gebhart/patrepeval huggingface dataset:
A Dataset and Exploration of Models for Understanding Video Data through Fill-in-the-Blank Question-Answering (2017)

While deep convolutional neural networks frequently approach or exceed human-level performance in benchmark tasks involving static images, extending this success to moving images is not straightforward. Video understanding is of interest for many applications, including content recommendation, prediction, summarization, event/object detection, and understanding human visual perception. However, many domains lack sufficient data to explore and perfect video models. In order to address the need for a simple, quantitative benchmark for developing and understanding video, we present MovieFIB, a fill-in-the-blank question-answering dataset with over 300,000 examples, based on descriptive video annotations for the visually impaired. In addition to presenting statistics and a description of the dataset, we perform a detailed analysis of 5 different models predictions, and compare these with human performance. We investigate the relative importance of language, static (2D) visual features, and moving (3D) visual features, the effects of increasing dataset size, the number of frames sampled, and of vocabulary size. We illustrate that: this task is not solvable by a language model alone, our model combining 2D and 3D visual information indeed provides the best result, all models perform significantly worse than human-level. We provide human evaluation for responses given by different models and find that accuracy on the MovieFIB evaluation corresponds well with human judgment. We suggest avenues for improving video models, and hope that the MovieFIB challenge can be useful for measuring and encouraging progress in this very interesting field.
Maintaining Reviews: Updates, Amendments and Feedback (2008)

This chapter contains sections titled: Introduction Some important definitions Important dates associated with Cochrane reviews Considerations when updating a Cochrane review ‘What's new’ and History tables Incorporating and addressing feedback in a Cochrane review Chapter information References
Granulocyte Colony-Stimulating Factor and Granulocyte-Macrophage Colony-Stimulating Factor (1992)

FOUR colony-stimulating factors influence the survival, proliferation, differentiation, and functional activation of myeloid hematopoietic cells: macrophage colony-stimulating factor (M-CSF), granulocyte colony-stimulating factor (G-CSF), granulocytemacrophage colony-stimulating factor (GM-CSF), and interleukin-3 (formerly known as multi-colony-stimulating factor).1 2 3 Various other cytokines and factors are also implicated in these processes, including interleukins 1, 5, 6, and 11 and the recently identified Steel factor (variously designated c-kit ligand, mast-cell growth factor, and stem-cell factor).4 , 5 Of these factors, only G-CSF and GM-CSF are commercially available for clinical use. G-CSF has been approved in the United States and major European countries for the reduction of infection after . . .
Activation of flavin-containing oxidases underlies light-induced production of H 2 O 2 in mammalian cells (1999)

Violet-blue light is toxic to mammalian cells, and this toxicity has been linked with cellular production of H2O2. In this report, we show that violet-blue light, as well as UVA, stimulated H2O2 production in cultured mouse, monkey, and human cells. We found that H2O2 originated in peroxisomes and mitochondria, and it was enhanced in cells overexpressing flavin-containing oxidases. These results support the hypothesis that photoreduction of flavoproteins underlies light-induced production of H2O2 in cells. Because H2O2 and its metabolite, hydroxyl radicals, can cause cellular damage, these reactive oxygen species may contribute to pathologies associated with exposure to UVA, violet, and blue light. They may also contribute to phototoxicity often encountered during light microscopy. Because multiphoton excitation imaging with 1,047-nm wavelength prevented light-induced H2O2 production in cells, possibly by minimizing photoreduction of flavoproteins, this technique may be useful for decreasing phototoxicity during fluorescence microscopy.
Matrix‐based comparative genomic hybridization: Biochips to screen for genomic imbalances (1997)

Comparative genomic hybridization (CGH) to metaphase chromosomes has been widely used for the genome-wide screening of genomic imbalances in tumor cells. Substitution of the chromosome targets by a matrix consisting of an ordered set of defined nucleic acid target sequences would greatly enhance the resolution and simplify the analysis procedure, both of which are prerequisites for a broad application of CGH as a diagnostic tool. However, hybridization of whole genomic human DNA to immobilized single-copy DNA fragments with complexities below the megabase pair level has been hampered by the low probability of specific binding because of the high probe complexity. We developed a protocol that allows CGH to chips consisting of glass slides with immobilized target DNAs arrayed in small spots. High-copy-number amplifications contained in tumor cells were rapidly scored by use of target DNAs as small as a cosmid. Low-copy-number gains and losses were identified reliably by their ratios by use of chromosome-specific DNA libraries or genomic fragments as small as 75 kb cloned in P1 or PAC vectors as targets, thus greatly improving the resolution achievable by chromosomal CGH. The ratios obtained for the same chromosomal imbalance by matrix CGH and by chromosomal CGH corresponded very well. The new matrix CGH protocol provides a basis for the development of automated diagnostic procedures with biochips designed to meet clinical needs. Genes Chromosomes Cancer 20:399–407, 1997. © 1997 Wiley-Liss, Inc.
Chemistry and electronic properties of metal-organic semiconductor interfaces: Al, Ti, In, Sn, Ag, and Au on PTCDA (1996)

The chemistry and electronic properties of interfaces formed between thin films of the archetype molecular organic semiconductor 3, 4, 9, 10 perylenetetracarboxylic dianhydride (PTCDA) and reactive and nonreactive metals are investigated via synchrotron radiation photoemission spectroscopy. In, Al, Ti, and Sn react at room temperature with the anhydride group of the PTCDA molecule, producing heavily oxidized interface metal species and thick interfacial layers with a high density of states in the PTCDA band gap. The penetration of the reactive metal species in the PTCDA film is found to be inversely related to their first ionization energy. The noble metals Ag and Au form abrupt, unreacted interfaces. The chemical and structural results correlate well with the electrical properties of the interfaces that show Ohmic behavior with the reactive metal contacts and blocking characteristics with the noble metals. The Ohmic behavior of the reactive metal contacts is ascribed to carrier hopping and/or tunneling through the reaction-induced interface states. \textcopyright{} 1996 The American Physical Society.
Identification, Genetic and Biochemical Analysis of Genes involved in Synthesis of Sugar Nucleotide Precursors of Xanthan Gum (1993)

A genetic and biochemical analysis of Xanthomonas campestris chromosomal functions required for xanthan polysaccharide synthesis (xps) was undertaken. Seven xps DNA regions were isolated after conjugation of chemically induced non-mucoid mutants with a genomic library of X. campestris DNA. No overlapping segments between regions were detected, based on physical mapping, indicating the unlinked character of these regions. Clones complementing several different mutants belonging to the same region contained overlapping segments of X. campestris chromosomal DNA. Complementation and biochemical analysis, and DNA mapping were used to identify and characterize xpsZZZ, ZV and VZ DNA regions. Mutants in these three regions were able to synthesize both lipid intermediates and xanthan gum in vitro when sugar nucleotides were provided as substrates. HPLC analysis of the intracellular sugar nucleotide content showed that the XpsIII group comprises two different classes of mutants : XpsIIIA, defective in UDP-glucose, UDP-glucuronic acid and GDP-mannose, and XpsIIIB,defective in GDP-mannose. XpsIV mutants were defective in UDP-glucose and UDP-glucuronic acid, and XpsVI mutants were defective only in UDP-glucuronic acid. Analysis of enzyme activities involved in the synthesis of UDP-glucose, GDP-mannose and UDP-glucuronic acid indicated that the xpsZZZA region affects the activity of the phosphoglucomutase/phosphomannomutase enzyme, and the xpsZZZB region affects the mannoisomerase/phosphomannoisomerase activities. The xpsZV mutations affect the activity of the UDPG-pyrophosphorylase enzyme, and the xps VZ mutations affect the activity of the UDPG-dehydrogenase enzyme.
A urinary Common Rejection Module (uCRM) score for non-invasive kidney transplant monitoring (2019)

A Common Rejection Module (CRM) consisting of 11 genes expressed in allograft biopsies was previously reported to serve as a biomarker for acute rejection (AR), correlate with the extent of graft injury, and predict future allograft damage. We investigated the use of this gene panel on the urine cell pellet of kidney transplant patients. Urinary cell sediments collected from patients with biopsy-confirmed acute rejection, borderline AR (bAR), BK virus nephropathy (BKVN), and stable kidney grafts with normal protocol biopsies (STA) were analyzed for expression of these 11 genes using quantitative polymerase chain reaction (qPCR). We assessed these 11 CRM genes for their abundance, autocorrelation, and individual expression levels. Expression of 10/11 genes were elevated in AR when compared to STA. Psmb9 and Cxcl10could classify AR versus STA as accurately as the 11-gene model (sensitivity = 93.6%, specificity = 97.6%). A uCRM score, based on the geometric mean of the expression levels, could distinguish AR from STA with high accuracy (AUC = 0.9886) and correlated specifically with histologic measures of tubulitis and interstitial inflammation rather than tubular atrophy, glomerulosclerosis, intimal proliferation, tubular vacuolization or acute glomerulitis. This urine gene expression-based score may enable the non-invasive and quantitative monitoring of AR.
<title>Picosecond characteristics of silicon-on-insulator metal-semiconductor-metal photodiodes</title> (1994)

A subpicosecond electro-optic sampling system was used to measure the picosecond characteristics of silicon-based, metal- semiconductor-metal photodiodes made on both bulk-silicon and silicon-on-sapphire (SOS) substrates with submicrometer finger spacings and widths. The temporal response of bulk-silicon diodes was strongly dependent on the wavelength of excitation light because of the effect of different penetration depths. On the other hand, for the SOS diodes, the device speed is nearly independent of wavelength since the thickness of the silicon layer limits the depth of photogenerated carriers. The external quantum efficiency of SOS diodes was measured at several selected wavelengths and shown to be dominated by the photon absorption coefficient.
Reputation-based framework for high integrity sensor networks (2004)

The traditional approach of providing network security has been to borrow tools from cryptography and authentication. However, we argue that the conventional view of security based on cryptography alone is not sufficient for the unique characteristics and novel misbehaviors encountered in sensor networks. Fundamental to this is the observation that cryptography cannot prevent malicious or non-malicious insertion of data from internal adversaries or faulty nodes.
Neurotrophic Factors Increase Axonal Growth after Spinal Cord Injury and Transplantation in the Adult Rat (1997)

The capacity of CNS neurons for axonal regrowth after injury decreases as the age of the animal at time of injury increases. After spinal cord lesions at birth, there is extensive regenerative growth into and beyond a transplant of fetal spinal cord tissue placed at the injury site. After injury in the adult, however, although host corticospinal and brainstem-spinal axons project into the transplant, their distribution is restricted to within 200 micron of the host/transplant border. The aim of this study was to determine if the administration of neurotrophic factors could increase the capacity of mature CNS neurons for regrowth after injury. Spinal cord hemisection lesions were made at cervical or thoracic levels in adult rats. Transplants of E14 fetal spinal cord tissue were placed into the lesion site. The following neurotrophic factors were administered at the site of injury and transplantation: brain-derived neurotrophic factor (BDNF), neurotrophin-3 (NT-3), neurotrophin-4 (NT-4), ciliary-derived neurotrophic factor (CNTF), or vehicle alone. After 1-2 months survival, neuroanatomical tracing and immunocytochemical methods were used to examine the growth of host axons within the transplants. The neurotrophin administration led to increases in the extent of serotonergic, noradrenergic, and corticospinal axonal ingrowth within the transplants. The influence of the administration of the neurotrophins on the growth of injured CNS axons was not a generalized effect of growth factors per se, since the administration of CNTF had no effect on the growth of any of the descending CNS axons tested. These results indicate that in addition to influencing the survival of developing CNS and PNS neurons, neurotrophic factors are able to exert a neurotropic influence on injured mature CNS neurons by increasing their axonal growth within a transplant.
The human liver‐specific proteome defined by transcriptomics and antibody‐based profiling (2014)

Human liver physiology and the genetic etiology of the liver diseases can potentially be elucidated through the identification of proteins with enriched expression in the liver. Here, we combined data from RNA sequencing (RNA-Seq) and antibody-based immunohistochemistry across all major human tissues to explore the human liver proteome with enriched expression, as well as the cell type-enriched expression in hepatocyte and bile duct cells. We identified in total 477 protein-coding genes with elevated expression in the liver: 179 genes have higher expression as compared to all the other analyzed tissues; 164 genes have elevated transcript levels in the liver shared with at least one other tissue type; and an additional 134 genes have a mild level of increased expression in the liver. We identified the precise localization of these proteins through antibody-based protein profiling and the subcellular localization of these proteins through immunofluorescent-based profiling. We also identified the biological processes and metabolic functions associated with these proteins, investigated their contribution in the occurrence of liver diseases, and identified potential targets for their treatment. Our study demonstrates the use of RNA-Seq and antibody-based immunohistochemistry for characterizing the human liver proteome, as well as the use of tissue-specific proteins in identification of novel drug targets and discovery of biomarkers.-Kampf, C., Mardinoglu, A., Fagerberg, L., Hallström, B. M., Edlund, K., Lundberg, E., Pontén, F., Nielsen, J., Uhlen, M. The human liver-specific proteome defined by transcriptomics and antibody-based profiling.
Droplet interface bilayers (1900)

Droplet interface bilayers (DIBs) provide a superior platform for the biophysical analysis of membrane proteins. The versatile DIBs can also form networks, with features that include built-in batteries and sensors.
2003 Evaluations of Fungicides for Control of Sclerotinia Stem Rot of Canola in North Dakota and Minnesota (2004)

PP-1263
User Location and Tracking in an In-Building Radio Network (1999)

The proliferation of mobile computing devices and local-area wireless networks has fostered a growing interest in location-aware systems and services. A key requirement for enabling such services is user location and tracking. In this paper we address this problem in the context of a popular radio-frequency wireless network technology. Our approach is based on recording and processing real-time signal strength information available at multiple base stations positioned to provide overlapping coverage in the area of interest. We employ techniques that combine empirical measurements with signal propagation modeling. We present concrete experimental results that demonstrate the feasibility of estimating user location with a high degree of accuracy. 1
LDPLFS: Improving I/O Performance without Application Modification (2012)

Input/Output (I/O) operations can represent a significant proportion of run-time when large scientific applications are run in parallel and at scale. In order to address the growing divergence between processing speeds and I/O performance, the Parallel Log-structured File System (PLFS) has been developed by EMC Corporation and the Los Alamos National Laboratory (LANL) to improve the performance of parallel file activities. Currently, PLFS requires the use of either (i) the FUSE Linux Kernel module, (ii) a modified MPI library with a customised ROMIO MPI-IO library, or (iii) an application rewrite to utilise the PLFS API directly. In this paper we present an alternative method of utilising PLFS in applications. This method employs a dynamic library to intercept the low-level POSIX operations and retarget them to use the equivalents offered by PLFS. We demonstrate our implementation of this approach, named LDPLFS, on a set of standard UNIX tools, as well on as a set of standard parallel I/O intensive mini-applications. The results demonstrate almost equivalent performance to a modified build of ROMIO and improvements over the FUSE-based approach. Furthermore, through our experiments we demonstrate decreased performance in PLFS when ran at scale on the Lustre file system.
Pivoted Document Length Normalization (2017)

Automatic information retrieval systems have to deal with documents of varying lengths in a text collection. Document length normalization is used to fairly retrieve documents of all lengths. In this study, we ohserve that a normalization scheme that retrieves documents of all lengths with similar chances as their likelihood of relevance will outperform another scheme which retrieves documents with chances very different from their likelihood of relevance. We show that the retrievaf probabilities for a particular normalization method deviate systematically from the relevance probabilities across different collections. We present pivoted normalization, a technique that can be used to modify any normalization function thereby reducing the gap between the relevance and the retrieval probabilities. Training pivoted normalization on one collection, we can successfully use it on other (new) text collections, yielding a robust, collectzorz independent normalization technique. We use the idea of pivoting with the well known cosine normalization function. We point out some shortcomings of the cosine function andpresent two new normalization functions--pivoted unique normalization and piuotert byte size normalization.
Structure of an unusually stable RNA hairpin (1991)

The structure of a very common RNA hairpin, 5'GGAC(UUCG)GUCC, has been determined in solution by NMR spectroscopy. The loop sequence, UUCG, occurs exceptionally often in ribosomal and other RNAs, and may serve as a nucleation site for RNA folding and as a protein recognition site. Reverse transcriptase cannot read through this loop, although it normally transcribes RNA secondary structure motifs. A hairpin with that loop displays unusually high thermodynamic stability; its stability decreases when conserved nucleotides are mutated. The three-dimensional structure for the hairpin was derived from interproton distances and scalar coupling constants determined by NMR using distance geometry, followed by restrained energy minimization. The structure was well-defined despite the conservative use of interproton distances, by constraining the backbone conformation by means of scalar coupling measurements. A mismatch G.U base pair, with syn-guanosine, closes the stem. This hairpin has a loop of only two nucleotides; both adopt C2'-endo sugar pucker. A sharp turn in the phosphodiester backbone is stabilized by a specific cytosine-phosphate contact, probably a hydrogen bond, and by stacking of the cytosine nucleotide on the G.U base pair. The structural features of the loop can explain the unusual thermodynamic stability of this hairpin and its sensitivity to mutations of loop nucleotides.
Therapeutic Implications of the Emerging Molecular Biology of Uveal Melanoma (2011)

Uveal melanoma represents the most common primary intraocular malignancy in adults. Although uveal and cutaneous melanomas both arise from melanocytes, uveal melanoma is clinically and biologically distinct from its more common cutaneous counterpart. Metastasis occurs frequently in this disease, and once distant spread occurs, outcomes are poor. No effective systemic therapies are currently available; however, recent advances in our understanding of the biology of this rare and devastating disease, combined with the growing availability of targeted agents, which can be used to rationally exploit these findings, hold the promise for novel and effective therapies in the foreseeable future. Herein, we review our rapidly growing understanding of the molecular biology of uveal melanoma, including the pathogenic roles of GNAQ (guanine nucleotide binding protein q polypeptide)/11, PTEN (phosphatase and tensin homolog), IGF (insulin-like growth factor)/IGF-1 receptor, MET (hepatocyte growth factor), BAP1 [breast cancer 1, early onset (BRCA1)-associated protein-1], and other key molecules, potential therapeutic strategies derived from this emerging biology, and the next generation of recently initiated clinical trials for the treatment of advanced uveal melanoma.
Increased Expression of Membrane Type 3-Matrix Metalloproteinase in Human Atherosclerotic Plaque (2002)

MT3-MMP is expressed by SMCs and Mphi in human atherosclerotic plaques. Proinflammatory molecules cause a progressive increase in the expression of MT3-MMP in cultured Mphi. Our results suggest a mechanism by which inflammatory molecules could promote Mphi-mediated degradation of extracellular matrix and thereby contribute to plaque destabilization.
An Exploratory Study of Systemic Administration of the Toll-like Receptor-7 Agonist 852A in Patients with Refractory Metastatic Melanoma (2008)

Intravenous 852A was well tolerated and induced systemic immune activation that eventually resulted in prolonged disease stabilization in some patients with stage IV metastatic melanoma who had failed chemotherapy.
Grain boundary topography in tungsten (1964)

Abstract Small ledges in grain boundaries have been postulated to play an important role in the nucleation of cavities in high temperature creep (Gifkins 1956, McLean 1963), in grain boundary sliding (Gifkins 1963) and in the yielding of metals (Li 1963). Direct experimental evidence of small grain boundary ledges is limited and comes mainly from electron micrographs, but since the dimensions of the postulated ledges are of the order of the limit of resolution of the electron microscope such evidence is not entirely convincing. However, the field ion microscope (Müller 1960) with its better resolution could be expected to provide unambiguous information concerning the existence or otherwise of ledges a few atoms in height and this note describes some observations made with such a microscope.