gebhart/patrepeval huggingface dataset:
Can Lower Resolution Be Better? (2008)

Recently, many researchers started to question a long-standing paradox in the engineering practice of digital photography: oversampling followed by compression, and pursue more intelligent sparse sampling techniques. In this research we take a practical approach of uniform down sampling in image space, and the sampling is made adaptive by a spatially varying directional low-pass prefiltering. Since the down-sampled prefiltered image is a low-resolution image of conventional square sample grid, it can be compressed and transmitted without any change to current image coding standards and systems. The decoder first decompresses the low-resolution image and then upsamples it to the original resolution by least-square estimation using a 2D piecewise autoregressive model and the knowledge of directional low-pass filter. The proposed joint adaptive down-sampling and up-sampling technique outperforms JPEG 2000 (the state-of-the-art in lossy image coding) in PSNR measure at low to modest bit rates and achieves superior visual quality at all bit rates. This work shows that oversampling not only increases cost and energy consumption, but it could, even when coupled with a sophisticated rate-distortion optimized compression scheme, cause inferior image quality at certain bit rates.
Structure and Physical Characteristics of Shell of Groundnut Pod, with Reference to Longevity of Seed-In-Shell (2006)

莢つきラッカセイ種子の寿命が小粒品種で優れることと莢の役割との関係を2実験で調べた. 実験1 : 外果皮, 中果皮, そして, 内果皮からなる未熟莢実の莢で, 外果皮と中果皮を加えた厚さは, 極小粒・薄莢の品種Chicoでは大粒・厚莢の品種ナカテユタカの約60％であったが, それぞれの細胞層の数には大きな差異が認められなかった. 外果皮と内果皮のほとんどが脱落, 崩壊している完熟莢実の莢で大部分を占める中果皮では, その最内層の厚膜組織が維管束の周辺に派生して隔壁状に発達していた. そして, 維管束と維管束の間に破生間隙様の空隙が観察されたが, それと莢の水分やガス交換におけるフィルター機能との関係が示唆された. 実験2 : 乾燥莢実1個あたりの, 莢実重, 子実重, 子実容積(VS), 胚室容積(VOC), 莢実表面積(PSA), 莢重(SHW), 莢の容積(PSA×ST), 及び胚室内空隙容積(VOC-VS)は, いずれも大～中粒性品種群h(バージニア・タイプと亜種間交雑育成の22品種)が小粒性品種群f(スパニッシュ・タイプ, 18品種)よりも約2倍と大きかったのに対して, 莢実表面積/胚室容積比は品種群fが品種群hよりも約30％大きく, 莢の厚さ(ST)では両品種群の差が小さく, そして, 莢密度(SHW/PSA×ST)では差がみられなかった. 莢つき種子の長期発芽力保持の品種間差異とその機構については, 莢の構造や物理的特性の差異が子実の水分やガス交換の動態に及ぼす影響の面からさらに詳しく調べる必要がある.
Upper airway response to electrical stimulation of the genioglossus in obstructive sleep apnea (2003)

Contraction of the genioglossus (GG) has been shown to improve upper airway patency. In the present study, we evaluated responses in upper airway pressure-flow relationships during sleep to electrical stimulation (ES) of the GG in patients with obstructive sleep apnea. Five patients with chronically implanted hypoglossal nerve (HG) electrodes and nine patients with fine-wire electrodes inserted into the GG were studied. Airflow was measured at multiple levels of nasal pressure, and upper airway collapsibility was defined by the nasal pressure below which airflow ceased ["critical" pressure (Pcrit)]. ES shifted the pressure-flow relationships toward higher flow levels in all patients over the entire range of nasal pressure applied. Pcrit decreased similarly during both HG-ES and GG-ES (deltaPcrit was 3.98 +/- 2.31 and 3.18 +/- 1.70 cmH2O, respectively) without a significant change in upstream resistance. The site of collapse (velo- vs. oropharynx) did not influence the response to GG-ES. Moreover, ES-induced reductions in the apnea-hypopnea index of the HG-ES patients were associated with substantial decreases in Pcrit. Our findings imply that responses in apnea severity to HG-ES can be predicted by characterizing the patient's baseline pressure-flow relationships and response to GG-ES.
Numbers, Point and Counterpoint (1985)

IF YOU PLAY a musical instrument and have some knowledge of mathematics, you probably know that mathematics and music have much in common. The connection between these two seemingly unrelated subjects may appear in the study of harmony or counterpoint, or in the laws of vibrating strings and physical resonance. Although musicians use musical laws without analyzing them too deeply, a mathematical glance at musical structure may be quite illuminating.KeywordsProjective GeometryArithmetic ProgressionWill EmitMusical StructureHarmonic SequenceThese keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.
Global kinomic and phospho-proteomic analyses of the human malaria parasite Plasmodium falciparum (2011)

The role of protein phosphorylation in the life cycle of malaria parasites is slowly emerging. Here we combine global phospho-proteomic analysis with kinome-wide reverse genetics to assess the importance of protein phosphorylation in Plasmodium falciparum asexual proliferation. We identify 1177 phosphorylation sites on 650 parasite proteins that are involved in a wide range of general cellular activities such as DNA synthesis, transcription and metabolism as well as key parasite processes such as invasion and cyto-adherence. Several parasite protein kinases are themselves phosphorylated on putative regulatory residues, including tyrosines in the activation loop of PfGSK3 and PfCLK3; we show that phosphorylation of PfCLK3 Y526 is essential for full kinase activity. A kinome-wide reverse genetics strategy identified 36 parasite kinases as likely essential for erythrocytic schizogony. These studies not only reveal processes that are regulated by protein phosphorylation, but also define potential anti-malarial drug targets within the parasite kinome.
Differential effects of B7-1 blockade in the rat experimental autoimmune encephalomyelitis model (1997)

Blocking the CD28-B7 T cell costimulatory activation pathway protects animals from developing experimental autoimmune encephalomyelitis (EAE). In the mouse EAE model, selective blockade of B7-1 by specific mAbs has been shown to protect animals from EAE. In the Lewis rat model, we have shown that CD28-B7 blockade by systemic administration of CTLA4Ig prevents actively induced EAE. Since CTLA4Ig binds to both B7-1 and B7-2, we used a mutant form of CTLA4Ig (CTLA4IgY100F) that binds only B7-1, to study the role of B7-1 blockade in this model. Such a reagent avoids the potential of signaling by mAbs. Systemic administration of CTLA4IgY100F in several dosing regimens did not protect from EAE, and in some protocols worsened disease, while CTLA4Ig was always protective. In contrast, systemic injection of APCs preincubated ex vivo with the encephalitogenic peptide of myelin basic protein and either CTLA4Ig or CTLA4IgY100F protected recipients from disease. In vitro studies confirmed the in vivo observations and showed that primed lymph node cells from protected animals had decreased proliferative responses to myelin basic protein as compared with controls, while lymphocytes from animals treated with systemic CTLA4gY100F did not. More importantly, systemic administration of CTLA4IgY100F abrogated the protective effect of ex vivo treated APCs. These data suggest an important regulatory role for B7-1, perhaps through binding to CTLA4, in this model of EAE. Understanding the role and mechanisms of selective blockade of costimulatory molecules has implications for therapy of autoimmune disease.
Preparation of Hela Cell Nuclear and Cytosolic S100 Extracts for In Vitro Splicing (2003)

Following the initial discovery of split genes in 1977, it took several years before in vitro systems were successfully developed to study the biochemistry of pre-mRNA splicing. The first systems relied on coupling of transcription and splicing in whole-cell extracts and were fairly inefficient, because of the different optima for these two reactions (1,2). It was later shown that these reactions could be uncoupled (3,4), but obtaining discrete pre-mRNAs in useful amounts remained an obstacle until in vitro transcription with bacteriophage RNA polymerases (3) was adopted for this purpose. Another useful development was a nuclear extract preparation procedure that was initially developed for in vitro transcription studies (5). No splicing was detected in this study. However, the same extract preparation procedure, in conjunction with pre-mRNAs transcribed from cloned genes by SP6 RNA polymerase, was used to define optimal conditions for in vitro splicing (6). This system results in relatively efficient and accurate splicing, and is now in wide use, with slight variations from laboratory to laboratory. Variations in extract preparation include primarily the use of slightly different buffers and salts for nuclear extraction or dialysis.
Human Type VI Collagen: Purification from Human Subcutaneous Fat Tissue and an Immunohistochemical Study of Morphea and Systemic Sclerosis (1995)

Collagen was isolated from human placenta by pepsin digestion and salt precipitation. This collagen was similar in its electrophoretic mobility and immunological reactivity with monoclonal antibody to form B of type VI collagen in the literature (Trueb B, Schreier T, Bruckner P and Winterhalter K. 1987. Eur. J. Biochem. 166: 699-703). We prepared polyclonal rabbit antiserum against alpha 2 chain of type VI collagen and performed an immunohistochemical study using this polyclonal antibody. It reacted in fat tissue and around vessels and peripheral nerves in normal human skin. To confirm the presence of type VI collagen in fat tissue, we isolated collagen from human subcutaneous tissue. This collagen showed a similar pattern in polyacrylamide gel electrophoresis with that from human placenta and cross-reacted with monoclonal or polyclonal antibody against type VI collagen. By immunohistochemical staining, abundant type VI collagen was observed in the septum of subcutaneous fat tissue in morphea or systemic sclerosis. In the mild hyalinizing areas or after treatment with 6M urea or hyaluronidase in highly hyalinized areas, the staining of type VI collagen increased. These data suggest that the amount of type VI collagen in subcutaneous tissue is involved in the early phases of these fibrosing disorders and that type VI collagen accumulates even more in hyalinizing tissue in late phases of these diseases.
High single mode operation from hybrid ion implanted/selectively oxidized VCSELs (2002)

The modal discrimination can be augmented by creating a central region of gain surrounded by a region of optical loss. We report single mode output of more than 5 mW for 850 nm VCSELs fabricated using a hybrid ion implantation and selective oxidation device structure designed to achieve this end.
Optical imaging techniques in microfluidics and their applications (2012)

Microfluidic devices have undergone rapid development in recent years and provide a lab-on-a-chip solution for many biomedical and chemical applications. Optical imaging techniques are essential in microfluidics for observing and extracting information from biological or chemical samples. Traditionally, imaging in microfluidics is achieved by bench-top conventional microscopes or other bulky imaging systems. More recently, many novel compact microscopic techniques have been developed to provide a low-cost and portable solution. In this review, we provide an overview of optical imaging techniques used in microfluidics followed with their applications. We first discuss bulky imaging systems including microscopes and interferometer-based techniques, then we focus on compact imaging systems that can be better integrated with microfluidic devices, including digital in-line holography and scanning-based imaging techniques. The applications in biomedicine or chemistry are also discussed along with the specific imaging techniques.
Unacylated ghrelin acts as a potent insulin secretagogue in glucose-stimulated conditions (2007)

Acylated and unacylated ghrelin (AG and UAG) are gut hormones that exert pleiotropic actions, including regulation of insulin secretion and glucose metabolism. In this study, we investigated whether AG and UAG differentially regulate portal and systemic insulin levels after a glucose load. We studied the effects of the administration of AG (30 nmol/kg), UAG (3 and 30 nmol/kg), the ghrelin receptor antagonist [D-Lys(3)]GHRP-6 (1 micromol/kg), or various combinations of these compounds on portal and systemic levels of glucose and insulin after an intravenous glucose tolerance test (IVGTT, d-glucose 1 g/kg) in anesthetized fasted Wistar rats. UAG administration potently and dose-dependently enhanced the rise of insulin concentration induced by IVGTT in the portal and, to a lesser extent, the systemic circulation. This UAG-induced effect was completely blocked by the coadministration of exogenous AG at equimolar concentrations. Similarly to UAG, [D-Lys(3)]GHRP-6, alone or in combination with AG and UAG, strongly enhanced the portal insulin response to IVGTT, whereas exogenous AG alone did not exert any further effect. Our data demonstrate that, in glucose-stimulated conditions, exogenous UAG acts as a potent insulin secretagogue, whereas endogenous AG exerts a maximal tonic inhibition on glucose-induced insulin release.
Anti-Mycobacterium leprae activity of several quinolones studied in the mouse. (1991)

The anti-Mycobacterium leprae activity of several fluoroquinolones (A-56619, A-56620, ofloxacin, fleroxacin, lomefloxacin, temafloxacin, tosufloxacin, and PD-117596) was studied in the mouse. In a dosage of 150 mg/kg administered daily, A-56619 is active and A-56620 is inactive against M. leprae. Ofloxacin administered daily for 2 weeks at 300 mg/kg is bactericidal. The minimal effective dose of PD-117596, lomefloxacin and temafloxacin is less than 37.5 mg/kg. When administered at 300 mg/kg at monthly intervals temafloxacin, PD-117596, and ofloxacin are bacteriostatic; while fleroxacin and lomefloxacin are bactericidal. Tosufloxacin is less active than the other quinolones included in the present study.
3D Point Cloud Classification and Segmentation using 3D Modified Fisher\n Vector Representation for Convolutional Neural Networks (2017)

The point cloud is gaining prominence as a method for representing 3D shapes,\nbut its irregular format poses a challenge for deep learning methods. The\ncommon solution of transforming the data into a 3D voxel grid introduces its\nown challenges, mainly large memory size. In this paper we propose a novel 3D\npoint cloud representation called 3D Modified Fisher Vectors (3DmFV). Our\nrepresentation is hybrid as it combines the discrete structure of a grid with\ncontinuous generalization of Fisher vectors, in a compact and computationally\nefficient way. Using the grid enables us to design a new CNN architecture for\npoint cloud classification and part segmentation. In a series of experiments we\ndemonstrate competitive performance or even better than state-of-the-art on\nchallenging benchmark datasets.\n
XRCE's Participation at Patent Image Classification and Image-based Patent Retrieval Tasks of the Clef-IP 2011 (2011)

The aim of this document is to describe the methods we used in the Patent Image Classification and Image-based Patent Retrieval tasks of the Clef-IP 2011 track. The patent image classification task consisted in categorizing patent images into predefined categories such as abstract drawing, graph, flowchart, table, etc. Our main aim in participating in this sub-task was to test how our image categorizer performs on this type of categorization problem. Therefore, we used SIFT-like local orientation histograms as low level features and on the top of that we built a visual vocabularies specific to patent images using Gaussian mixture model (GMM). This allowed us to represent images with Fisher Vectors and to use linear classifiers to train one-versusall classifiers. As the results show, we obtain very good classification performance. Concerning the Image-based Patent Retrieval task, we kept the same image representation as for the Image Classification task and used dot product as similarity measure. Nevertheless, in the case of patents the aim was to rank patents based on patent similarities, which in the case of pure image-based retrieval implies to be able to compare a set of images versus another set of images. Therefore, we investigated dierent strategies such as averaging Fisher Vector representation of an image set or considering the maximum similarity between pairs of images. Finally, we also built runs where the predicted image classes were considered in the retrieval process. For the text-based patent retrieval, we decided simply to weight dierently the different fields of the patent, giving more weight to some of them, before concatenating the dierent fields. Monolingually, we then used the standard cosine measure, after applying the tf-idf weighting scheme, to compute the similarity between the query and the documents of the collection. To handle the multi-lingual aspect, we either used late fusion of monolingual similarities (French / English / German) or translated non-English fields into English (and then computed simple monolingual similarities). In addition to these standard textual similarities, we also computed similarities between patents based on the IPC-categories they share and similarities based on the patent citation graph; we used late fusion to merge these new similarities with the former ones. Finally to combine the image-based and the text-based rankings, we normalized the ranking scores and used again weighted late fusion strategy. As our expectation for the visual expert was low, we used a much stronger weight for the textual expert, than for the visual one. We have shown that while indeed the visual expert performed poorly, combined with text experts the multi-modal system outperformed the corresponding text-only based retrieval system.
Multifunctional RNA Nanoparticles (2014)

Our recent advancements in RNA nanotechnology introduced novel nanoscaffolds (nanorings); however, the potential of their use for biomedical applications was never fully revealed. As presented here, besides functionalization with multiple different short interfering RNAs for combinatorial RNA interference (e.g., against multiple HIV-1 genes), nanorings also allow simultaneous embedment of assorted RNA aptamers, fluorescent dyes, proteins, as well as recently developed RNA-DNA hybrids aimed to conditionally activate multiple split functionalities inside cells.
PCR with Q5® High-Fidelity 2X Master Mix (M0492) v1 (2014)

This protocol is for PCR with Q5® High-Fidelity 2X Master Mix (M0492)
Two interferon mRNAs in human fibroblasts: in vitro translation and Escherichia coli cloning studies. (1980)

Two mRNA species that produce biologically active interferon were isolated from human fibroblasts and studied by size fractionation and cloning in Escherichia coli plasmid pBR322. The major fibroblast interferon (Hu IFN-beta 1) is coded for by the smaller of the two mRNAs, an 11S species, 900 nucleotides long, which in cell-free systems yields a 20,000 Mr protein. The second interferon mRNA species (Hu IFN-beta 2) is 14S, about 1300 nucleotides long, and codes for another protein of 23,000-26,000 Mr. The two interferon mRNAs do not cross-hybridize. Both are induced by poly(rI.rC), but IFN-beta 2 mRNA is induced to about 10% in cells by cycloheximide treatment alone whereas under these conditions IFN-beta 1 is not induced.
Spatiotemporal patterns of expression of NGF and the low-affinity NGF receptor in rat embryos suggest functional roles in tissue morphogenesis and myogenesis (1992)

We show here that NGF and its low-affinity receptor (p75NGFR) are expressed during rat embryogenesis at sites that are known to have important roles in tissue morphogenesis and myogenesis. The developing skin of the maxilla, the mandible, and the limb showed very similar patterns of NGF and p75NGFR expression. However, NGF and p75NGFR expression in the developing limb initiated at the limb bud stage and was concentrated at proximal and distal developmental sites that have been reported to be involved in limb morphogenesis. Expression at the proximal/distal ends of the limb persisted throughout limb development, with some of the highest levels of expression occurring at the limb axillary sites, which were not highly innervated. We have also found p75NGFR expression at sites of mesenchymal/epithelial interactions in several developing organs that do not appear to have an adjacent source of NGF and may therefore be sites that bind and respond to the other members of the NGF family (brain-derived neurotrophic factor and neurotrophin-3). These organs include the lung, testes, and kidney, where expression of p75NGFR occurred during the morphogenesis of specific epithelial structures and was coexpressed with the cell adhesion molecule NCAM. In addition, we found that NGF and p75NGFR were expressed during myogenesis. p75NGFR was observed in myoblast cells expressing MyoD1, a myoblast differentiation marker, and NGF transcripts in cells just adjacent to the developing myoblasts. When the myoblasts differentiate into myotubes, p75NGFR and MyoD1 cease to be expressed and the adjacent cells concomitantly cease to be make NGF. However, NGF and p75NGFR were not present in the early muscle precursor cells of the myotome of the somites but were observed in the dermatome and sclerotome, respectively. These results suggest that NGF and p75NGFR have functional roles in developmental processes that affect morphogenesis and cell differentiation.
The Effect of Occlusal Discrepancies on Periodontitis. II. Relationship of Occlusal Treatment to the Progression of Periodontal Disease (2001)

This study provides strong evidence of an association between untreated occlusal discrepancies and the progression of periodontal disease. In addition, this study shows that occlusal treatment significantly reduces the progression of periodontal disease over time and can be an important adjunct therapy in the comprehensive treatment of periodontal disease.
Diabetes and cardiovascular risk factors: the Framingham study. (1979)

The impact of cardiovascular disease was compared in non-diabetics and diabetics in the Framingham cohort. In the first 20 years of the study about 6% of the women and 8% of the men were diagnosed as diabetics. The incidence of cardiovascular disease among diabetic men was twice that among non-diabetic men. Among diabetic women the incidence of cardiovascular disease was three times that among non-diabetic women. Judging from a comparison of standardized coefficients for the regression of incidence of cardiovascular disease on specified risk factors, there is no indication that the relationship of risk factors to the subsequent development of cardiovascular disease is different for diabetics and non-diabetics. This study suggests that the role of diabetes as a cardiovascular risk factor does not derive from an altered ability to contend with known risk factors.
Therapeutics targeting Bcl-2 in hematological malignancies (2017)

Members of the <i>B-cell lymphoma 2</i> (<i>BCL-2</i>) gene family are attractive targets for cancer therapy as they play a key role in promoting cell survival, a long-since established hallmark of cancer. Clinical utility for selective inhibition of specific anti-apoptotic Bcl-2 family proteins has recently been realized with the Food and Drug Administration (FDA) approval of venetoclax (formerly ABT-199/GDC-0199) in relapsed chronic lymphocytic leukemia (CLL) with 17p deletion. Despite the impressive monotherapy activity in CLL, such responses have rarely been observed in other B-cell malignancies, and preclinical data suggest that combination therapies will be needed in other indications. Additional selective antagonists of Bcl-2 family members, including Bcl-X<sub>L</sub> and Mcl-1, are in various stages of preclinical and clinical development and hold the promise of extending clinical utility beyond CLL and overcoming resistance to venetoclax. In addition to direct targeting of Bcl-2 family proteins with BH3 mimetics, combination therapies that aim at down-regulating expression of anti-apoptotic <i>BCL-2</i> family members or restoring expression of pro-apoptotic BH3 family proteins may provide a means to deepen responses to venetoclax and extend the utility to additional indications. Here, we review recent progress in direct and selective targeting of Bcl-2 family proteins for cancer therapy and the search for rationale combinations.