gebhart/patrepeval huggingface dataset:
Continuous Representations of Time-Series Gene Expression Data (2003)

We present algorithms for time-series gene expression analysis that permit the principled estimation of unobserved time points, clustering, and dataset alignment. Each expression profile is modeled as a cubic spline (piecewise polynomial) that is estimated from the observed data and every time point influences the overall smooth expression curve. We constrain the spline coefficients of genes in the same class to have similar expression patterns, while also allowing for gene specific parameters. We show that unobserved time points can be reconstructed using our method with 10-15% less error when compared to previous best methods. Our clustering algorithm operates directly on the continuous representations of gene expression profiles, and we demonstrate that this is particularly effective when applied to nonuniformly sampled data. Our continuous alignment algorithm also avoids difficulties encountered by discrete approaches. In particular, our method allows for control of the number of degrees of freedom of the warp through the specification of parameterized functions, which helps to avoid overfitting. We demonstrate that our algorithm produces stable low-error alignments on real expression data and further show a specific application to yeast knock-out data that produces biologically meaningful results.
On approximating multicriteria TSP (2012)

We present approximation algorithms for almost all variants of the multicriteria traveling salesman problem (TSP). First, we devise randomized approximation algorithms for multicriteria maximum traveling salesman problems (Max-TSP). For multicriteria Max-STSP where the edge weights have to be symmetric, we devise an algorithm with an approximation ratio of 2/3 - ε. For multicriteria Max-ATSP where the edge weights may be asymmetric, we present an algorithm with a ratio of 1/2 - ε. Our algorithms work for any fixed number k of objectives. Furthermore, we present a deterministic algorithm for bicriteria Max-STSP that achieves an approximation ratio of 7/27. Finally, we present a randomized approximation algorithm for the asymmetric multicriteria minimum TSP with triangle inequality (Min-ATSP). This algorithm achieves a ratio of log n + ε.
A simple speed estimation algorithm for mobility-aware SON RRM strategies in LTE (2013)

Mobility management in so-called heterogeneous networks (HetNets) becomes a complicated issue because of the increased complexity of inter-layer Radio Resource Management (RRM) techniques. Frequent inter-layer reselections and handovers should be minimized when dealing with high-speed users by taking into account both user speeds and relative cell sizes. In this paper we propose a simple User Equipment (UE) speed estimation algorithm for application in mobility-aware cell reselection and handover strategies in Long Term Evolution (LTE) wireless networks where Self-Organising Networks (SON) are intended to play a key role. The suitability of mobility-aware RRM strategies based on the exchange of speed and cell size information between terminals and base stations is analysed. A simple structure for speed detection is proposed that relies on the analysis of the downlink Doppler spread spectrum. Simulations show that the proposed algorithm is accurate enough for performing advanced RRM techniques based on user speed.
22q11 deletion syndrome in adults with schizophrenia (1998)

Genetic syndromes associated with deletions at chromosome 22q11 generally have been diagnosed during childhood based on a constellation of physical features. To investigate a reported association of velocardiofacial syndrome with psychotic disorders in adults, we assessed subjects with DSM-IV schizophrenia or schizoaffective disorder who were referred with two or more syndromal features (palatal, cardiac, facial, or other congenital anomalies, and/or learning difficulties). We report on 10 subjects (5 men and 5 women), mean age 27.2 (SD 6.0) years, who were found to have a 22q11 deletion at locus D22S75 using fluorescence in-situ hybridization (FISH). The mean age at onset of psychosis was 19.6 (SD 4.6) years. Symptoms and course of the psychotic illnesses were unremarkable, but additional signs such as temper outbursts were common. These adult subjects had significantly fewer major palatal (P = .0001) and conotruncal cardiac (P = .05) anomalies but the same high rate of learning difficulties as a sample with deletion 22q11 ascertained through a pediatric clinic [Lindsay et al. (1995): Am J Med Genet 57:514-522]. Minor congenital features and rate of transmitted cases were similar to those previously reported. These results replicate the association of a 22q11 deletion syndrome with schizophrenia and confirm the importance of ascertainment in influencing the phenotype found. The findings support a developmental gene in the 22q11 deletion region causing a complex phenotype which may include significant behavioral components that emerge over time. We support using the term "22q11 deletion syndrome (22DS)," which would encompass physical and psychiatric features, and could also be applied to describe a genetic subtype of schizophrenia.
Quick and easy measurement of the band gap in semiconductors (1983)

A simple method for measuring band gap in semiconductors is described, involving transport measurement in a p-n junction. Fairly accurate results are given for germanium, silicon and gallium arsenide.
Graphene Oxide as a Practical Solution to High Sensitivity Gas Sensing (2013)

Graphene and its related materials have attracted much interest in sensing applications because of their optimized ratio between active surface and bulk volume. In particular, several forms of oxidized graphene have been studied to optimize the sensing efficiency, sometimes moving away from practical solutions to boost performance. In this paper, we propose a practical, high-sensitivity, and easy to fabricate gas sensor based on high quality graphene oxide (GO), and we give the rationale to the high performance of the device. The device is fabricated by drop-casting water-dispersed single-layer GO flakes on standard 30 mu m spaced interdigitated Pt electrodes. The exceptional size of the GO flakes (27 mu m mean size and similar to 500 mu m maximum size) allows single GO flake to bridge electrodes. A typical p-type response is observed by testing the device in both reducing and oxidizing environments. The specific response to NO2 is studied by varying the operating temperature and the gas concentration. Sensing activity is demonstrated to be mainly mediated by the oxygen functional groups. A 20 ppb detection limit is measured. Besides illustrating a simple and efficient approach to gas sensing, this work is an example of the versatility of graphene oxide, accomplishing tasks that are complementary to graphene. adjacent
Epitopes Recognized by Human T Cells Map Within the Conserved Part of the GP190 of <i>P. Falciparum</i> (1988)

In a study aimed at developing a vaccine against the asexual blood stages of Plasmodium falciparum, two T cell epitopes were identified within a nonpolymorphic region of gp190 of Plasmodium falciparum merozoites. The two epitopes, which were revealed by deletion analysis, stimulated human T cell clones. Peptides containing sequences of the epitopes stimulated the cloned T cells and peripheral blood mononuclear cells (PBMC) from malaria-infected individuals. Moreover, the T cell clones responded to 11 different Plasmodium falciparum isolates in culture, showing that the epitopes are recognized in native parasites.
Advanced Integrated Workflows for Incorporating Both Production and 4D Seismic-Related Data into Reservoir Models (2012)

Reservoir models are used for predicting future oil recovery or for evaluating alternative field management scenarios. They can be considered as reliable when they account for all available data collected on the field: data are split into static data such as logs or measurements carried out on cores extracted from wells and dynamic data such as pressures and flow rates. Since the late nineties, the latter also consist of 4D seismic data. This motivated the development of very specific workflows, which yield reservoir models respecting all collected data. In this paper, we focus on workflows for building reservoir models consistent with both production and inverted 4D seismic data. Seismic data are referred to as inverted since we do not consider the amplitudes of the seismic traces, but the acoustic impedances or velocities derived from amplitudes. Then, two application cases are presented. The first one is a synthetic case inspired by typical North Sea Brent fields. It aims to stress the potential of the proposed approach for determining reservoir models respecting production data. The second one is also rooted in a real field case, but focuses on the matching of impedances.
A standard for architecture description (1999)

A profitable information technology (IT) services organization is dependent on widespread asset harvesting (from previous engagements) and scalable asset deployment (into current and future engagements). This activity demands consistency of terminology and notation in the creation and use of engagement artifacts, including work products. This paper presents a standard for architecture description in which a set of conventions for terminology and notation is used to describe and to express the organization of the architecture for an IT system. This standard, the Architecture Description Standard (ADS), is intended to be used by the IBM architecture community. The emphasis is on a minimal set of shared concepts that can be effectively taught to a broad range of IT architects with different skills and that is usable in practice.
Free-Space Transparency: Exposing Hidden Content Through Unimportant Screen Space (2003)

We present free-space transparency, a method that renders unimportant regions of a window as transparent. This allows users to view screen content that lies beneath these regions. By maximizing the amount of simultaneously visible content, while keeping window sizes and locations constant, users can be made more productive with minimal window layout manipulation.
Occurrence of human papillomavirus type 16 DNA sequences and c-myc oncogene alterations in uterine-cervix carcinoma. (1991)

Using genetic engineering and molecular biology techniques, we have examined sixteen human carcinomas in the uterine-cervix tumors (the most frequent tumor in México, representing 34% of malignant tumors in women), for the presence of Human Papillomavirus type 16 (HPV-16) DNA sequences and possible alterations of the cellular myc (c-myc) proto-oncogene. In this study we have analyzed cervical carcinomas from patient with clinical stage II. We detected in 31% of these samples, the presence of HPV-16 sequences (2-100 copies). In addition, an elevated amplification (up to 80-fold in one tumor) and/or rearrangement of the c-myc oncogene was detected in most tumors (more than 90% of the samples). These results suggest that either c-myc oncogene and/or HPV-16 could play an important role in the development of uterine-cervix carcinoma.
High‐sensitivity TFA‐free LC‐MS for profiling histones (2011)

The analysis of proteins by RPLC commonly involves the use of TFA as an ion-pairing agent, even though it forms adducts and suppresses sensitivity. The presence of adducts can complicate protein molecular weight assignment especially when protein isoforms coelute as in the case of histones. To mitigate the complicating effects of TFA adducts in protein LC-MS, we have optimized TFA-free methods for protein separation. Protein standards and histones were used to evaluate TFA-free separations using capillary (0.3 mm id) and nanoscale (0.1 mm id) C(8) columns with the ion-pairing agents, formic acid or acetic acid. The optimized method was then used to examine the applicability of the approach for histone characterization in human cancer cell lines and primary tumor cells from chronic lymphocytic leukemia patients.
Enhancement of x-ray damage in HeLa cells by exposure to lucanthone (Miracil D) following radiation. (1970)

Summary The colony-forming ability of HeLa cells that survived an initial dose of X-irradiation proved abnormally sensitive to lucanthone. Surviving cells gradually regained normal resistance to lucanthone treatment, which implied that lucanthone was acting to inhibit a postradiation repair process. Enhancement of cell killing by lucanthone was comparable in degree to that induced by actinomycin D, with which it shares many properties. Lucanthone merits further study as a possible adjunct in clinical radiation therapy, since it is a relatively safe drug which has been widely used for many years in the treatment of human schistosomiasis.
Association of common polymorphisms in inflammatory genes interleukin (IL)6, IL8, tumor necrosis factor alpha, NFKB1, and peroxisome proliferator-activated receptor gamma with colorectal cancer. (2003)

Animal models and epidemiological observations suggest that a continuous inflammatory condition predisposes to colorectal cancer (CRC), but the roles of different elements participating in inflammatory responses have been little investigated in relation to CRC. We have studied the association between single nucleotide polymorphisms in the interleukin (IL)-6 (-174 G>C), IL8 (-251T>A), tumor necrosis factor alpha (-308G>A), and PPARG (Pro12Ala) genes and the risk of CRC in a group of 377 cases and 326 controls from Barcelona, Spain. These genes are known to be important for inflammation of the colorectum and common allelic variants have been shown to have a biological effect. The PPARG Ala12 and IL8-251A genotypes are associated with reduced risk of disease (0.56, 95% CI, 0.37-0.85, P = 0.0056, and 0.70, 95% CI, 0.50-0.99, P = 0.043, respectively), whereas the IL6-174C genotype is associated with increased risk (1.53, 95% CI, 1.12-2.09, P = 0.0073). We also studied a single nucleotide polymorphism in intron 11 of the NFKB1 gene (rs1020759), which probably lacks any functional role, and found no significant association with the disease. This is the first report that IL6, IL8, and PPARG genes are important in relation to inflammation-related risk of sporadic CRC.
Detection of Counterfeit by the Usage of Product Inherent Features (2015)

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Optical Properties of Polymer-Based Photonic Nanocomposite Materials (2003)

Designing metallodielectric nanocomposite materials for photonic applications implies the ability to reliably model and predict the effect of metallic inclusions on the optical properties of a microstructured composite material. We present a detailed analysis of the optical properties of block copolymer based, multilayered metallodielectric Bragg reflectors and discuss the implications of nanosize-specific effects on the design of composite materials for photonic applications. A series of lamellar poly(styrene-b-ethylene/propylene) copolymer thin films with varying filling fraction of gold nanocrystals preferentially but randomly distributed within the poly(styrene) domains have been studied by reflectometry. The reflective properties are compared to model calculations based on effective medium concepts taking into account confinement effects on the dielectric function of the nanocrystals. The particle size causes strong alterations in the dielectric function of the metal inclusions that have relevance for the attainable dielectric contrast within periodic nanocomposites.
Nitrogen-Containing Compounds from <i>Salvia </i><i>m</i><i>iltiorrhiza</i> (2005)

Five new N-containing compounds, neosalvianen (1), salvianen (2), salvianan (3), salviadione (4), and 5-(methoxymethyl)-1H-pyrrole-2-carbaldehyde (5), were isolated from Salvia miltiorrhiza. Their structures were mainly established by spectroscopic methods. Neosalvianen (1) and its analogues (6a, 6b) were synthesized for spectroscopic data comparison. Compounds 1, 2, 4, and 6a were evaluated for their cytotoxic activities against selected cancer cell lines. Among these components, salvianen (2) exhibited the most potent cytotoxicity with a CD50 range of 30.4-39.5 microM against HeLa (cervical epitheloid carcinoma), HepG2 (hepatocellular carcinoma), and OVCAR-3 (ovarian adenocarcinoma) cell lines in a dose-dependent manner. The cytotoxicities of the tested compounds were not specific and showed similar activities to the selected cancer cell lines.
What makes ImageNet good for transfer learning? (2016)

The tremendous success of ImageNet-trained deep features on a wide range of transfer tasks begs the question: what are the properties of the ImageNet dataset that are critical for learning good, general-purpose features? This work provides an empirical investigation of various facets of this question: Is more pre-training data always better? How does feature quality depend on the number of training examples per class? Does adding more object classes improve performance? For the same data budget, how should the data be split into classes? Is fine-grained recognition necessary for learning good features? Given the same number of training classes, is it better to have coarse classes or fine-grained classes? Which is better: more classes or more examples per class? To answer these and related questions, we pre-trained CNN features on various subsets of the ImageNet dataset and evaluated transfer performance on PASCAL detection, PASCAL action classification, and SUN scene classification tasks. Our overall findings suggest that most changes in the choice of pre-training data long thought to be critical do not significantly affect transfer performance.? Given the same number of training classes, is it better to have coarse classes or fine-grained classes? Which is better: more classes or more examples per class?
Accuracy and precision of dual energy CT imaging for the quantification of tissue fat content (2006)

We present the analysis of the accuracy and precision of dual energy material basis decomposition for the quantification of tissue fat content in computed tomography. We compare the benefits of a pre-reconstruction (sinogram-based) dual energy imaging technique versus a post-reconstruction (image) based dual energy decomposition technique using a numerical simulation. A phantom containing plastics of known composition is measured to validate the technique. The accuracy of the image based dual energy decomposition technique is contingent on the amount of beam hardening encountered in the phantom. The accuracy of the pre-reconstruction dual energy technique depends on how accurately the system spectral response can be modeled. In both cases the precision of the dual energy imaging is determined by the photon flux.
Genome‐wide selection for increased copy number in <i>Acinetobacter baylyi</i> ADP1: locus and context‐dependent variation in gene amplification (2011)

Renewed interest in gene amplification stems from its importance in evolution and a variety of medical problems ranging from drug resistance to cancer. However, amplified DNA segments (amplicons) are not fully characterized in any organism. Here we report a novel Acinetobacter baylyi system for genome-wide studies. Amplification mutants that consume aromatic compounds were selected under conditions requiring high-level expression from three promoters in a linked set of chromosomal genes. Tools were developed to relocate these catabolic genes to any non-essential chromosomal position, and 49 amplification mutants from five genomic contexts were characterized. Amplicon size (18-271 kb) and copy number (2-105) indicated that 30% of mutants carried more than 1 Mb of amplified DNA. Amplification features depended on genomic position. For example, amplicons from one locus were similarly sized but displayed variable copy number, whereas those from another locus were differently sized but had comparable copy number. Additionally, the importance of sequence context was highlighted in one region where amplicons differed depending on the presence of a promoter mutation in the strain from which they were selected. DNA sequences at amplicon boundaries in 19 mutants reflected illegitimate recombination. Furthermore, steady-state duplication frequencies measured under non-selective conditions (10(-4) to 10(-5) ) confirmed that spontaneous gene duplication is a major source of genetic variation.
Integrating device monitoring into the infrastructure and workflow of routine practice. (2006)

Monitoring strategies for patients with heart failure vary. Physical assessment and patient reporting are often unreliable and inconsistent. Continuous physiologic information from implanted devices identifies the progression to congestion in patients with chronic heart failure earlier in the process than traditional methods. Common themes of a successful system will require a means to provide device-based data to interested providers who then can interpret the information in the context of either remote or face-to-face clinical assessment.
Design of 60GHz planar array antennas using PCB-based microstrip-ridge gap waveguide and SIW (2014)

A wideband 2×2-slot element for a 60 GHz antenna array is designed by making use of two double-sided printed circuit boards (PCBs). The upper PCB contains the four radiating cavity-backed slots backed by a substrate-integrated waveguide (SIW) cavity. The SIW cavity is excited by a coupling slot fed by a microstrip-ridge gap waveguide formed in the air gap between the upper and lower PCBs. The designed 2×2-slot element is considered in an infinite array environment. A sample 32×32 slot array aperture is simulated using infinite array approach and the relative bandwidth of 16% over 57-66GHz frequency range with the directivity of more than 38 dBi over the operating bandwidth is obtained. The simulations are verified by measurements on a smaller 4×4 slot array surrounded by dummy elements.
Adhesion property of novel polyimides containing fluorine and phosphine oxide moieties (2001)

Novel diamine monomers containing fluorine and phosphine oxide - bis(3-aminophenyl)-3,5-bis(trifluoromethyl)phenyl phosphine oxide (mDA6FPPO) and bis(3-aminophenyl)-4-(trifluoromethyl)phenyl phosphine oxide (mDAFPPO) - were utilized to prepare polyimides with dianhydrides such as 6FDA, BTDA or ODPA by the conventional two-step route, i.e. preparation of poly(amic acid) followed by solution imidization. The polyimides were characterized by FT-IR, NMR, DSC, and intrinsic viscosity measurements. The adhesion property of the polyimides was evaluated via a peel test with bare Cu foil, as well as silane/Cr-coated Cu foil, and failure surfaces were analyzed by SEM/EDX to elucidate the failure mechanism. The results were compared with those from the polyimides prepared from bis(3-aminophenyl)phenyl phosphine oxide (mDAPPO) containing only the phosphine oxide moiety, 1,1-bis(4-aminophenyl)-1-phenyl-2,2-trifluoroethane (3FDAm) containing only the fluorine moiety, and a commercial 3,3′-diaminodiphenylsulfone (mDDS). The polyimides with 3FDAm exhibited the highest T g, followed by the mDAPPO-, mDA3FPPO-, and mDA6FPPO-based polyimides, but the mDAPPO-based polyimides exhibited the highest adhesion properties, followed by mDA3FPPO, mDA6FPPO, mDDS, and 3FDAm, which is attributed to the phosphine oxide and fluorine moieties.