gebhart/patrepeval huggingface dataset:
One-way Loss Pattern Sample Metrics (2002)

Using the base metric defined in RFC 2680, this document defines two derived metrics loss distance and loss period, and the associated statistics that together capture patterns experienced by packet streams on the Internet. The Internet exhibits certain specific types of behavior (e.g., bursty packet loss) that can affect the performance seen by the users as well as the operators. The pattern or distribution is a key parameter that determines the performance observed by the users for certain real-time applications such as packet voice and video. For the same rate, two different distributions could potentially produce widely different perceptions of performance.
Transcriptional Activity of the Herpes Simplex Virus Genome during Establishment, Maintenance, and Reactivation of in vitro Virus Latency (1989)

We previously have described a model of in vitro herpes simplex virus (HSV) latency in which latent infection was (i) established with human leukocyte interferon (IFN-alpha) in combination with (E)-5-(2-bromovinyl)-2'-deoxyuridine (BVDU) or 9-[(2-hydroxyethoxy)methyl]guanine (acyclovir); (ii) maintained after termination of combined inhibitor treatment by incubation at 40.5 degrees, and (iii) reactivated by either reducing the incubation temperature to 37 degrees or by superinfecting at the elevated temperature with human cytomegalovirus (HCMV). We now report the use of this system to examine the transcriptional activity of the HSV genome during establishment, maintenance, and reactivation of HSV latency in vitro. Numerous species of virus-specific polyadenylated RNAs were present during the first 3 days of combined BVDU and IFN-alpha treatment of HSV type 1 (HSV-1)-infected human fetus lung fibroblast cells. However, after 7 days of combined inhibitor treatment, only a very small quantity of virus-specific RNA could be detected utilizing the short unique region of the HSV-1 genome as probe. After terminating combined BVDU and IFN-alpha treatment and increasing the temperature from 37 to 40.5 degrees on day 7 after infection, virus-specific RNA was undetectable by RNA blot hybridization analysis; however, a small amount of HSV-specific RNA was detected in 2% of the cells by in situ hybridization. The HSV-1 transcriptional products produced after HCMV superinfection in the presence of selected inhibitors of macromolecular synthesis also were examined and demonstrated that the efficient activation of HSV-1 immediate-early gene transcription required the expression of not only immediate-early HCMV gene product(s), but also at least a subset of early-late gene products.
THE RELATIONSHIP BETWEEN RELIGION, SELF-ESTEEM, AND DELINQUENCY (1996)

ABSTRACT The impact of religious and self-esteem factors on delinquency has received considerable attention. Despite significant contributions, however, few studies have explored whether the combined effects of religion and self-esteem influence crime/delinquency. The present study examines (a) whether religion, self-esteem, and delinquency are interrelated, and (b) whether the interaction of religion and self-esteem, as well as the main effects of these factors, affects delinquency. Through an examination of 15 OLS regression models, the findings are twofold: (a) main effects of religion and self-esteem affect certain forms of delinquency, and (b) the combined effects of religion and self-esteem do not affect delinquency. The impact of religion and self-esteem on delinquency has received considerable attention. Much of this attention, however, has been devoted to one of two relationships: (a) the impact of religion on delinquency, and (b) the impact of self-esteem on delinquency. Although these studies have made significant contributions to knowledge, few scholars (if any) have explored whether the combined effects of religion and self-esteem influence crime/delinquency.
Expression and ultrastructural immunolocalization of a major 66 kDa phosphoprotein synthesized by chicken osteoblasts during mineralization in vitro (1990)

Embryonic chicken osteoblasts cultured over a 30 day period were used as a model system for studying the expression of bone phosphoproteins during cellular differentiation and the possible role of these proteins in extracellular matrix mineralization. Accumulation of total phosphoprotein in the cultures, as determined by O-phosphoserine (Ser-P) and O-phosphothreonine (Thr-P) amino acid analysis, revealed a greater than 10-fold increase over the 30 day period. Total phosphoprotein synthesis, as assessed by (32P)-, (3H)-Ser-P, and (14C)-Thr-P protein labeling, showed the highest levels concurrent with initial mineral deposition within the matrix. The major phosphoprotein present in chicken bones and synthesized by the cultured osteoblasts had a molecular weight of approximately 66 kDa. This 66 kDa bone phosphoprotein (66 kDa BPP) was purified to homogeneity and was used for antibody production. Application of this antibody in Western blot analysis revealed that 66 kDa BPP was present only in protein extracts of mineralizing cultured osteoblasts and was absent in cultures of non-mineralizing chondrocytes, myoblasts, and tendon fibroblasts. The 66 kDa BPP in vitro accumulated continuously in the extracellular matrix in a manner that paralleled both phosphoprotein synthesis and total phospho-amino acid production. A comparison of the results obtained in vitro to those from developing embryonic tibiae in vivo demonstrated a similar qualitative and temporal expression of phosphoprotein and a continual accumulation of 66 kDa BPP in the matrix with advancing mineralization and developmental age. Ultrastructural immunocytochemistry using the 66 kDa BPP antibody and the protein A-gold technique revealed specific immunolabeling over electron-dense regions of mineralization in the cultures that appeared identical to the distribution of labeling observed in vivo (McKee et al.: Connect. Tissue Res., 21:21-29, 1989; Anat. Rec., 228:77-92, 1990). These results demonstrate that this major 66 kDa BPP was expressed concurrently with other differentiated osteoblast functions and suggests that it may play a role in the initiation or regulation of mineralization.
Long-Term Stable Correction of Low-Density Lipoprotein Receptor–Deficient Mice With a Helper-Dependent Adenoviral Vector Expressing the Very Low-Density Lipoprotein Receptor (2001)

HD-Ad-mediated intravenous delivery of VLDLR to hepatocytes is well tolerated. It produces long-term lowering of plasma cholesterol and prevents atherosclerosis development in LDLR-deficient mice. These data provide support for the feasibility and safety of this approach for therapy of human subjects.
Recombinant soluble low-density lipoprotein receptor fragment inhibits common cold infection (1998)

A fragment of the human low-density lipoprotein receptor encompassing the seven ligand-binding repeats fused to a C-terminal oligo-His tag was expressed in Sf9 insect cells. The melittin signal sequence encoded in the baculovirus vector led to secretion of the protein into the cell supernatant in a soluble form. The receptor fragment bound its natural ligand beta-migrating very-low-density lipoprotein and human rhinovirus serotype 2 in non-reducing ligand blots. Infection of all minor group human rhinovirus serotypes investigated was inhibited by the presence of the receptor fragment during viral challenge of HeLa cells. Infection is inhibited by aggregation of the virions.
Thinking Outside the Box—Novel Antibacterials To Tackle the Resistance Crisis (2018)

The public view on antibiotics as reliable medicines changed when reports about "resistant superbugs" appeared in the news. While reasons for this resistance development are easily spotted, solutions for re-establishing effective antibiotics are still in their infancy. This Review encompasses several aspects of the antibiotic development pipeline from very early strategies to mature drugs. An interdisciplinary overview is given of methods suitable for mining novel antibiotics and strategies discussed to unravel their modes of action. Select examples of antibiotics recently identified by using these platforms not only illustrate the efficiency of these measures, but also highlight promising clinical candidates with therapeutic potential. Furthermore, the concept of molecules that disarm pathogens by addressing gatekeepers of virulence will be covered. The Review concludes with an evaluation of antibacterials currently in clinical development. Overall, this Review aims to connect select innovative antimicrobial approaches to stimulate interdisciplinary partnerships between chemists from academia and industry.
Polymer derived ceramics : from nano-structure to applications (2010)

This book presents the foundations of the science of polymer derived ceramics, enriched with many descriptions of applications. Written by a team of selected researchers, the text is a systematic, comprehensive introduction to all phases of polymer derived ceramics from synthesis strategies through properties measurement, and applications. New material is given on the nanolevel structure of PDCs, and it is shown how nano-sized modifications can alter and improve the properties of polymer derived ceramics, including high chemical durability, oxidation resistance, luminescence, and piezo-resistivity. Groundbreaking work is also described on novel precursors such as stoichiometric SiC, BN, and SiBCN ceramics. In terms of technology, this volume explains how PDCs are fabricated and how these novel materials are used in membranes, filters, MEMS, fibers, and micro-components.
Practical points in understanding local anesthetics. (1992)

It has been the purpose of this article to discuss the pharmacology and physiology of local anesthetics. By having an understanding of local anesthetics at this level, the PACU nurse should have a better understanding of the consequences of employing local anesthetics in regional anesthesia.
Granulocyte function disorders: aspects of development, genetics and management (2001)

The field of phagocytic disorders has attained major biologic and clinical significance in the past 40 years. The development of exciting new techniques in molecular biology and the cellular physiology of signal transduction have made it possible to identify the genetic defects involved in many of these disorders. Moreover through immunopharmacologic intervention, bone marrow or peripheral or cord blood stem cell transplantation along with the prospect of gene therapy, we have begun attempts to at least partially correct genetic defects in cell development and activation pathways in the entire spectrum of phagocyte disorders. Carrier detection and prenatal diagnosis employing with chain reaction techniques or direct nucleotide sequencing in fetal blood have made these diseases potentially preventable or treatable in utero or shortly after birth.
Facies and development of the Middle Jurassic Brent Delta near the northern limit of its progradation, UK North Sea (1989)

Summary The lithofacies patterns in the Middle Jurassic Brent Group, the principal hydrocarbon reservoir in the UK northern North Sea, are examined in seven wells. The sections, from the area of the Don and Murchison oil fields, record the nature of the Brent Delta near the northern limit of its progradation. Here the deltaic deposits of the Brent Group, which regionally constitute a major regressive-transgressive clastic wedge, progressively lose the interbedded sands and muds of the delta plain which characterize the middle part of the succession further S. This leads locally to a maximum sand-to-mud ratio for the Brent Group reservoir interval. A regressive storm-wave-influenced marine succession, from offshore transition-zone silts and muds up to hummocky cross-stratified nearshore sand, is overlain in turn by stacked distributary channel sands. Distributary mouth deposits are absent. The interbedded delta-plain succession, where it occurs, exhibits some marine influence and records wave reworking of interdistributary bay or lagoonal sediments. The Brent Group succession is capped by transgressive sands which were deposited in a storm-wave-influenced nearshore environment. Delta-plain drowning is also evident in the gradual marine incursions into distributary channels at the northern limit of the study area. The character of the delta locally is compared with the nature of the wave-dominated Brent Delta elsewhere on its progradational path. High energy nearshore deposits in both regressive and transgressive phases are widely distributed, but there is a contrast between the dominance of fluvial processes in the study area and the development elsewhere of a barrier island complex in front of a coastal plain.
Mechanism and clinical significance of cyclooxygenase-2 expression in gastric cancer (2005)

The demethylation of 5' CpG island of gene is necessary for COX-2 expression in human gastric cancer. The expression status of COX-2 may provide theoretical basis for COX-2 targeting gastric cancer treatments.
Biologically derived melanin electrodes in aqueous sodium-ion energy storage devices (2013)

Significance Here we present important findings related to biologically derived pigments for potential use as battery electrodes. Namely, we report the synthesis, fabrication, and characterization of melanins as materials for use in aqueous sodium-ion batteries. We demonstrate the use of naturally occurring melanins as active electrode materials in charge storage devices. Furthermore, the performance of melanin anodes is comparable to many commonly available synthetic organic electrode materials. The structure–property relationships that govern the storage capacity in melanin materials were also elucidated. These findings suggest that the unique chemistry and nanostructure in natural melanins increase the charge storage capacity compared with synthetic melanin analogues.
The biological action of saponins in animal systems: a review (2002)

Saponins are steroid or triterpenoid glycosides, common in a large number of plants and plant products that are important in human and animal nutrition. Several biological effects have been ascribed to saponins. Extensive research has been carried out into the membrane-permeabilising, immunostimulant, hypocholesterolaemic and anticarcinogenic properties of saponins and they have also been found to significantly affect growth, feed intake and reproduction in animals. These structurally diverse compounds have also been observed to kill protozoans and molluscs, to be antioxidants, to impair the digestion of protein and the uptake of vitamins and minerals in the gut, to cause hypoglycaemia, and to act as antifungal and antiviral agents. These compounds can thus affect animals in a host of different ways both positive and negative.
Bacteriology of Urinary Tract Infection Associated with Indwelling J Ureteral Stents (2004)

An indwelling J ureteral stent carries a significant risk of bacteriuria and stent colonization. The sensitivity of urine culture to stent colonization is low, and therefore, a negative culture does not rule out a colonized stent. Bacteria cultured from urine after stent insertion and from the stents are more resistant to antibiotics than are those cultured from urine before stent insertion. Norfloxacin or ciprofloxacin is recommended as prophylaxis prior to stent insertion, and an aminoglycoside can be added to treat symptomatic patients with severe infections.
Erythrocyte Mr 28,000 transmembrane protein exists as a multisubunit oligomer similar to channel proteins. (1991)

A novel Mr 28,000 erythrocyte transmembrane protein was recently purified and found to exist in two forms, "28kDa" and "gly28kDa," the latter containing N-linked carbohydrate (Denker, B. M., Smith, B. L., Kuhajda, F. P., and Agre, P. (1988) J. Biol. Chem. 263, 15634-15642). Although 28kDa protein resembles the Rh polypeptides biochemically, structural homologies were not identified by immunoblot or two-dimensional iodopeptide maps. The NH2-terminal amino acid sequence for the first 35 residues of purified 28kDa protein is 37% identical to the 26-kDa major intrinsic protein of lens (Gorin, M. B., Yancey, S. B., Cline, J., Revel, J.-P., and Horwitz, J. Cell 39, 49-59). Antisera to a synthetic peptide corresponding to the NH2-terminus of 28kDa protein gave a single reaction of molecular mass 28kDa on immunoblots of erythrocyte membranes. Selective digestions of intact erythrocytes and inside-out membrane vesicles with carboxypeptidase Y indicated the existence of a 5-kDa COOH-terminal cytoplasmic domain. Multiple studies indicated that 28kDa and gly28kDa proteins exist together as a multisubunit oligomer: 1) similar partial solubilizations in Triton X-100; 2) co-purification during ion exchange and lectin affinity chromatography; 3) cross-linking in low concentrations of glutaraldehyde; and 4) physical analyses of purified proteins and solubilized membranes in 1% (v/v) Triton X-100 showed 28kDa and gly28kDa proteins behave as a large single unit with Stokes radius of 61 A and sedimentation coefficient of 5.7 S. These studies indicate that the 28kDa and gly28kDa proteins are distinct from the Rh polypeptides and exist as a multisubunit oligomer. The 28kDa protein has NH2-terminal amino acid sequence homology and membrane organization similar to major intrinsic protein and other members of a newly recognized family of transmembrane channel proteins.
Deflection-based force sensing for continuum robots: A probabilistic approach (2011)

The inherent flexibility of continuum robots allows them to interact with objects in a safe and compliant way. This flexibility also makes it possible to use robot deflection to estimate external forces applied to the robot. This ¿intrinsic force sensing¿ concept is particularly useful for thin continuum robots where application constraints preclude the use of traditional force sensors. This paper describes an Extended Kalman Filter approach to estimate forces applied at the tip of a continuum robot using only uncertain pose measurements and a kinematic-static model of the robot with uncertainty.
Phenolic Constituents of Cassia Seeds and Antibacterial Effect of Some Naphthalenes and Anthraquinones on Methicillin-Resistant Staphylococcus aureus. (1999)

Thirteen phenolic glycosides including six new compounds were isolated from seeds of Cassia tora (Leguminosae). The structures of the new compounds, rubrofusarin triglucoside (7), nor-rubrofusarin gentiobioside (9), demethylflavasperone gentiobioside (10), torachrysone gentiobioside (11), torachrysone tetraglucoside (12) and torachrysone apioglucoside (13), were elucidated on the basis of spectroscopic and chemical evidence. The effects of the phenolic glycosides, their aglycones and several other compounds structurally related to them on Escherichia coli K12, Pseudomonas aeruginosa PAO1 and some strains of Staphylococcus aureus were then examined. Among them, torachrysone (15), toralactone (16), aloe-emodin (18), rhein (19) and emodin (20) showed noticeable antibacterial effects on four strains of methicillin-resistant Staphylococcus aureus with a minimum inhibitory concentration of 2-64 micrograms/ml. On the other hand, the phenolic compounds tested did not show strong antibacterial effects on E. coli and P. aeruginosa.
Ranking Measures and Loss Functions in Learning to Rank (2009)

Learning to rank has become an important research topic in machine learning. While most learning-to-rank methods learn the ranking functions by minimizing loss functions, it is the ranking measures (such as NDCG and MAP) that are used to evaluate the performance of the learned ranking functions. In this work, we reveal the relationship between ranking measures and loss functions in learningto-rank methods, such as Ranking SVM, RankBoost, RankNet, and ListMLE. We show that the loss functions of these methods are upper bounds of the measurebased ranking errors. As a result, the minimization of these loss functions will lead to the maximization of the ranking measures. The key to obtaining this result is to model ranking as a sequence of classification tasks, and define a so-called essential loss for ranking as the weighted sum of the classification errors of individual tasks in the sequence. We have proved that the essential loss is both an upper bound of the measure-based ranking errors, and a lower bound of the loss functions in the aforementioned methods. Our proof technique also suggests a way to modify existing loss functions to make them tighter bounds of the measure-based ranking errors. Experimental results on benchmark datasets show that the modifications can lead to better ranking performances, demonstrating the correctness of our theoretical analysis. 1
Holins: The Protein Clocks of Bacteriophage Infections (2000)

Two proteins, an endolysin and a holin, are essential for host lysis by bacteriophage. Endolysin is the term for muralytic enzymes that degrade the cell wall; endolysins accumulate in the cytosol fully folded during the vegetative cycle. Holins are small membrane proteins that accumulate in the membrane until, at a specific time that is "programmed" into the holin gene, the membrane suddenly becomes permeabilized to the fully folded endolysin. Destruction of the murein and bursting of the cell are immediate sequelae. Holins control the length of the infective cycle for lytic phages and so are subject to intense evolutionary pressure to achieve lysis at an optimal time. Holins are regulated by protein inhibitors of several different kinds. Holins constitute one of the most diverse functional groups, with >100 known or putative holin sequences, which form >30 ortholog groups.
Stampy: A statistical algorithm for sensitive and fast mapping of Illumina sequence reads (2010)

High-volume sequencing of DNA and RNA is now within reach of any research laboratory and is quickly becoming established as a key research tool. In many workflows, each of the short sequences ("reads") resulting from a sequencing run are first "mapped" (aligned) to a reference sequence to infer the read from which the genomic location derived, a challenging task because of the high data volumes and often large genomes. Existing read mapping software excel in either speed (e.g., BWA, Bowtie, ELAND) or sensitivity (e.g., Novoalign), but not in both. In addition, performance often deteriorates in the presence of sequence variation, particularly so for short insertions and deletions (indels). Here, we present a read mapper, Stampy, which uses a hybrid mapping algorithm and a detailed statistical model to achieve both speed and sensitivity, particularly when reads include sequence variation. This results in a higher useable sequence yield and improved accuracy compared to that of existing software.