gebhart/patrepeval huggingface dataset:
Whole-genome maps of USF1 and USF2 binding and histone H3 acetylation reveal new aspects of promoter structure and candidate genes for common human disorders (2008)

Transcription factors and histone modifications are crucial regulators of gene expression that mutually influence each other. We present the DNA binding profiles of upstream stimulatory factors 1 and 2 (USF1, USF2) and acetylated histone H3 (H3ac) in a liver cell line for the whole human genome using ChIP-chip at a resolution of 35 base pairs. We determined that these three proteins bind mostly in proximity of protein coding genes transcription start sites (TSSs), and their bindings are positively correlated with gene expression levels. Based on the spatial and functional relationship between USFs and H3ac at protein coding gene promoters, we found similar promoter architecture for known genes and the novel and less-characterized transcripts human mRNAs and spliced ESTs. Furthermore, our analysis revealed a previously underestimated abundance of genes in a bidirectional conformation, where USFs are bound in between TSSs. After taking into account this promoter conformation, the results indicate that H3ac is mainly located downstream of TSS, and it is at this genomic location where it positively correlates with gene expression. Finally, USF1, which is associated to familial combined hyperlipidemia, was found to bind and potentially regulate nuclear mitochondrial genes as well as genes for lipid and cholesterol metabolism, frequently in collaboration with GA binding protein transcription factor alpha (GABPA, nuclear respiratory factor 2 [NRF-2]). This expands our understanding about the transcriptional control of metabolic processes and its alteration in metabolic disorders.
DeepReID: Deep Filter Pairing Neural Network for Person Re-identification (2014)

Person re-identification is to match pedestrian images from disjoint camera views detected by pedestrian detectors. Challenges are presented in the form of complex variations of lightings, poses, viewpoints, blurring effects, image resolutions, camera settings, occlusions and background clutter across camera views. In addition, misalignment introduced by the pedestrian detector will affect most existing person re-identification methods that use manually cropped pedestrian images and assume perfect detection. In this paper, we propose a novel filter pairing neural network (FPNN) to jointly handle misalignment, photometric and geometric transforms, occlusions and background clutter. All the key components are jointly optimized to maximize the strength of each component when cooperating with others. In contrast to existing works that use handcrafted features, our method automatically learns features optimal for the re-identification task from data. The learned filter pairs encode photometric transforms. Its deep architecture makes it possible to model a mixture of complex photometric and geometric transforms. We build the largest benchmark re-id dataset with 13, 164 images of 1, 360 pedestrians. Unlike existing datasets, which only provide manually cropped pedestrian images, our dataset provides automatically detected bounding boxes for evaluation close to practical applications. Our neural network significantly outperforms state-of-the-art methods on this dataset.
Using AOP for detailed runtime monitoring instrumentation (2009)

Although AOP has long been used for monitoring purposes, the level of detail that virtually all AOP frameworks support is not enough to support broad classes of monitoring applications. Often the method or function call is the basic unit of code weaving, and if some data access weaving is supported it is usually very limited, e.g., to object field access. In this paper we demonstrate the need for AOP to be extended if it is to support broad runtime monitoring needs, and then present two new joinpoint types for AspectJ, the basic block and loop back edge types. These allow much more fine-grained weaving of advice, which in turn supports a much larger category of runtime monitoring applications. We demonstrate the feasibility of these extensions with example prototype implementations using the AspectBench Compiler (abc).
A Compact Tri-Band Monopole Antenna With Single-Cell Metamaterial Loading (2010)

A compact tri-band planar monopole antenna is proposed that employs reactive loading and a ¿defected¿ ground-plane structure. The reactive loading of the monopole is inspired by transmission-line based metamaterials (TL-MTM), which enables the loaded antenna to operate in two modes. The first resonance exhibits a dipolar mode over the lower WiFi band of 2.40 GHz - 2.48 GHz, and the second resonance has a monopolar mode over the 5.15-5.80 GHz upper WiFi band. Full-wave analysis shows that the currents of the two modes are orthogonal to each other, resulting in orthogonal radiation patterns in the far field. The feature of a ¿defected¿ ground-plane, formed by appropriately cutting an L-shaped slot out of one of the CPW ground-planes, leads to the third resonance that covers the WiMAX band at 3.30-3.80 GHz. Air bridges at the intersection between the antenna and the CPW feedline ensure a balanced current. A fabricated prototype has compact dimensions of 20.0 mm × 23.5 mm × 1.59 mm, and exhibits good agreement between the measured and simulated <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">S</i> parameters and radiation patterns. The measured radiation efficiencies are 67.4% at 2.45 GHz, 86.3% at 3.50 GHz and 85.3% at 5.50 GHz.
Structural analysis of the glycoprotein allergen Art v II from the pollen of mugwort (Artemisia vulgaris L.) (1991)

The glycoprotein allergen Art v II, from the pollen of mugwort (Artemisia vulgaris L.) was treated with peptide:N-glycosidase F (PNGase F) to release asparagine-linked oligosaccharides. The oligosaccharides were isolated by gel permeation chromatography and their structures determined by 500-MHz 1H NMR spectroscopy, fast atom bombardment-mass spectrometry, and high-pH anion-exchange chromatography. The high-mannose oligosaccharides Man5GlcNAc2, Man6GlcNAc2, Man7GlcNAc2, Man8GlcNAc2, and Man9GlcNAc2 were present in the ratios 2:49:19:24:6 and accounted for all the asparagine-linked oligosaccharides released from Art v II by PNGase F. The NH2-terminal amino acid sequences of Art v II and of four peptides generated by cyanogen bromide (CNBr) cleavage of deglycosylated Art v II were determined. The first 30 amino acid residues of Art v II did not contain any potential N-glycosylation sites. One potential N-glycosylation site was identified in one of the CNBr fragments. The native protein conformation was shown by enzyme-linked immunosorbent assay inhibition assays to be essential for the binding of rabbit IgG to Art v II and for the binding of human IgE to the major IgE-binding epitope(s) in this allergen. At least one minor IgE-binding epitope still bound IgE after denaturation of the allergen. Removal of the high-mannose chains from denatured Art v II had no significant effect on the binding of human IgE to the minor IgE-binding epitope(s).
Mechanism of Prostaglandin E2 Transport across the Plasma Membrane of HeLa Cells and Xenopus Oocytes Expressing the Prostaglandin Transporter “PGT” (1998)

We recently identified a novel prostaglandin transporter called PGT (Kanai, N., Lu, R., Satriano, J. A., Bao, Y., Wolkoff, A. W., and Schuster, V. L. (1995) Science 268, 866-869). Based on initial functional studies, we have hypothesized that PGT might mediate the release of newly synthesized prostaglandins (PG), epithelial transport of PGs, or metabolic clearance of PGs. Here we examined the mechanism of PGT transport as expressed in HeLa cells and Xenopus oocytes, using isotopic PG influx and efflux studies. In both native HeLa cells and oocytes, cell membranes were poorly permeable to PGs. In contrast, in oocytes injected with PGT mRNA, the PG influx permeability coefficient was 90-157 times that of oocytes injected with water. The rank order substrate profile was PGF2alpha approximately PGE2 > TXB2 >> 6 keto-PGF1alpha. PG influx displayed an overshoot with rapid accumulation of tracer PGE2, followed by a gradual return to baseline. Based on estimated oocyte volumes, the PGT-mediated accumulation of PGE2 reached steady state at intra-oocyte concentrations 25-fold higher than the external media. The accumulation of PG was not due to intracellular binding or metabolism. PGT-mediated uptake was ATP- and temperature-dependent, but not sodium-dependent, and was inhibited by disulfonic stilbenes, niflumic acid, and the thiol reactive anion MTSES (Na(2-sulfonatoethyl)methanethiosulfonate). [3H]PGE2 efflux from PGT-transfected HeLa cells was stimulated by external (trans) PGE2 in a dose-dependent fashion and was inhibited by bromcresol green and 4,4'-diisothiocyanatostilbene-2,2'-disulfonate. Membrane depolarization inhibited uptake of [3H]PGE2, consistent with a model of net outward movement of negative charge during the translocation event. These findings suggest that PGT mediates [3H]PGE2 accumulation via obligatory, electrogenic anion exchange.
MovieGraphs: Towards Understanding Human-Centric Situations from Videos (2018)

There is growing interest in artificial intelligence to build socially intelligent robots. This requires machines to have the ability to "read" people's emotions, motivations, and other factors that affect behavior. Towards this goal, we introduce a novel dataset called MovieGraphs which provides detailed, graph-based annotations of social situations depicted in movie clips. Each graph consists of several types of nodes, to capture who is present in the clip, their emotional and physical attributes, their relationships (i.e., parent/child), and the interactions between them. Most interactions are associated with topics that provide additional details, and reasons that give motivations for actions. In addition, most interactions and many attributes are grounded in the video with time stamps. We provide a thorough analysis of our dataset, showing interesting common-sense correlations between different social aspects of scenes, as well as across scenes over time. We propose a method for querying videos and text with graphs, and show that: 1) our graphs contain rich and sufficient information to summarize and localize each scene; and 2) subgraphs allow us to describe situations at an abstract level and retrieve multiple semantically relevant situations. We also propose methods for interaction understanding via ordering, and reason understanding. MovieGraphs is the first benchmark to focus on inferred properties of human-centric situations, and opens up an exciting avenue towards socially-intelligent AI agents.
Inhibitory Effects of MLDG-containing Heterodimeric Disintegrins Reveal Distinct Structural Requirements for Interaction of the Integrin α9β1 with VCAM-1, Tenascin-C, and Osteopontin (2000)

The integrin alpha9beta1 is expressed on epithelial cells, smooth muscle cells, skeletal muscle, and neutrophils and recognizes at least three distinct ligands: vascular cell adhesion molecule 1 (VCAM-1), tenascin-C, and osteopontin. The alpha9 subunit is structurally similar to the integrin alpha4 subunit, and alpha9beta1 and alpha4beta1 both recognize VCAM-1 as a ligand. We therefore examined whether the disintegrin EC3, which we have recently shown specifically inhibits the binding of alpha4 integrins to ligands, would also be a functional inhibitor of alpha9beta1. EC3 and a novel heterodimeric disintegrin that we identified, EC6, both were potent inhibitors of alpha9beta1-mediated adhesion to VCAM-1 and of neutrophil migration across tumor necrosis factor-activated endothelial cells. A peptide containing a novel MLDG motif shared by both of these disintegrins also inhibited alpha9beta1- and alpha4beta1-mediated adhesion to VCAM-1. Surprisingly though, concentrations of EC3 that completely inhibited adhesion of alpha9-transfected cells to VCAM-1 had little or no effect on adhesion to either of the other alpha9beta1 ligands, osteopontin and tenascin-C. Furthermore, peptides AEIDGIEL and SVVYGLR, which we have previously shown inhibit binding of alpha9beta1-expressing cells to tenascin-C and osteopontin, respectively, had no effect on adhesion to VCAM-1. These data suggest that there are structurally distinct requirements for interactions of the alpha9beta1 integrin with VCAM-1 and the extracellular matrix ligands osteopontin and tenascin-C.
Isolation and characterization of full-length cDNA clones for human alpha-, beta-, and gamma-actin mRNAs: skeletal but not cytoplasmic actins have an amino-terminal cysteine that is subsequently removed. (1983)

cDNA clones encoding three classes of human actins have been isolated and characterized. The first two classes (gamma and beta, cytoplasmic actins) were obtained from a cDNA library constructed from simian virus 40-transformed human fibroblast mRNA, and the third class (alpha, muscle actin) was obtained from a cDNA library constructed from adult human muscle mRNA. A new approach was developed to enrich for full-length cDNAs. The human fibroblast cDNA plasmid library was linearized with restriction enzymes that did not cut the inserts of interest; it was then size-fractionated on gels, and the chimeric molecules of optimal length were selected for retransformation of bacteria. When the resulting clones were screened for actin-coding sequences it was found that some full-length cDNAs were enriched as much as 50- to 100-fold relative to the original frequency of full-length clones in the total library. Two types of clones were distinguished. One of these clones encodes gamma actin and contains 100 base pairs of 5' untranslated region, the entire protein coding region, and the 3' untranslated region. The second class encodes beta actin, and the longest such clone contains 45 base pairs of 5' untranslated region plus the remainder of the mRNA extending to the polyadenylic acid tail. A third class, obtained from the human muscle cDNA library, encodes alpha actin and contains 100 base pairs of 5' untranslated region, the entire coding region, and the 3' untranslated region. Analysis of the DNA sequences of the 5' end of the clones demonstrated that although beta- and gamma-actin genes start with a methionine codon (MET-Asp-Asp-Asp and MET-Glu-Glu-Glu, respectively), the alpha-actin gene starts with a methionine codon followed by a cysteine codon (MET-CYS-Asp-Glu-Asp-Glu). Since no known actin proteins start with a cysteine, it is likely that post-translational removal of cysteine in addition to methionine accompanies alpha-actin synthesis but not beta- and gamma-actin synthesis. This observation has interesting implications both for actin function and actin gene regulation and evolution.
Structural and optical properties of europium doped zirconia single crystals fibers grown by laser floating zone (2011)

Yttria stabilized zirconia single crystal fibers doped with europium ions were developed envisaging optical applications. The laser floating zone technique was used in order to grow millimetric high quality single crystal fibers. The as-grown fibers are completely transparent and inclusion free, exhibiting a cubic structure. Under ultraviolet (UV) excitation, a broad emission band appears at 551 nm. The europium doped fibers are translucent with a tetragonal structure and exhibit an intense red emission at room temperature under UV excitation. The fingerprint transition lines between the D50 and F7J(0–4) multiplets of the Eu3+ ions are observed with the main emission line at ∼606 nm due to D50→F72 transition. Photoluminescence excitation and wavelength dependent the photoluminescence spectra confirm the existence of different Eu3+ optical centers.
Quantitative Analysis of Orofacial Thermoreceptive Neurons in the Superficial Medullary Dorsal Horn of the Rat (1997)

Surprisingly little is known concerning the central processing of innocuous thermal somatosensory information. The aim of the present study was to obtain quantitative data on the characteristics of neurons in the rat superficial medullary dorsal horn (sMDH) that responded to innocuous thermal stimulation of the rat's face and tongue. Single-unit extracellular recordings were obtained in chloralose-urethane anesthetized rats. A total of 153 thermoreceptive neurons was studied. Of these, 146 were excited by cooling and inhibited by warming and were classified as COLD cells. The remaining seven cells were excited by innocuous warming of the skin or tongue. Of 123 COLD cells tested, 33% were excited by touch and 22% by pinch stimuli delivered to the thermoreceptive field. Of the 50 COLD cells tested, 46% were excited also by noxious heating (> or = 50 degrees C for 5 s). Most (82/121) of the receptive fields were located on the upper lip, 25 on the tongue, and most of the remaining on the lower lip. Receptive fields were generally small (1-5 mm2). In some experiments, electrical stimulation in the thalamus was performed, and nine COLD cells could be activated antidromically. The responses of 38 COLD cells to incremental 5 degrees C cooling steps were examined quantitatively. Thermal stimuli were applied to facial or lingual receptive fields of sMDH neurons with a computer-controlled Peltier thermode starting from 33 degrees C, decreasing to 8 or 3 degrees C, and returning to 33 degrees C. Most COLD cells (26/38) had both static and dynamic responses; 7 had mainly dynamic and 5 mainly static responses to step decreases in temperature. Rat sMDH COLD cells could be classified into three groups depending on their stimulus-response functions. The first group (Type 1, n = 19) had a bell-shaped static stimulus response function. The second group (Type 2) had a high maintained or increasing static firing rate as the temperature decreased < 18 degrees C (n = 10). Type 3 COLD cells had mainly dynamic properties (n = 7). Many of the cells in all groups were excited by noxious mechanical stimulation. Type 2 cells differed from the other two groups in that most did not respond to noxious thermal stimuli (hot) and many responded to innocuous tactile stimuli. Neurons from each of the three groups of COLD cells could be activated antidromically from contralateral thalamus. These data suggest that there is little central processing of thermal information at the first central synapse for Type 1 neurons, however, the responses of the other two types may be due to central processing and convergence. The demonstration of rat sMDH COLD cells with distinctive stimulus-response functions to thermal shifts suggests separate functional roles of these neurons in the ascending thermal sensory pathway.
Image reconstruction from highly undersampled (k,t)-space data with joint partial separability and sparsity constraints (2012)

Partial separability (PS) and sparsity have been previously used to enable reconstruction of dynamic images from undersampled (k,t)-space data. This paper presents a new method to use PS and sparsity constraints jointly for enhanced performance in this context. The proposed method combines the complementary advantages of PS and sparsity constraints using a unified formulation, achieving significantly better reconstruction performance than using either of these constraints individually. A globally convergent computational algorithm is described to efficiently solve the underlying optimization problem. Reconstruction results from simulated and in vivo cardiac MRI data are also shown to illustrate the performance of the proposed method.
The structure of the tetrasaccharide unit of camellidins, saponins possessing antifungal activity (1986)

By successful application of recently developed 1H n.m.r. techniques, the structure of the tetrasaccharide unit of camellidin-I (1) and -II (2), saponins having antifungal activity, was elucidated as β-D-glucopyranosyl-(1→2)-β-D-galactopyranosyl-(1→4)-[α-D-galactopyranosyl-(1→2)]-β-D-glucuronopyranoside, without degradation of the glycosidic linkages.
Connective tissue in female urinary incontinence (1999)

An effective closure of the female urethra in stress situations is dependent on an integrated action of various anatomical structures connected to the organ. The most important of these structures - from a functional aspect - are the suburethral vaginal wall, the pubourethral ligaments, the pubococcygeus muscles and the paraurethral connective tissues. In all these structures connective tissue is an essential ingredient. Hence, defects in the actual connective tissue - in particular the paraurethral connective tissue that connects the aforementioned structures to each other and to the urethra - will bring about an ineffective urethral closure. Female urinary incontinence may then be caused by defective connective tissue per se and/or by a disconnection of the aforementioned structures, whereby the urethra cannot be 'kinked' - that is, closed off in stress situations.
Molecular genetics of myeloid leukemia: identification of the commonly deleted segment of chromosome 20. (1993)

A deletion of the long arm of chromosome 20 [del(20q)] is a recurring abnormality in malignant myeloid disorders. The occurrence of the del(20q) in a broad spectrum of myeloid disorders suggests that the loss of genetic material on 20q could provide a proliferative advantage to myeloid cells, possibly through the loss of a tumor-suppressor gene. We have examined a series of patients with the del(20q) using fluorescence in situ hybridization (FISH) with unique sequence probes that map along the length of 20q, and have delineated a segment that is deleted in 95% of all patients examined (18 of 19). In addition, we have shown that the deletions are interstitial rather than terminal. This region of deletion extends from 20q11.2 to q12, and is flanked by the RPN2 (proximal) and D20S17 loci (distal). The SRC and ADA genes are located within the commonly deleted segment. Our findings emphasize the importance of FISH and other molecular mapping techniques in defining such a region. The delineation of a commonly deleted segment in 20q11.2-q12 will facilitate the identification of candidate tumor-suppressor genes on 20q.
Overview and emerging challenges in mechanical dicing of silicon wafers (2006)

An overview and emerging challenges in mechanical dicing of silicon (Si) wafer are discussed from view point of narrow kerf, thin wafer, chip strength enhancement, Copper (Cu)/low-k wafers and dicing challenges for emerging technologies.
Long-Term Stimulation and Recording With a Penetrating Microelectrode Array in Cat Sciatic Nerve (2004)

We studied the consequences of long-term implantation of a penetrating microelectrode array in peripheral nerve over the time course of 4-6 mo. Electrode arrays without lead wires were implanted to test the ability of different containment systems to protect the array and nerve during contractions of surrounding muscles. Treadmill walking was monitored and the animals showed no functional deficits as a result of implantation. In a different set of experiments, electrodes with lead wires were implanted for up to 7 mo and the animals were tested at 2-4 week intervals at which time stimulation thresholds and recorded sensory activity were monitored for every electrode. It was shown that surgical technique highly affected the long-term stimulation results. Results between measurement sessions were compared, and in the best case, the stimulation properties stabilized in 80% of the electrodes over the course of the experiment (162 days). The recorded sensory signals, however, were not stable over time. A histological analysis performed on all implanted tissues indicated that the morphology and fiber density of the nerve around the electrodes were normal.