gebhart/patrepeval huggingface dataset:
Epstein-Barr virus DNA in serum/plasma as a tumor marker for nasopharyngeal cancer. (2000)

Nasopharyngeal cancer (NPC) constitutes a type of carcinoma encountered frequently in Southern China, among Eskimos of the Arctic region, and to a lesser extent in Southeast Asia. Because EBV DNA present in plasma or serum of NPC patients has proven to represent a promising noninvasive tumor marker, the present study was designed to determine the incidence of serum/plasma EBV DNA by nested PCR during various disease management stages. By this method, we could detect EBV DNA in plasma/serum of 98 of 167 NPC patients prior to treatment, compared with 10 of 77 samples derived from healthy blood donors serving as controls, with a similar prevalence observed in plasma versus serum. Investigation of 13 patients subjected to radiotherapy revealed plasma EBV DNA to persist in the plasma of one case, whereas among the remaining patients, it had vanished during the early phase of treatment. Finally, with 52 samples derived from 37 NPC patients during follow-up, we established 100% specificity and 0% false-positive rate for plasma DNA detection by nested PCR. Moreover, we subjected 24 known EBV DNA-positive serum samples to DNase digestion prior to DNA extraction and amplification to differentiate between free and encapsulated viral DNA, which demonstrated complete absence of the human beta-globin genomic DNA in contrast to EBV DNA detectable in 14 samples. In conclusion, applying this noninvasive method, serum/plasma EBV DNA constitutes a reliable tumor marker prior to, during, and after treatment of NPC.
Free‐living amoebae: pathogenicity and immunity (1991)

Free-living amoebae causes three well-defined disease entities: (i) primary amoebic meningoencephalitis, caused by Naegleria fowleri, (ii) granulomatous amoebic encephalitis and (iii) chronic amoebic keratitis, caused by species of Acanthamoeba. Both Naegleria infections and chronic amoebic keratitis occur in healthy individuals while granulomatous amoebic encephalitis is often associated with patients with acquired immunodeficiencies. The different pathogenic behaviour of these organisms is associated with differences in life cycle, amoeboidal locomotion, enzyme composition (such as phospholipase A), and cytotoxins, as well as natural host immunity. Immunity against these amoebae (whether acquired or natural) involves a combination of complement, antibody and cell-mediated immunity. Evidence suggests that the major mechanisms of immunity against these amoebae is activation of phagocytic cells, especially neutrophils, by lymphokines and opsonization of the amoebae by antibody which promote an antibody dependent cellular destruction of the organism.
Toward a national public key infrastructure (1994)

Reliance on electronic communications makes information more vulnerable, and users will require confidentiality, message integrity, sender authentication, and sender non-repudiation. Public key cryptography will play an important role in providing these services.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Mutations in the regulatory domain of cystathionine beta-synthase can functionally suppress patient-derived mutations in cis (2001)

Human cystathionine beta--synthase (CBS) is an S-adenosylmethionine-regulated enzyme that plays a key role in the metabolism of homocysteine. Mutations in CBS are known to cause homocystinuria, an inborn error in metabolism. We previously developed a yeast functional assay for CBS and used it to characterize mutations found in homocystinuric patients. We discovered that many patient-derived mutations are functionally suppressed by deletion of the C-terminal 142 amino acids, which contain a 53 amino acid motif known as the CBS domain. This domain is found in a wide variety of proteins of diverse biological function. Here we have used a genetic screen to identify missense mutations in the C-terminal region of CBS that can suppress the most common patient mutation, I278T. Seven suppressor mutations were identified, four of which map to the CBS domain. When combined in cis with another pathogenic mutation, V168M, six of seven of the suppressor mutations rescued the yeast phenotype. Enzyme activity analyses indicate that the suppressors restore activity from <2% to 17--64% of the wild-type levels. Analysis of the suppressor mutations in the absence of the pathogenic mutation shows that six of the seven suppressor alleles have lost enzymatic responsiveness to S-adenosylmethionine. Using homology modeling, we show that the suppressor mutations appear to map on one face of the CBS domain. Our results indicate that subtle changes to the C-terminus of CBS can restore activity to mutant proteins and provide a rationale for screening for compounds that can activate mutant CBS alleles.
Enhancing Internet streaming media with cueing protocols (2002)

We propose a new, media-independent protocol for including program timing, structure and identity information in Internet media streams. The protocol uses signaling messages called cues to indicate events whose timing is significant to receivers, such as the start or stop time of a media program. We describe the implementation and operation of a prototype Internet radio station which transmits program cues in audio broadcasts using the Real-Time Transport Protocol. A collection of simple yet powerful stream processing applications we implemented demonstrate how application creation is greatly eased when media streams are enriched with program cues.
Conformational behavior of ionic self‐complementary peptides (2000)

Several de novo designed ionic peptides that are able to undergo conformational change under the influence of temperature and pH were studied. These peptides have two distinct surfaces with regular repeats of alternating hydrophilic and hydrophobic side chains. This permits extensive ionic and hydrophobic interactions resulting in the formation of stable beta-sheet assemblies. The other defining characteristic of this type of peptide is a cluster of negatively charged aspartic or glutamic acid residues located toward the N-terminus and positively charged arginine or lysine residues located toward the C-terminus. This arrangement of charge balances the alpha-helical dipole moment (C --> N), resulting in a strong tendency to form stable alpha-helices as well. Therefore, these peptides can form both stable alpha-helices and beta-sheets. They are also able to undergo abrupt structural transformations between these structures induced by temperature and pH changes. The amino acid sequence of these peptides permits both stable beta-sheet and alpha-helix formation, resulting in a balance between these two forms as governed by the environment. Some segments in proteins may also undergo conformational changes in response to environmental changes. Analyzing the plasticity and dynamics of this type of peptide may provide insight into amyloid formation. Since these peptides have dynamic secondary structure, they will serve to refine our general understanding of protein structure.
Immunodetection of the metastasis-associated laminin receptor in human breast cancer cells obtained by fine-needle aspiration biopsy. (1990)

Fine-needle aspiration biopsy of the breast is a very useful technique for the evaluation of a suspect lesion before surgical removal. Increased expression of the 67-kd laminin receptor has been associated with the metastatic phenotype of cancer cells, particularly in colon and breast cancers. In this study, the expression of laminin receptor was evaluated using the immunoperoxidase technique in 81 breast aspirates (26 benign and 55 neoplastic lesions). Cells obtained from benign samples exhibited a low level of laminin receptor antigen detected by affinity-purified antibody raised against a cDNA-derived laminin receptor peptide. In contrast, 71% of smears obtained from malignant breast lesions contained cells that were strongly stained by the antibody. Heterogeneous expression of the laminin receptor was noted in both breast aspirates and fixed tissue specimens. These data suggest that the immunodetection of laminin receptor in cells obtained by fine-needle aspiration of breast lesions could be a valuable adjunct in the prognostic evaluation of breast lesions.
Drowning in triangle soup: the quest for a better 3-D printing file format (2016)

File formats for additive manufacturing are lagging behind the capabilities of 3-D printing technology itself, and no one is doing anything about it.
High expression of ACE2 receptor of 2019-nCoV on the epithelial cells of oral mucosa (2020)

It has been reported that ACE2 is the main host cell receptor of 2019-nCoV and plays a crucial role in the entry of virus into the cell to cause the final infection. To investigate the potential route of 2019-nCov infection on the mucosa of oral cavity, bulk RNA-seq profiles from two public databases including The Cancer Genome Atlas (TCGA) and Functional Annotation of The Mammalian Genome Cap Analysis of Gene Expression (FANTOM5 CAGE) dataset were collected. RNA-seq profiling data of 13 organ types with para-carcinoma normal tissues from TCGA and 14 organ types with normal tissues from FANTOM5 CAGE were analyzed in order to explore and validate the expression of ACE2 on the mucosa of oral cavity. Further, single-cell transcriptomes from an independent data generated in-house were used to identify and confirm the ACE2-expressing cell composition and proportion in oral cavity. The results demonstrated that the ACE2 expressed on the mucosa of oral cavity. Interestingly, this receptor was highly enriched in epithelial cells of tongue. Preliminarily, those findings have explained the basic mechanism that the oral cavity is a potentially high risk for 2019-nCoV infectious susceptibility and provided a piece of evidence for the future prevention strategy in dental clinical practice as well as daily life.
Processing of Electric Arc Furnace Dust using Deep Eutectic Solvents (2009)

The present paper describes the design and operation of the first large-scale extraction and separation of metals from a complex matrix using an ionic liquid. The liquid was a deep eutectic solvent based on choline chloride. The hydrogen-bond donors were mixed to optimize solubility and fluid viscosity. It was found that the incorporation of a fine particulate dust actually decreased the viscosity of the fluid. The present paper shows that selective extraction of zinc and lead can be achieved through judicious choice of the hydrogen-bond donor and it is also shown that metals in solution can be separated using cementation with zinc powder. Electrowinning of pure zinc is demonstrated but scale-up tests suggest that the process is relatively slow and has poor current efficiency. An alternative methodology was developed to rapidly recover the zinc from solution using dilute ammonia solution. It is also shown for the first time that cementation can be efficiently carried out in ionic liquids because the recovered metal is porous and allows thick layers to be deposited.
Portable X-ray Fluorescence Spectrometry Analysis of Soils (2016)

Portable X-ray fluorescence (PXRF) spectrometry is a proximal sensing technique whereby low-power X-rays are used to make elemental determinations in soils. The technique is rapid, portable, and provides multi-elemental analysis with results generally comparable to traditional laboratory-based techniques. Elemental data from PXRF can then be either used directly for soil parameter assessment (e.g., total Ca, total Fe) or as a proxy for predicting other soil parameters of interest (e.g., soil cation-exchange capacity [CEC], soil reaction, soil salinity) via simple or multiple linear regression. Importantly, PXRF does have some limitations that must be considered in the context of soil analysis. Those notwithstanding, PXRF has proven effective in numerous, agronomic, pedological, and environmental quality assessment applications.
Synthesis of Isobrassilexin, a Biologically Active Isomer of Brassilexin, a Cruciferac Phytoalexin (1993)

Abstract The synthesis of isobrassilexin 2, a hitherto non natural indoloisothiazole is reported (two steps, 43% yield). This substance, an isomer of brassilexin 1 has shown important biological properties in vitro.
Towards High-Resolution Salient Object Detection (2019)

Deep neural network based methods have made a significant breakthrough in salient object detection. However, they are typically limited to input images with low resolutions ($400\times400$ pixels or less). Little effort has been made to train deep neural networks to directly handle salient object detection in very high-resolution images. This paper pushes forward high-resolution saliency detection, and contributes a new dataset, named High-Resolution Salient Object Detection (HRSOD). To our best knowledge, HRSOD is the first high-resolution saliency detection dataset to date. As another contribution, we also propose a novel approach, which incorporates both global semantic information and local high-resolution details, to address this challenging task. More specifically, our approach consists of a Global Semantic Network (GSN), a Local Refinement Network (LRN) and a Global-Local Fusion Network (GLFN). GSN extracts the global semantic information based on down-sampled entire image. Guided by the results of GSN, LRN focuses on some local regions and progressively produces high-resolution predictions. GLFN is further proposed to enforce spatial consistency and boost performance. Experiments illustrate that our method outperforms existing state-of-the-art methods on high-resolution saliency datasets by a large margin, and achieves comparable or even better performance than them on widely-used saliency benchmarks. The HRSOD dataset is available at https://github.com/yi94code/HRSOD.
Retinoic acid alters photoreceptor development  in vivo (1996)

Application of exogenous retinoic acid (RA) to zebrafish during the initial stages of photoreceptor differentiation results in a precocious development of rod photoreceptors and an inhibition of cone photoreceptor maturation. The acceleration of rod differentiation is observed initially within the ventral retina 3 days after fertilization, following 24 hr of RA application, and within the dorsal retina 4 days after fertilization, following 48 hr of RA application. The differentiation of rods was impeded significantly when the synthesis of endogenous retinoic acid was inhibited by citral prior to the initial stage of rod differentiation. RA-treated embryos labeled for bromodeoxyuridine (BrdU) uptake revealed that RA exerts its effect on a postmitotic cell population within the developing retina. During normal development in zebrafish, rod differentiation is most robust within the ventral retina, a region previously shown to be rich in RA. Our data suggest that the RA signaling pathway is involved in the differentiation and maturation of both the rod and cone photoreceptors within the developing zebrafish retina.
Clinical and serological differences between systemic lupus erythematosus patients with antibodies to Ro versus patients with antibodies to Ro and La. (1982)

Among 55 systemic lupus erythematosus patients having antibodies to Ro and/or La, two major groups were distinguished by titration of sera in counterimmunoelectrophoresis. The first group (30 patients) had antibodies to Ro alone. This was associated with a high incidence of antibodies to DNA (77%) and serious renal disease (53%). The second group (23 patients) had antibodies to Ro and La, and this was associated with a lower incidence of antibodies to DNA (30%) and a very low incidence of nephritis (9%). In this group a phenomenon of linkage of anti- Ro and anti-La titers was observed. Additionally two patients with only anti-La were found. Neither had clinically apparent renal disease. Thus, systemic lupus erythematosus patients with anti-Ro fall into two subgroups that differ considerably in their prevalence of anti-DNA and serious renal disease.
Cyclosporin A inhibits Coccidioides immitis in vitro and in vivo (1983)

BALB/c mice infected intraperitoneally with Coccidioides immitis were treated with cyclosporin (CyA) subcutaneously. CyA prevented infection when treatment was started at day zero. When treatment was delayed until day 6 after infection, the mice that received either 75 or 25 mg/kg per day survived, but those treated with 7.5 mg/kg per day had the same mortality rate as controls. The higher doses of CyA prevented dissemination of the fungus from the peritoneum to the lung but did not eliminate the peritoneal infection. In vitro, CyA inhibited the growth of the mycelial phase of eight test strains of C. immitis at a concentration of 1.0 microgram/ml. One or two strains of 10 other fungi were tested for susceptibility to CyA; only Aspergillus niger was inhibited, at a concentration of 0.1 microgram/ml. CyA is structurally unrelated to the polyenes and imidazoles and has a very restricted spectrum of antifungal activity. CyA may represent a new class of antifungal agents with a novel mechanism of antifungal activity.
word2ket: Space-efficient Word Embeddings inspired by Quantum Entanglement (2019)

Deep learning natural language processing models often use vector word embeddings, such as word2vec or GloVe, to represent words. A discrete sequence of words can be much more easily integrated with downstream neural layers if it is represented as a sequence of continuous vectors. Also, semantic relationships between words, learned from a text corpus, can be encoded in the relative configurations of the embedding vectors. However, storing and accessing embedding vectors for all words in a dictionary requires large amount of space, and may stain systems with limited GPU memory. Here, we used approaches inspired by quantum computing to propose two related methods, {\em word2ket} and {\em word2ketXS}, for storing word embedding matrix during training and inference in a highly efficient way. Our approach achieves a hundred-fold or more reduction in the space required to store the embeddings with almost no relative drop in accuracy in practical natural language processing tasks.
Molecular characterization of Dau c 1, the Bet v 1 homologous protein from carrot and its cross‐reactivity with Bet v 1 and Api g 1 (1999)

Purified recombinant Dau c 1.2 was tested in immunoblots displaying IgE-binding capacity comparable to its natural counterpart. Cross-inhibition assays verified the existence of common B-cell epitopes present on Dau c 1, Api g 1 as well as on Bet v 1.
Normal Ligand Binding and Signaling by CD47 (Integrin-associated Protein) Requires a Long Range Disulfide Bond between the Extracellular and Membrane-spanning Domains (2001)

CD47 is a unique member of the Ig superfamily with a single extracellular Ig domain followed by a multiply membrane-spanning (MMS) domain with five transmembrane segments, implicated in both integrin-dependent and -independent signaling cascades. Essentially all functions of CD47 require both the Ig and MMS domains, raising the possibility that interaction between the two domains is required for normal function. Conservation of Cys residues among CD47 homologues suggested the existence of a disulfide bond between the Ig and MMS domains that was confirmed by chemical digestion and mapped to Cys(33) and Cys(263). Subtle changes in CD47 conformation in the absence of the disulfide were suggested by decreased binding of two anti-Ig domain monoclonal antibodies, decreased SIRPalpha1 binding, and reduced CD47/SIRPalpha1-mediated cell adhesion. Mutagenesis to prevent formation of this disulfide completely disrupted CD47 signaling independent of effects on ligand binding, as assessed by T cell interleukin-2 secretion and Ca(2+) responses. Loss of the disulfide did not affect membrane raft localization of CD47 or its association with alpha(v)beta(3) integrin. Thus, a disulfide bond between the Ig and MMS domains of CD47 is required for normal ligand binding and signal transduction.
Recent Development of High Quality LCDTV (2005)

The production technologies of the flat panel display in the large-size liquid crystal TVs have been developed remarkably. The importance of evaluation method of the display has been also increased. Using the new indexes for evaluations of the motion picture quality and the viewing angle characteristic of the liquid crystal TVs, we review the developments of the recent liquid crystal television technology . 大型液晶TVにおいて,平面ディスプレイの生産技術が飛躍的に発展しています。同時にディ スプレイの評価方法の重要性も益々高まっています。本論文では,液晶TVの応答特性と視野角 特性について,新しい評価法を提案し,その評価結果に基づき,最近の液晶TV技術の進展状況 をレヴューします。
Content-Aware Prediction Algorithm With Inter-View Mode Decision for Multiview Video Coding (2008)

3-D video will become one of the most significant video technologies in the next-generation television. Due to the ultra high data bandwidth requirement for 3-D video, effective compression technology becomes an essential part in the infrastructure. Thus multiview video coding (MVC) plays a critical role. However, MVC systems require much more memory bandwidth and computational complexity relative to mono-view video coding systems. Therefore, an efficient prediction scheme is necessary for encoding. In this paper, a new fast prediction algorithm, content-aware prediction algorithm (CAPA) with inter-view mode decision, is proposed. By utilizing disparity estimation (DE) to find corresponding blocks between different views, the coding information, such as rate-distortion cost, coding modes, and motion vectors, can be effectively shared and reused from the coded view channel. Therefore, the computation for motion estimation (ME) in most view channels can be greatly reduced. Experimental results show that compared with the full search block matching algorithm (FSBMA) applied to both ME and DE, the proposed algorithm saves 98.4-99.1% computational complexity of ME in most view channels with negligible quality loss of only 0.03-0.06 dB in PSNR.