, eigenvalue minimization, and computing the Lovasz capacity number of a graph, and these are illustrated by numerical experiments with large-scale matrix games and Lovasz capacity problems.
A RUNX2-Mediated Epigenetic Regulation of the Survival of p53 Defective Cancer Cells (2016)

The inactivation of p53 creates a major challenge for inducing apoptosis in cancer cells. An attractive strategy is to identify and subsequently target the survival signals in p53 defective cancer cells. Here we uncover a RUNX2-mediated survival signal in p53 defective cancer cells. The inhibition of this signal induces apoptosis in cancer cells but not non-transformed cells. Using the CRISPR technology, we demonstrate that p53 loss enhances the apoptosis caused by RUNX2 knockdown. Mechanistically, RUNX2 provides the survival signal partially through inducing MYC transcription. Cancer cells have high levels of activating histone marks on the MYC locus and concomitant high MYC expression. RUNX2 knockdown decreases the levels of these histone modifications and the recruitment of the Menin/MLL1 (mixed lineage leukemia 1) complex to the MYC locus. Two inhibitors of the Menin/MLL1 complex induce apoptosis in p53 defective cancer cells. Together, we identify a RUNX2-mediated epigenetic mechanism of the survival of p53 defective cancer cells and provide a proof-of-principle that the inhibition of this epigenetic axis is a promising strategy to kill p53 defective cancer cells.
Concepts to automate the theoretical design of effective antisense oligonucleotides (2001)

Among the large number of possible antisense species against a given target RNA, only a small number shows effective suppression of the target gene in living cells. In the case of short-chain antisense oligonucleotides (asON) which usually comprise less than approximately 25 nucleotides, local structures of the target RNA seem to be of particular importance for the extent of gene suppression. Experimental approaches to identify promising local target sequences and, hence, complementary asON sequences, have provided tools to define asON that are biologically active at higher than statistical probability. However, experimental protocols are expensive, time consuming, and are associated with intrinsic basic and technical limitations. As insights into the structure-function relationship of asON as well as the role of sequence motifs increase, it becomes feasible to consider computer-based theoretical approaches for the design of effective asON. In the following we describe how individual steps of the theoretical design of asON may be automated by establishing and implementing suitable algorithms.
Füllungsmaterialien für das Milchgebiss (2009)

Trotz aller Praventionserfolge in den letzten Jahren ist der Kariesbefall im Milchgebiss nach wie vor hoch. Trotzdem spielt die Sanierung von kariosen Milchzahnen in der Bundesrepublik nach wie vor eine untergeordnete Rolle. Dies ist umso erstaunlicher, als fur die Fullungstherapie in den letzten Jahren erfolgreiche Konzepte vorgestellt wurden. Die einfache Handhabung und die Weiterentwicklung von Fullungsmaterialien mit verbesserten asthetischen und werkstoffkundlichen Eigenschaften ermoglichen eine defektorientierte und minimal-invasive Therapie auch in der ersten Dentition. Aufgrund der positiven klinischen Ergebnisse gelten Kompomere heute fur die Fullungstherapie im Front- und Seitenzahnbereich des Milchgebisses als Mittel der Wahl. Je nach Compliance der Kinder und der Aktivitat und Grose der kariosen Lasion ist jedoch an eine alternative Versorgung zu denken. Bei groseren Defekten und erhohtem Kariesrisiko sollten Milchzahne mit konfektionierten Kronen versorgt werden. Bei schlechter Compliance sind Glasionomerzemente der adhasiven Versorgung vorzuziehen, um zumindest Zeit zu uberbrucken und den „Infektionsherd“ Karies aus der Mundhohle zu eliminieren.
Light dosimetry: effects of dehydration and thermal damage on the optical properties of the human aorta (1993)

The influences of dehydration and thermal damage on in vitro optical properties of human aorta were studied. The absorption coefficient increased by 20-50%, especially in the visible range when at least 40% of total tissue weight was lost as a result of dehydration. The reduced scattering coefficient increased by 10-45% in the visible and 30% to over 150% in the near IR after the tissue samples were heated in a constant temperature water bath at 100 degrees C for 300 +/- 10 s. This study implies that dehydration and protein coagulation during photothermal treatment of tissue are important factors altering optical properties of tissue.
Hydrogen-Bonding Effects on the Fluorescence versus Electron-Transfer-Initiated Chemiluminescence Spectra of the <i>m</i>-Oxybenzoate Ion Derived from a Bicyclic Dioxetane (2000)

A comparative spectral study of the fluorescence of the m-oxybenzoate anion versus the electron-transfer-initiated chemiluminescence (CIEEL) of the same anion derived from the bicyclic dioxetanes in various solvents is reported. The present study reveals that the fluorescence of this oxyanion is blue-shifted in protic versus aprotic solvents, while the CIEEL-spectral maximum is independent of the medium. The same phenomenon has been recently observed for the m-oxybenzoate ion derived from CIEEL-active spiroadamantyl dioxetanes. The reported spectral differences between the fluorescence and chemiluminescence emissions cannot be attributed to exciplex formation in the CIEEL process, but result from the differences in hydrogen-bonding effects on the photo- and chemiexcited oxyanion species. The observed solvatochromism is qualitatively rationalized in terms of the semiempirical AM1 calculations.
Palladium metal nanoparticles stabilized by ionophilic ligands in ionic liquids: synthesis and application in hydrogenation reactions (2014)

The selectivity of the hydrogenation of 1,3-cyclohexadiene and 2-pentyne by Pd nanoparticles in an ionic liquid can be modulated by the addition of N- or P-containing ionophilic ligands.