gebhart/patrepeval huggingface dataset:
First isolation of an aquatic birnavirus from farmed and wild fish species in Australia (2000)

During routine sampling and testing, as part of a systematic surveillance program (the Tasmanian Salmonid Health Surveillance Program), an aquatic birnavirus was isolated from 'pin-head' (fish exhibiting deficient acclimatisation on transfer to saltwater) Atlantic salmon Salmo salar, approximately 18 mo old, farmed in net-pens located in Macquarie Harbour on the west coast of Tasmania, Australia. The isolate grows readily in a range of fish cell lines including CHSE-214, RTG-2 and BF-2 and is neutralised by a pan-specific rabbit antiserum raised against infectious pancreatic necrosis virus (IPNV) Ab strain and by a commercial pan-specific IPNV-neutralising monoclonal antibody. Presence of the virus was not associated with gross clinical signs. Histopathological examination revealed a range of lesions particularly in pancreatic tissue. The virus was localised in pancreas sections by immunoperoxidase staining using the polyclonal antiserum and by electron microscopy. Examination by electron microscopy demonstrated that the virus isolated in cell culture (1) belongs to the family Birnaviridae, genus Aquabirnaviridae; (2) was ultrastructurally and antigenically similar to virus identified in the index fish; (3) is related to IPNV. Western blot analysis using the polyclonal rabbit antiserum confirmed the cross-reactions between various aquatic birnavirus isolates. In addition, PCR analysis of isolated viral nucleic acid from the index case indicated that the virus is more closely related to IPNV fr21 and N1 isolates than to other birnavirus isolates available for comparison. Sampling of other fish species within Macquarie Harbour has demonstrated that the virus is present in several other species of fish including farmed rainbow trout Oncorhynchus mykiss, wild flounder Rhombosolea tapirina, cod Pseudophycis sp., spiked dogfish Squalus megalops and ling Genypterus blacodes.
Structure−Activity Relationship Study on a Simple Cationic Peptide Motif for Cellular Delivery of Antisense Peptide Nucleic Acid (2005)

Improving cellular uptake and biodistribution remains one of the major obstacles for a successful and broad application of peptide nucleic acids (PNAs) as antisense therapeutics. Recently, we reported the identification and functional characterization of an antisense PNA, which redirects splicing of murine CD40 pre-mRNA. In this context, it was discovered that a simple octa(l-lysine) peptide covalently linked to the PNA is capable of promoting free uptake of the conjugate into BCL1 cells as well as primary murine macrophages. On the basis of this peptide motif, the present study aimed at identifying the structural features, which define effective peptide carriers for cellular delivery of PNA. While the structure-activity relationship study revealed some clear correlations, only a few modifications actually led to an overall improvement as compared to the parent octa(l-lysine) conjugate. In a preliminary PK/tissue distribution study in healthy mice, the parent conjugate exhibited relatively broad tissue distribution and only modest elimination via excretion within the time frame of the study.
Fast CU size decision and mode decision algorithm for HEVC intra coding (2013)

The emerging international standard of High Efficiency Video Coding (HEVC) is a successor to H.264/AVC. In the joint model of HEVC, the tree structured coding unit (CU) is adopted, which allows recursive splitting into four equally sized blocks. At each depth level, it enables up to 34 intra prediction modes. The intra mode decision process in HEVC is performed using all the possible depth levels and prediction modes to find the one with the least rate distortion (RD) cost using Lagrange multiplier. This achieves the highest coding efficiency but requires a very high computational complexity. In this paper, we propose a fast CU size decision and mode decision algorithm for HEVC intra coding. Since the optimal CU depth level is highly content-dependent, it is not efficient to use a fixed CU depth range for a whole image. Therefore, we can skip some specific depth levels rarely used in spatially nearby CUs. Meanwhile, there are RD cost and prediction mode correlations among different depth levels or spatially nearby CUs. By fully exploiting these correlations, we can skip some prediction modes which are rarely used in the parent CUs in the upper depth levels or spatially nearby CUs. Experimental results demonstrate that the proposed algorithm can save 21% computational complexity on average with negligible loss of coding efficiency.
Calibration of angle encoders using transfer functions (2006)

Classical approaches to the calibration of angle encoders typically make use of circle division by means of an auxiliary artefact and apply linear equation systems constrained by circle closure which are solved for the errors of the encoder and those of the artefact simultaneously. Lately, emphasis has been placed on Fourier methods, as Fourier approaches involving transfer functions have proved to be a powerful tool applicable to various high-precision measurement tasks. We present an in-depth treatment of the use of the Fourier approach including transfer functions for the calibration of angle encoders. Different weighting schemes for combining the measurements will be presented by which the uncertainty of the calibration of angle encoders can be substantially reduced. The method utilizes angle difference measurements and it can therefore also be applied to the calibration of angle encoders using suitable arrangements of multiple reading heads. The approach is used for calibrating an angle encoder in an experimental set-up by means of a five-sided calibration polygon with angle differences between the optical faces that are not integer fractions of the full circle. The calibration results, including an evaluation of the measurement uncertainty, are presented for different weighting schemes and it is shown that appropriate weighting leads to a reduction in the uncertainty up to a factor of 4.
Amine-Grafted MCM-48 and Silica Xerogel as Superior Sorbents for Acidic Gas Removal from Natural Gas (2002)

In an effort to develop selective solid sorbents for acidic gas (CO2 and H2S) removal from natural gas mixtures, we synthesized amine-surface-modified silica xerogel and MCM-48 materials. With large amounts of basic amine groups on the surface, the sorbents are able to selectively bind the acidic gases CO2 and H2S. High adsorption capacities and adsorption rates were obtained for both gases. The adsorption−desorption isotherms of the gases and thermogravimetric analysis of the sorbents showed that these sorbents can be regenerated completely under mild conditions such as those used in pressure swing or temperature swing adsorption processes. We have also investigated the effect of moisture on the adsorption of CO2 and H2S by TPD-MS and infrared spectroscopy. The results indicated that the presence of water vapor doubled the amount of CO2 adsorbed and barely affected the H2S adsorption.
Virtual basestation (2010)

This paper presents the architecture and performance evaluation of a virtualized wide-area "4G" cellular wireless network. Specifically, it addresses the challenges of virtualization of resources in a cellular base station to enable shared use by multiple independent slice users (experimenters or mobile virtual network operators), each with possibly distinct flow types and network layer protocols. The proposed virtual basestation architecture is based on an external substrate which uses a layer-2 switched datapath, and an arbitrated control path to the WiMAX basestation. The framework implements virtualization of base station's radio resources to achieve isolation between multiple virtual networks. An algorithm for weighted fair sharing among multiple slices based on an airtime fairness metric has been implemented for the first release. Preliminary experimental results from the virtual basestation prototype are given, demonstrating mobile network performance, isolation across slices with different flow types, and custom flow scheduling capabilities.
Underwater acoustic communication by passive-phase conjugation: theory and experimental results (2001)

A new method for coherent underwater acoustic communication called passive phase conjugation is evaluated. The method is so named because of conceptual similarities to active phase conjugation methods that have been demonstrated in the ocean. In contrast to active techniques, however, the array in passive phase conjugation needs only receive. The procedure begins with a source transmitting a single probe pulse. After waiting for the multipathed arrivals to clear, the source then transmits the data stream. At each element in the distant receiving array, the received probe is cross-correlated with the received data stream. This cross-correlation is done in parallel at each array element and the results are summed across the array to achieve the final communication signal suitable for demodulation. As the ocean changes, it becomes necessary to break up the data stream and insert new probe pulses. Results from an experiment conducted in Puget Sound near Seattle are reported. Measurements were made at multiple ranges and water depths in range-dependent environments.
Cooperativity in protein-folding kinetics. (1993)

How does a protein find its native state without a globally exhaustive search? We propose the "HZ" (hydrophobic zipper) hypothesis: hydrophobic contacts act as constraints that bring other contacts into spatial proximity, which then further constrain and zip up the next contacts, etc. In contrast to helix-coil cooperativity, HZ-heteropolymer collapse cooperativity is driven by nonlocal interactions, causes sheet and irregular conformations in addition to helices, leads to secondary structures concurrently with early hydrophobic core formation, is much more sequence dependent than helix-coil processes, and involves compact intermediate states that have much secondary--but little tertiary--structure. Hydrophobic contacts in the 1992 Protein Data Bank have the type of "topological localness" predicted by the hypothesis. The HZ paths for amino acid sequences that mimic crambin and bovine pancreatic trypsin inhibitor are quickly found by computer; the best configurations thus reached have single hydrophobic cores that are within about 3 kcal/mol of the global minimum. This hypothesis shows how proteins could find globally optimal states without exhaustive search.
Dynamic release of nuclear RanGTP triggers TPX2-dependent microtubule assembly during the apoptotic execution phase (2009)

During apoptosis, the interphase microtubule network is dismantled then later replaced by a novel, non-centrosomal microtubule array. These microtubules assist in the peripheral redistribution of nuclear fragments in the apoptotic cell; however, the regulation of apoptotic microtubule assembly is not understood. Here, we demonstrate that microtubule assembly depends upon the release of nuclear RanGTP into the apoptotic cytoplasm because this process is blocked in apoptotic cells overexpressing dominant-negative GDP-locked Ran (T24N). Actin-myosin-II contractility provides the impetus for Ran release and, consequently, microtubule assembly is blocked in blebbistatin- and Y27632-treated apoptotic cells. Importantly, the spindle-assembly factor TPX2 (targeting protein for Xklp2), colocalises with apoptotic microtubules, and siRNA silencing of TPX2, but not of the microtubule motors Mklp1 and Kid, abrogates apoptotic microtubule assembly. These data provide a molecular explanation for the assembly of the apoptotic microtubule network, and suggest important similarities with the process of RanGTP- and TPX2-mediated mitotic spindle formation.
Targeted gene therapy (1995)

Melanin biosynthesis is limited to melanocytes partly as a consequence of transcriptional regulation of the enzymes involved in this pathway. Promoter sequences of these enzyme genes may be utilised to drive expression of complementary DNA coding for therapeutic genes so as to provide transcriptional targeting. We have used the 5'-flanking sequences of the murine tyrosinase or tyrosinase-related protein 1 (TRP-1) genes to show that such transcriptional targeting can be achieved both in vitro and in vivo. Using IL-2 as an example of an immunostimulatory gene and Herpes Simplex Virus thymidine kinase (HSVtk) as an example of a prodrug-activating gene we have shown, in murine model systems, that substantial anti-tumour effects can be achieved by targeted gene therapy approaches. The stage now is set for initial clinical evaluations in human patients.
Pathogenicity in POLG syndromes: DNA polymerase gamma pathogenicity prediction server and database (2017)

DNA polymerase gamma (POLG) is the replicative polymerase responsible for maintaining mitochondrial DNA (mtDNA). Disorders related to its functionality are a major cause of mitochondrial disease. The clinical spectrum of POLG syndromes includes Alpers-Huttenlocher syndrome (AHS), childhood myocerebrohepatopathy spectrum (MCHS), myoclonic epilepsy myopathy sensory ataxia (MEMSA), the ataxia neuropathy spectrum (ANS) and progressive external ophthalmoplegia (PEO). We have collected all publicly available POLG-related patient data and analyzed it using our pathogenic clustering model to provide a new research and clinical tool in the form of an online server. The server evaluates the pathogenicity of both previously reported and novel mutations. There are currently 176 unique point mutations reported and found in mitochondrial patients in the gene encoding the catalytic subunit of POLG, <i>POLG</i>. The mutations are distributed nearly uniformly along the length of the primary amino acid sequence of the gene. Our analysis shows that most of the mutations are recessive, and that the reported dominant mutations cluster within the polymerase active site in the tertiary structure of the POLG enzyme. The POLG Pathogenicity Prediction Server (http://polg.bmb.msu.edu) is targeted at clinicians and scientists studying POLG disorders, and aims to provide the most current available information regarding the pathogenicity of <i>POLG</i> mutations.
A Virtual Screening Approach for Thymidine Monophosphate Kinase Inhibitors as Antitubercular Agents Based on Docking and Pharmacophore Models. (2005)

Docking and pharmacophore screening tools were used to examine the binding of ligands in the active site\nof thymidine monophosphate kinase of &lt;i&gt;Mycobacterium tuberculosis&lt;/i&gt;. Docking analysis of deoxythymidine\nmonophosphate (dTMP) analogues suggests the role of hydrogen bonding and other weak interactions in\nenzyme selectivity. Water-mediated hydrogen-bond networks and a halogen-bond interaction seem to stabilize\nthe molecular recognition. A pharmacophore model was developed using 20 dTMP analogues. The\npharmacophoric features were complementary to the active site residues involved in the ligand recognition.\nOn the basis of these studies, a composite screening model that combines the features from both the docking\nanalysis and the pharmacophore model was developed. The composite model was validated by screening a\ndatabase spiked with 47 known inhibitors. The model picked up 42 of these, giving an enrichment factor of\n17. The validated model was used to successfully screen an in-house database of about 500 000 compounds.\nSubsequent screening with other filters gave 186 hit molecules.
Long-term Cognitive Impairment and Functional Disability Among Survivors of Severe Sepsis (2010)

Severe sepsis in this older population was independently associated with substantial and persistent new cognitive impairment and functional disability among survivors. The magnitude of these new deficits was large, likely resulting in a pivotal downturn in patients' ability to live independently.
CHEMISTRY OF THE TRIFLUOROMETHYL GROUP: PART IV. DIPHENYLTRIFLUOROMETHYLPHOSPHINE AND COMPLEX FORMATION BY PHENYLTRIFLUOROMETHYLPHOSPHINES (1962)

Three methods of preparing diphenyltrifluoromethylphosphine are described. The hydrolysis of the phosphine to diphenylphosphinic acid and fluoroform, and the formation of dibromo-and diiodo-phosphoranes from the phosphine are reported. The adducts (C 6 H 5 ) 3 P • BF 3 and (C 6 H 5 ) 2 CF 3 P • BF 3 are described and the latter is found to be the less stable. With platinum (II) chloride, the complexes trans-[(C 6 H 5 ) 2 PCF 3 ] 2 PtCl 2 and trans-[C 6 H 5 PCF 3 ) 2 ] 2 PtCl 2 are formed. The properties of the BF 3 adducts and PtCl 2 complexes are interpreted in terms of the electronegativity and size of the trifluoromethyl group.
The dynamics of gene expression in vertebrate embryogenesis at single-cell resolution (2018)

Time series of single-cell transcriptome measurements can reveal dynamic features of cell differentiation pathways. From measurements of whole frog embryos spanning zygotic genome activation through early organogenesis, we derived a detailed catalog of cell states in vertebrate development and a map of differentiation across all lineages over time. The inferred map recapitulates most if not all developmental relationships and associates new regulators and marker genes with each cell state. We find that many embryonic cell states appear earlier than previously appreciated. We also assess conflicting models of neural crest development. Incorporating a matched time series of zebrafish development from a companion paper, we reveal conserved and divergent features of vertebrate early developmental gene expression programs.
Glucagon-Like Peptides (1998)

Proglucagon contains the sequence of two glucagon-like peptides, GLP-1 and GLP-2, secreted from enteroendocrine cells of the small and large intestine. GLP-1 lowers blood glucose in both NIDDM and IDDM patients and may be therapeutically useful for treatment of patients with diabetes. GLP-1 regulates blood glucose via stimulation of glucose-dependent insulin secretion, inhibition of gastric emptying, and inhibition of glucagon secretion. GLP-1 may also regulate glycogen synthesis in adipose tissue and muscle; however, the mechanism for these peripheral effects remains unclear. GLP-1 is produced in the brain, and intracerebroventricular GLP-1 in rodents is a potent inhibitor of food and water intake. The short duration of action of GLP-1 may be accounted for in part by the enzyme dipeptidyl peptidase 4 (DPP-IV), which cleaves GLP-1 at the NH2-terminus; hence GLP-1 analogs or the lizard peptide exendin-4 that are resistant to DPP-IV cleavage may be more potent GLP-1 molecules in vivo. GLP-2 has recently been shown to display intestinal growth factor activity in rodents, raising the possibility that GLP-2 may be therapeutically useful for enhancement of mucosal regeneration in patients with intestinal disease. This review discusses recent advances in our understanding of the biological activity of the glucagon-like peptides.
BCMAp: an integral membrane protein in the Golgi apparatus of human mature B lymphocytes (1995)

BCMA is a human gene expressed preferentially in mature B lymphocytes as a 1.2 kb mRNA, which encodes a 184 amino acid peptide (BCMAp). The study of BCMA mRNA expression, using human malignant B cell lines characteristic of different stages of B lymphocyte differentiation, demonstrated that the BCMA mRNA is absent in the pro-B lymphocyte stage. It is expressed faintly at the pre-B cell stage and its expression increases with B lymphocyte maturation. Polyclonal antibodies were used to show, by cellular fractionation and immunoprecipitation, that BCMAp is a non-glycosylated integral membrane protein. Furthermore, BCMAp inserts, in vitro, into canine microsomes, as a type I integral membrane protein. Cell surface labeling showed that BCMAp is not expressed in the plasma membrane of mature B lymphocytes. Immunofluorescence studies revealed that BCMAp lies in a cap-like structure near the nucleus, that was identified as the Golgi apparatus by co-localization of BCMAp with CTR433, a marker of the medial cisternae of the Golgi apparatus. Confocal scanning laser microscopy of U266 plasma cells labeled with markers of various Golgi apparatus subcompartments strongly suggests that BCMAp is located in the cis part of the Golgi apparatus. Thus, BCMAp is the first Golgi resident protein with a tissue specificity and whose expression is linked to the stage of differentiation of B lymphocytes. The location of BCMAp in the Golgi apparatus and its high expression in plasmocytes (secreting large amounts of Ig) suggest that BCMAp is implicated in the intracellular traffic of Ig.
Plasma Volume, Blood Volume and Transcapillary Escape Rate (TER) of Albumin in Young Spontaneously Hypertensive Rats (SHR) as Compared with Normotensive Controls (NCR) (1978)

A detailed comparison of blood and plasma volumes and of the transcapillary escape rate (TER) of albumin was performed in SHR and matched NCR, particularly during the phase of rapid pressure rise in SHR. Throughout this early phase of life, the relative plasma and blood volumes tend to be lower, and TER higher in SHR, as would be expected when neurogenic mechanisms dominate the initiation of hypertension. Only in late established SHR hypertension, with increasing signs of cardiovascular complications, blood volume tends to be higher in SHR than in NCR. These results are in general agreement with most observations in early essential hypertension in man. They are of interest in contrast to recent findings in another variant of primary hypertension in rats, MHS. Also the apparently quite different initiating mechanisms in SHR and MHS primary hypertension are discussed.
The fibronectin-binding protein of Streptococcus pyogenes, SfbI, is involved in the internalization of group A streptococci by epithelial cells (1997)

Streptococcus pyogenes organisms (group A streptococci) are considered to be highly adhesive extracellular pathogens. However, it has recently been reported that S. pyogenes has the capacity to efficiently invade eukaryotic cells. In this study, we demonstrate that the interaction of S. pyogenes fibronectin-binding protein (SfbI) with fibronectin on nonphagocytic HEp-2 cells triggers bacterial internalization. Blocking of the SfbI adhesin by either antibodies against the whole protein or antibodies against the fibronectin-binding domains of SfbI, as well as pretreatment of HEp-2 cells with purified SfbI protein, prevents both S. pyogenes attachment and internalization. Inert latex beads precoated with the purified SfbI protein are ingested by eukaryotic cells, demonstrating that SfbI is per se enough to trigger the internalization process. Experiments performed with a recombinant SfbI domain encompassing the two fibronectin-binding regions of the SfbI molecule demonstrated that these binding regions are essential and sufficient to activate uptake by HEp-2 cells. These results demonstrate that the fibronectin-binding protein SfbI is involved in both S. pyogenes' attachment to and ingestion by HEp-2 cells and contribute to elucidation of the underlying molecular events leading to eukaryotic cell invasion by S. pyogenes.