gebhart/patrepeval huggingface dataset:
Intra Coding With Adaptive Partial Reconstruction (2012)

Intra prediction improves coding performance by reducing inter pixel redundancy. However, to accommodate the use of block transforms, not all pixels can be predicted from reconstructed pixels that are located close to themselves. This causes prediction performance to suffer as pixel values further apart are less correlated. This paper presents additional intra coding modes designed with the goal of improving prediction performance. Experimental results show an average gain of about 2% in the key technical area software when the new modes are incorporated in the current 8 <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">$\,\times\,$</tex></formula> 8 prediction modes. Since the new coding modes (8 <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">$\,\times\,$</tex></formula> 8) are designed with transform size smaller than coding block size, the modes can also be useful when the source block is larger than the maximum transform size.
Cyclobenzaprine Overdosage (1983)

The clinical findings in three patients who ingested 260-900 mg cyclobenzaprine (Flexeril) consisted of delayed onset and long duration of anticholinergic symptomatology. In two of these patients, symptoms responded to treatment with physostigmine. The third patient recovered without specific therapy. Despite its structural similarity to amitriptyline, cyclobenzaprine overdosage did not result in coma, seizures, or cardiac toxicity. The pharmacological properties of cyclobenzaprine may account for the observed toxicity.
Nucleotide sequence analysis of the BALB/c murine sarcoma virus transforming gene (1985)

We determined the nucleotide sequence of the v-H-ras-related oncogene of BALB/c murine sarcoma virus. This oncogene contains an open reading frame of 189 amino acids that initiates and terminates entirely within the mouse cell-derived ras sequence. The protein encoded by this open reading frame matches the sequence predicted for the T24 human bladder carcinoma oncogene product, p21, in all but two positions. The presence of a lysine residue in position 12 of BALB/c murine sarcoma virus p21 likely accounts for its oncogenic properties.
Mu Opioid Receptor Antagonists: Recent Developments (2007)

For thousands of years mu opioid agonists such as morphine have been utilized for their analgesic properties. Today, morphine and related compounds are still used as a first line therapy in the treatment of moderate to severe pain. However, despite the clear benefits of mu agonists in pain management, severe side effects such as dependence and respiratory depression are associated with use of these drugs. To date, there are only two approved mu opioid antagonists for use in the treatment of these adverse effects, that is, naloxone and naltrexone. However, many other clinical and therapeutic areas have been linked to mu opioid receptor antagonism. These include treatment of opioid induced pruritus of the skin, obesity, and Parkinson-induced tardive dyskinesia. Currently there are two compounds, N-methylnaltrexone and alvimopan, under FDA review as possible treatments for opioid induced bowel dysfunction and postoperative ileus. These compounds are of special interest as they are peripherally restricted. This attribute enables treatment of peripheral side effects induced by opioid agonists without reversal of the centrally mediated analgesia of the agonist. In this article we discuss the structural classes of mu opioid antagonists, their potential clinical applications, and review the relevant patents of the last ten years.
Mosquito repellents: a review of chemical structure diversity and olfaction (2010)

Research on mosquito chemical repellents continues to advance, along with knowledge of mosquito olfaction and behavior, mosquito-host interactions and chemical structure. New tools and technologies have revealed information about insect olfactory mechanisms and processing, providing a more complex approach for the interpretation of how chemical repellents influence host-seeking and feeding behavior. Even with these advances, there is still a large amount of information contained in the early works on insect repellents. Many of the standard test methods and chemicals that are still used for evaluating active repellents were developed in the 1940s. These studies contain valuable references to the activity of different structural classes of chemicals, and serve as a guide to optimization of select compounds for insect repellency effects.
Salmonella Pathogenicity Island 2 (2000)

Systemic infections by Salmonella enterica, such as typhoid fever, are a significant threat to human health. Recent studies indicate that the function of a type III secretion system encoded by Salmonella Pathogenicity Island 2 (SPI2) is central for the ability of S. enterica to cause systemic infections and for intracellular pathogenesis. This review summarizes approaches leading to the identification of SPI2, the molecular genetics and evolution of SPI2, and the current understanding of the regulation of gene expression. Recent studies have indicated that SPI2 is used by intracellular Salmonella to actively modify functions of the host cells. The role of SPI2 during pathogenesis of salmonellosis and current models regarding function will be discussed.
Consensus-degenerate hybrid oligonucleotide primers for amplification of distantly related sequences (1998)

We describe a new primer design strategy for PCR amplification of unknown targets that are related to multiply-aligned protein sequences. Each primer consists of a short 3' degenerate core region and a longer 5' consensus clamp region. Only 3-4 highly conserved amino acid residues are necessary for design of the core, which is stabilized by the clamp during annealing to template molecules. During later rounds of amplification, the non-degenerate clamp permits stable annealing to product molecules. We demonstrate the practical utility of this hybrid primer method by detection of diverse reverse transcriptase-like genes in a human genome, and by detection of C5DNA methyltransferase homologs in various plant DNAs. In each case, amplified products were sufficiently pure to be cloned without gel fractionation. This COnsensus-DEgenerate Hybrid Oligonucleotide Primer (CODEHOP) strategy has been implemented as a computer program that is accessible over the World Wide Web (http://blocks.fhcrc.org/codehop.html) and is directly linked from the BlockMaker multiple sequence alignment site for hybrid primer prediction beginning with a set of related protein sequences.
Down-Regulation of Overexpressed Sp1 Protein in Human Fibrosarcoma Cell Lines Inhibits Tumor Formation (2005)

Sp1 is a transcription factor for many genes, including genes involved in tumorigenesis. We found that human fibroblast cells malignantly transformed in culture by a carcinogen or by stable transfection of an oncogene express Sp1 at 8-fold to 18-fold higher levels than their parental cells. These cell lines form fibrosarcomas in athymic mice with a very short latency, and the cells from the tumors express the same high levels of Sp1. Similar high levels of Sp1 were found in the patient-derived fibrosarcoma cell lines tested, and in the tumors formed in athymic mice by these cell lines. To investigate the role of overexpression of Sp1 in malignant transformation of human fibroblasts, we transfected an Sp1 U1snRNA/Ribozyme into two human cell lines, malignantly transformed in culture by a carcinogen or overexpression of an oncogene, and into a patient-derived fibrosarcoma cell line. The level of expression of Sp1 in these transfected cell lines was reduced to near normal. The cells regained the spindle-shaped morphology and exhibited increased apoptosis and decreased expression of several genes linked to cancer, i.e., epithelial growth factor receptor, urokinase plasminogen activator, urokinase plasminogen activator receptor, and vascular endothelial growth factor. When injected into athymic mice, these cell lines with near normal levels of Sp1 failed to form tumors or did so only at a greatly reduced frequency and with a much longer latency. These data indicate that overexpression of Sp1 plays a causal role in malignant transformation of human fibroblasts and suggest that for cancers in which it is overexpressed, Sp1 constitutes a target for therapy.
COMPLEMENT INHIBITION WITH AN ANTI-C5 MONOCLONAL ANTIBODY PREVENTS HYPERACUTE REJECTION IN A XENOGRAFT HEART TRANSPLANTATION MODEL1 (1999)

We conclude that (1) anti-C5 mAb prevents HAR, (2) AVR/DXR still occurs when HAR is prevented by complement inactivation, and (3) AVR/DXR cannot be overcome by conventional immunosuppression. These data suggest that anti-C5 mAb may be valuable for preventing HAR in future clinical xenotransplantation and that additional interventions may be required to address AVR/DXR.
Photo-tuning of highly selective wetting in inverse opals (2013)

Crack-free inverse opals exhibit a sharply defined threshold wettability for infiltration that has enabled their use as colourimetric indicators for liquid identification. Here we demonstrate direct and continuous photo-tuning of this wetting threshold in inverse opals whose surfaces are functionalized with a polymer doped with azobenzene chromophores.
Peripheral Nerve Stimulation for Neuropathic Pain (2011)

Over the last two decades, electrical neuromodulation has become a dominant approach in surgical treatment of medically refractory neuropathic pain, essentially eclipsing multiple available neuroablative procedures. Among different types of neuromodulation, peripheral nerve stimulation (PNS) holds the unique position of being the least invasiveand at the same time the least established in terms of scientific evidence and regulatory approvals. However, it is now gaining tremendous momentum in terms of accumulation of clinical experience and development of new indications. As a matter of fact, recent European approval of PNS for treatment of chronic low back pain and intractable migraine headaches is expected to add legitimacy and marketing support to the entire field of PNS. This article provides an overview of PNS history, reviews current thoughts regarding its mechanism of action, summarizes common indications, clinical outcomes, technical procedural details, and complications, and suggests future directions for PNS development. It appears that PNS today is the most rapidly growing field of neuromodulationand that does not come as a surprise, considering its potential for treatment of very prevalent and hard-to-treat conditions, such as back pain and headaches. From the point of view of a practicing neurologist, PNS presents an attractive pain management option that combines a high level of efficacy and reproducibility of results with low invasiveness and minimal morbidity. As the worldwide experience with PNS continues to grow, one may expect to see it becoming a widely accepted treatment approach in a variety of clinical conditions.
Patients with chronic hepatitis C have circulating cytotoxic T cells which recognize hepatitis C virus-encoded peptides binding to HLA-A2.1 molecules (1995)

Antiviral cytotoxic T lymphocytes (CTL) may play a role in clearance of hepatitis C virus (HCV)-infected cells and thereby cause hepatocellular injury during acute and chronic HCV infection. The aim of this study was to identify HLA-A2.1-restricted HCV T-cell epitopes and to evaluate whether anti-HCV-specific CTL are present during chronic hepatitis C. Peripheral blood mononuclear cells from four HLA-A2-positive patients with chronic hepatitis C and from two individuals after recovery from HCV infection were tested against a panel of HCV-encoded peptides derived from different regions of the genome, including some peptides containing HLA-A2.1 binding motifs. HLA-A2-negative patients with chronic hepatitis C as well as healthy HLA-A2-positive (anti-HCV-negative) donors served as controls. Peripheral blood mononuclear cells stimulated repeatedly with several HCV-encoded peptides (three in core, one in NS4B, and one in NS5B) yielded cytolytic responses. All four HLA-A2-positive patients with active infection had CTL specific for at least one of the identified epitopes, whereas two patients who had recovered from HCV infection had almost no CTL responses. Monoclonal antibody blocking experiments performed for two epitopes demonstrated a class I- and HLA-A2-restricted CTL response. CTL epitopes could partially be predicted by HLA-A2 binding motifs and more reliably by quantitative HLA-A2.1 molecule binding assays. Most of the identified epitopes could also be produced via the endogenous pathway. Specific CTL against multiple, mostly highly conserved epitopes of HCV were detected during chronic HCV infection. This finding may be important for further investigations of the immunopathogenesis of HCV, the development of potential therapies against HCV on the basis of induction or enhancement of cellular immunity, and the design of vaccines.
Buprenorphine given after surgery does not alter renal ischemia/reperfusion injury. (2000)

Buprenorphine should be given after renal ischemia-reperfusion surgery because administration of the proper analgesic improved animal health without interfering with the renal ischemia/reperfusion model. Analgesic treatment at the time of the operation and 12 hours after was sufficient. Buprenorphine may reduce the post-surgical stress response, and thus potentially improve the specificity of testing for drugs that reduce or treat renal injury.
Distal-less homeobox transcription factors regulate development and maturation of natural killer cells (2008)

Natural killer (NK) cells constitute a subpopulation of lymphocytes that develop from precursors in the bone marrow (BM), but the transcriptional regulation of their development and maturation is only beginning to be understood, in part due to their relatively rare abundance, especially of developmental subsets. Using a mouse model in which NK cells are arrested at an immature stage of development, and a gene expression profiling approach, we uncovered transient normal NK cell expression of a homeobox transcription factor (TF) family, called Distal-less (Dlx), which had been primarily implicated in murine CNS, craniofacial, limb, and skin development. Our studies demonstrate that Dlx1, Dlx2, and Dlx3 are transiently expressed in immature Mac-1(lo) NK cells within the BM, with Dlx3 being the predominantly expressed member. These genes are expressed in a temporally regulated pattern with overlapping waves of expression, and they display functional redundancy. Expression is extinguished in fully mature splenic NK cells, and persistent expression of Dlx genes leads to functionally immature NK cells arrested at the Mac-1(lo) stage. Whereas conventional splenic NK cells develop but are arrested at an immature stage, there appears to be a complete failure to develop CD127(+) thymic NK cells when Dlx genes are persistently expressed. We also observed that T and B cells fail to develop in the context of persistent Dlx1 expression. Thus, these studies indicate that Dlx TFs play a functional role in lymphocyte development.
Expression of a cytoplasmic LINE-1 transcript is regulated in a human teratocarcinoma cell line. (1985)

The major primate family of highly repeated, long interspersed DNA sequences (LINE-1, previously Kpn I, family) includes several thousand 6-kilobase-pair long units that terminate in an A-rich stretch. Recent evidence indicates that long open reading frames occur in at least some family members. These results suggested that one or more LINE-1 family members might be structural genes. Accordingly, a variety of human cell lines was analyzed for the presence of a cytoplasmic, polyadenylylated RNA homologous to LINE-1 sequences. Such a transcript was detected in a human pluripotent teratocarcinoma cell line (NTera2 clone D1). The RNA is approximately 6.5 kilobases long and is homologous to the LINE-1 strand with the open reading frames. The abundance of the transcript varies markedly with previously described variations in the phenotype of these cells and is highest when the cells display the embryonal carcinoma morphology. This RNA may represent a mRNA transcribed from one or more functional genes in the LINE-1 family.
Central Nervous System Pharmacology of Antileukemic Drugs (1989)

The blood-brain barrier provides a pharmacologic sanctuary for leukemic cells within the central nervous system (CNS), protecting them from the cytotoxic effects of systemic antileukemic therapy. Attempts to overcome this problem have included specific CNS-directed treatment in the form of direct intrathecal drug injection, cranial irradiation, and alteration in the dose and schedule of systemic agents to enhance their CNS penetration. Use of these treatments and strategies has led to the effective prevention and control of meningeal leukemia. Intrathecal therapy, primarily with methotrexate or cytosine arabinoside, is a form of regional chemotherapy that can achieve very high drug concentrations at the target site [i.e., in the meninges and cerebrospinal fluid (CSF)] with a low total dose. Therefore, there is minimal systemic toxicity. The dose and schedules, clinical pharmacology, and toxicities of the commonly used intrathecal agents are discussed in detail in this article. Another approach to overcoming the limited penetration of antileukemic drugs into the CNS has been the use of high-dose systemic therapy. Methotrexate and cytosine arabinoside in high doses have produced favorable clinical responses in patients with overt meningeal disease, and pharmacokinetic studies have documented cytotoxic concentrations of these drugs within the cerebrospinal fluid. A clear understanding of the CNS pharmacology of the antileukemic drugs is required in order to use these agents in the safest and most efficacious manner for the treatment of meningeal leukemia.
The Molecular Mechanism of Natural Killer Cells Function and Its Importance in Cancer Immunotherapy (2017)

Natural killer (NK) cells are innate immune cells that show strong cytolytic function against physiologically stressed cells such as tumor cells and virus-infected cells. NK cells show a broad array of tissue distribution and phenotypic variability. NK cells express several activating and inhibitory receptors that recognize the altered expression of proteins on target cells and control the cytolytic function. NK cells have been used in several clinical trials to control tumor growth. However, the results are encouraging only in hematological malignancies but not very promising in solid tumors. Increasing evidence suggests that tumor microenvironment regulate the phenotype and function of NK cells. In this review, we discussed the NK cell phenotypes and its effector function and impact of the tumor microenvironment on effector and cytolytic function of NK cells. We also summarized various NK cell-based immunotherapeutic strategies used in the past and the possibilities to improve the function of NK cell for the better clinical outcome.
A 500 MHz carbon nanotube transistor oscillator (2008)

Operation of a carbon nanotube field effect transistor (FET) oscillator at a record frequency of 500 MHz is described. The FET was fabricated using a large parallel array of single-walled nanotubes grown by chemical vapor deposition on ST-quartz substrates. Matching of the gate capacitance with a series inductor enabled greater than unity net oscillator loop gain to be achieved at 500 MHz.
Mechanisms Underlying Coagulation Abnormalities in Ebola Hemorrhagic Fever: Overexpression of Tissue Factor in Primate Monocytes/Macrophages Is a Key Event (2003)

Disseminated intravascular coagulation is a prominent manifestation of Ebola virus (EBOV) infection. Here, we report that tissue factor (TF) plays an important role in triggering the hemorrhagic complications that characterize EBOV infections. Analysis of samples obtained from 25 macaques showed increased levels of TF associated with lymphoid macrophages, whereas analysis of peripheral blood-cell RNA showed increased levels of TF transcripts by day 3. Plasma from macaques contained increased numbers of TF-expressing membrane microparticles. Dysregulation of the fibrinolytic system developed during the course of infection, including a rapid decrease in plasma levels of protein C. Infection of primary human monocytes/macrophages (PHMs) was used to further evaluate the role of TF in EBOV infections. Analysis of PHM RNA at 1-48 h showed increased TF transcripts, whereas levels of TF protein were dramatically increased by day 2. Thus, chemotherapeutic strategies aimed at controlling overexpression of TF may ameliorate the effects of EBOV hemorrhagic fever.
Structure of Marek's disease virus DNA: detailed restriction enzyme map (1984)

Purified virion DNA (120 X 10(6) molecular weight [MW]) of Marek's disease virus strain GA was cleaved with BamHI restriction endonuclease, and 27 out of the 29 fragments were cloned into bacterial plasmids. Restriction maps for BamHI, BglI, and SmaI endonucleases were constructed. The genomic structure of Marek's disease virus DNA was found to be similar to that of herpes simplex virus types 1 and 2. A long unique region (75 X 10(6) MW, located at 10 X 10(6) to 85 X 10(6) MW [10-85] from the left end of the genome), which was subdivided into segment 1 (22 X 10(6) MW, located at 10-32) and segment 2 (51 X 10(6) MW, located at 34-85) by direct repeats (32-34), was flanked by a long terminal region (10 X 10(6) MW, located at 0-10) and a long inverted region (10 X 10(6) MW, located at 85-95). A short unique region (8 X 10(6) MW, located at 103-111) was flanked by a short terminal region (8 X 10(6) MW, located at 111-119) and a short inverted region (8 X 10(6) MW, located at 95-103). The direct repeat fragments (0.9 X 10(6) could be isolated by cleavage with SmaI. The right terminal end was found to be heterogenous .
A Unique Form of Terminal Redundancy in Adenovirus DNA Molecules (1972)

A unique form of terminal redundancy has been observed in DNA molecules extracted from several human adenovirus serotypes. Electron microscopic studies reveal that single-stranded circular molecules are formed when native DNA is denatured and then annealed. Temperatures approaching the T(m) of native DNA are required to convert circles to linear molecules, indicating a high degree of self-complementarity between terminal base sequences of DNA strands. Single-stranded circles are not generated if a limited number of nucleotides (2-4%) are removed from the 3' ends of native DNA by digestion with Escherichia coli exonuclease III before denaturation and annealing. The lenght of the redundant segment appears to differ among major serotypic groups, and a possible association between increased length of the redundant segment and increased oncogenic capability of virus serotype is suggested. Evidence for the configuration of the duplex closure region of circular molecules is also presented.