gebhart/patrepeval huggingface dataset:
Essential PHP Security (2005)

Being highly flexible in building dynamic, database-driven web applications makes the PHP programming language one of the most popular web development tools in use today. It also works beautifully with other open source tools, such as the MySQL database and the Apache web server. However, as more web sites are developed in PHP, they become targets for malicious attackers, and developers need to prepare for the attacks. Security is an issue that demands attention, given the growing frequency of attacks on web sites. Essential PHP Security explains the most common types of attacks and how to write code that isn't susceptible to them. By examining specific attacks and the techniques used to protect against them, you will have a deeper understanding and appreciation of the safeguards you are about to learn in this book. In the much-needed (and highly-requested) Essential PHP Security, each chapter covers an aspect of a web application (such as form processing, database programming, session management, and authentication). Chapters describe potential attacks with examples and then explain techniques to help you prevent those attacks. Topics covered include: Preventing cross-site scripting (XSS) vulnerabilities Protecting against SQL injection attacks Complicating session hijacking attempts You are in good hands with author Chris Shiflett, an internationally-recognized expert in the field of PHP security. Shiflett is also the founder and President of Brain Bulb, a PHP consultancy that offers a variety of services to clients around the world.
Relation Between Infantile Colic and Asthma/Atopy: A Prospective Study in an Unselected Population (2001)

Our data cannot support the hypothesis that infantile colic provides increased risk for subsequent allergic disease or atopy.
Nasal saline irrigations for the symptoms of chronic rhinosinusitis (2007)

This is a protocol for a Cochrane Review (Intervention). The objectives are as follows: To evaluate the effectiveness and safety of topical saline in the management of chronic rhinosinusitis.
Classifying and segmenting microscopy images with deep multiple instance learning (2016)

oren.kraus@mail.utoronto.ca.
Effects of Chronic Pelvic Pain on Heart Rate Variability in Women (2015)

Subjects with interstitial cystitis/bladder pain syndrome had diminished vagal activity and a shift toward sympathetic nervous system dominance. Overall these data support the hypothesis that changes in autonomic function occur in interstitial cystitis/bladder pain syndrome but not in myofascial pelvic pain. These changes may result from interstitial cystitis/bladder pain syndrome or contribute to its pathophysiology through abnormal self-regulatory function.
Primer design versus PCR bias in methylation independent PCR amplifications (2009)

Many protocols in methylation studies utilize one primer set to generate a PCR product from bisulfite modified template regardless of its methylation status (methylation independent amplification MIP). However, proportional amplification of methylated and unmethylated alleles is hard to achieve due to PCR bias favoring amplification of unmethylated relatively GC poor sequence. Two primer design systems have been proposed to overcome PCR bias in methylation independent amplifications. The first advises against including any CpG dinucleoteides into the primer sequence (CpG-free primers) and the second, recently published by us, is based on inclusion of a limited number of CpG sites into the primer sequence. Here we used the Methylation Sensitive High Resolution Melting (MS-HRM) technology to investigate the ability of primers designed according to both of the above mentioned primer design systems to proportionally amplify methylated and unmethylated templates. Ten "CpG-free" primer pairs and twenty primers containing limited number of CpGs were tested. In reconstruction experiments the "CpG-free" primers showed primer specific sensitivity and allowed us to detect methylation levels in the range from 5 to 50%. Whereas while using primers containing limited number of CpG sites we were able to consistently detect 1-0.1% methylation levels and effectively control PCR amplification bias. In conclusion, the primers with limited number of CpG sites are able to effectively reverse PCR bias and therefore detect methylated templates with significantly higher sensitivity than CpG free primers.
Complement fraction 3 binding on erythrocytes as additional mechanism of disease in paroxysmal nocturnal hemoglobinuria patients treated by eculizumab (2009)

Abstract In paroxysmal nocturnal hemoglobinuria (PNH) hemolytic anemia is due mainly to deficiency of the complement regulator CD59 on the surface of red blood cells (RBCs). Eculizumab, an antibody that targets complement fraction 5 (C5), has proven highly effective in abolishing complement-mediated intravascular hemolysis in PNH; however, the hematologic benefit varies considerably among patients. In the aim to understand the basis for this variable response, we have investigated by flow cytometry the binding of complement fraction 3 (C3) on RBCs from PNH patients before and during eculizumab treatment. There was no evidence of C3 on RBCs of untreated PNH patients; by contrast, in all patients on eculizumab (n = 41) a substantial fraction of RBCs had C3 bound on their surface, and this was entirely restricted to RBCs with the PNH phenotype (CD59−). The proportion of C3+ RBCs correlated significantly with the reticulocyte count and with the hematologic response to eculizumab. In 3 patients in whom 51Cr labeling of RBCs was carried out while on eculizumab, we have demonstrated reduced RBC half-life in vivo, with excess 51Cr uptake in spleen and in liver. Binding of C3 by PNH RBCs may constitute an additional disease mechanism in PNH, strongly enhanced by eculizumab treatment and producing a variable degree of extravascular hemolysis.
PathwayVoyager: pathway mapping using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database (2005)

PathwayVoyager represents an alternative approach to many already existing, more complex pathway reconstructions software solutions. This software does not require any dedicated hardware or software and is flexible and straightforward to use. It is ideally suited for environments where analyses on variable datasets are desired.
Blocking stress response for better memory? (2015)

A drug that affects memory targets a constituent of a cellular stress response mechanism [Also see Report by Sekine et al. ]
tRNomics: Analysis of tRNA genes from 50 genomes of Eukarya, Archaea, and Bacteria reveals anticodon-sparing strategies and domain-specific features (2002)

From 50 genomes of the three domains of life (7 eukarya, 13 archaea, and 30 bacteria), we extracted, analyzed, and compared over 4,000 sequences corresponding to cytoplasmic, nonorganellar tRNAs. For each genome, the complete set of tRNAs required to read the 61 sense codons was identified, which permitted revelation of three major anticodon-sparing strategies. Other features and sequence peculiarities analyzed are the following: (1) fit to the standard cloverleaf structure, (2) characteristic consensus sequences for elongator and initiator tDNAs, (3) frequencies of bases at each sequence position, (4) type and frequencies of conserved 2D and 3D base pairs, (5) anticodon/tDNA usages and anticodon-sparing strategies, (6) identification of the tRNA-Ile with anticodon CAU reading AUA, (7) size of variable arm, (8) occurrence and location of introns, (9) occurrence of 3'-CCA and 5'-extra G encoded at the tDNA level, and (10) distribution of the tRNA genes in genomes and their mode of transcription. Among all tRNA isoacceptors, we found that initiator tDNA-iMet is the most conserved across the three domains, yet domain-specific signatures exist. Also, according to which tRNA feature is considered (5'-extra G encoded in tDNAs-His, AUA codon read by tRNA-Ile with anticodon CAU, presence of intron, absence of "two-out-of-three" reading mode and short V-arm in tDNA-Tyr) Archaea sequester either with Bacteria or Eukarya. No common features between Eukarya and Bacteria not shared with Archaea could be unveiled. Thus, from the tRNomic point of view, Archaea appears as an "intermediate domain" between Eukarya and Bacteria.
Characterization and epitope mapping of a human monoclonal antibody reactive with the envelope glycoprotein of human immunodeficiency virus. (1987)

A human monoclonal antibody (IgG2, lambda), 1B8.env, was produced, reactive with the envelope glycoprotein of human immunodeficiency virus (HIV). The antibody specifically stains cells infected with HIV, as assessed by indirect immunofluorescence analysis and reacts with determinants displayed on the surface of infected cells. In Western blot analysis, the antibody reacts with bands of 160 and 41 kD, consistent with the precursor and transmembrane forms of the HIV envelope glycoprotein. The antibody also reacts specifically in immunofluorescence and Western blot analysis with cells infected with the recombinant vaccinia virus VSC-25, which contains the envelope gene of HIV. With the lambda gt11 expression vector, the epitope recognized by 1B8.env was mapped to a region of 11 amino acids in the coding region of gp41. This domain is highly conserved between several otherwise highly variable HIV isolates. In addition, this epitope appears to be recognized by the vast majority of HIV seropositive individuals. Although antibody IB8.env does not neutralize HIV virion infectivity or virally mediated cell fusion, the results presented here demonstrate the feasibility of generating and characterizing human monoclonal antibodies to HIV with these techniques. Additional antibodies produced in this manner will help to further characterize the humoral response to HIV infection, define biologically significant determinants on HIV proteins, and may be useful in clinical applications.
Facilitated Target Location in Biological Systems (1989)

In this minireview we have attempted to provide some overall perspective on the question of how various forms of diffusion in reduced dimensions, or diffusion within a nonspecifically bound state, can speed biological interactions beyond the limits normally set by three-dimensional diffusion processes. To this end we began by discussing the rates expected for small molecules engaged in classical elastic collisions. We then proceeded to modify this picture by introducing first the features of inelastic macromolecular collisions in solution, then the effects of specific electrostatic fields set up around macromolecules of known structure at low ionic strengths, and finally the special rate enhancements available to DNA-protein interactions because of the particular geometry of the DNA molecule and the multiple conformations that can be assumed by the protein component. We hope that this exposition will help to clarify the subject for others and also will stimulate more focused examination of this type of problem, both in DNA-protein interaction systems and in other biological systems where such rate facilitation might apply.
An Investigation of Genome-Wide Studies Reported Susceptibility Loci for Ulcerative Colitis Shows Limited Replication in North Indians (2011)

Genome-Wide Association studies (GWAS) of both Crohn's Disease (CD) and Ulcerative Colitis (UC) have unearthed over 40 risk conferring variants. Recently, a meta-analysis on UC revealed several loci, most of which were either previously associated with UC or CD susceptibility in populations of European origin. In this study, we attempted to replicate these findings in an ethnically distinct north Indian UC cohort. 648 UC cases and 850 controls were genotyped using Infinium Human 660W-quad. Out of 59 meta-analysis index SNPs, six were not in the SNP array used in the study. Of the remaining 53 SNPs, four were found monomorphic. Association (p<0.05) at 25 SNPs was observed, of which 15 were CD specific. Only five SNPs namely rs2395185 (HLA-DRA), rs3024505 (IL10), rs6426833 (RNF186), rs3763313 (BTNL2) and rs2066843 (NOD2) retained significance after Bonferroni correction. These results (i) reveal limited replication of Caucasian based meta-analysis results; (ii) reiterate overlapping molecular mechanism(s) in UC and CD; (iii) indicate differences in genetic architecture between populations; and (iv) suggest that resources such as HapMap need to be extended to cover diverse ethnic populations. They also suggest a systematic GWAS in this terrain may be insightful for identifying population specific IBD risk conferring loci and thus enable cross-ethnicity fine mapping of disease loci.
Senescent intimal foam cells are deleterious at all stages of atherosclerosis (2016)

Advanced atherosclerotic lesions contain senescent cells, but the role of these cells in atherogenesis remains unclear. Using transgenic and pharmacological approaches to eliminate senescent cells in atherosclerosis-prone low-density lipoprotein receptor-deficient (Ldlr<sup>-/-</sup>) mice, we show that these cells are detrimental throughout disease pathogenesis. We find that foamy macrophages with senescence markers accumulate in the subendothelial space at the onset of atherosclerosis, where they drive pathology by increasing expression of key atherogenic and inflammatory cytokines and chemokines. In advanced lesions, senescent cells promote features of plaque instability, including elastic fiber degradation and fibrous cap thinning, by heightening metalloprotease production. Together, these results demonstrate that senescent cells are key drivers of atheroma formation and maturation and suggest that selective clearance of these cells by senolytic agents holds promise for the treatment of atherosclerosis.
Thermal Therapy, Part 1: An Introduction to Thermal Therapy (2006)

Thermal therapy is widely known and electromagnetic (EM) energy, ultrasonic waves, and other thermal-conduction-based devices have been used as heating sources. In particular, advances in EM technology have paved the way for promising trends in thermotherapeutical applications such as oncology, physiotherapy, urology, cardiology, ophthalmology, and in other areas of medicine as well. This series of articles is generally written for oncologists, cancer researchers, medical students, biomedical researchers, clinicians, and others who have an interest in this topic. This article reviews key processes and developments in thermal therapy with emphasis on two techniques, namely, hyperthermia [including long-term low-temperature hyperthermia (40-41 degrees C for 6-72 hr), moderate-temperature hyperthermia (42-45 degrees C for 15-60 min), and thermal ablation, or high-temperature hyperthermia (> 50 degrees C for > 4-6 min)]. The article will also provide an overview of a wide range of possible mechanisms and biological effects of heat. This information will be discussed in light of what is known about the degree of temperature rise that is expected from various sources of energy. The review concludes with an evaluation of human exposure risk to EM energy or the corresponding heat, trends in equipment development, and future research directions.
<title>High-resolution, multiple optical mode confocal microscope: I. System design, image acquisition and 3D visualization</title> (1994)

We have designed and constructed an experimental confocal specimen-scanning microscope which has the capability of producing high resolution 3D images in a variety of optical modes, many of which are not currently available on commercial confocal microscopes. The transmission Nomarski differential interference contrast mode is particularly interesting because it can be utilized to image small changes in refractive index within complex biological specimens which are transparent in standard brightfield. The three-color reflection configuration can produce a color 3D image, which means that stained or pigmented objects will be similar in appearance to images obtained from conventional white light microscopes which makes them more recognizable.
GUIDED NANOSTRUCTURES USING ANODIZED ALUMINUM OXIDE TEMPLATES (2011)

In this paper, we review recent advances in nanotemplate fabrication using anodized aluminum oxide (AAO). In addition to self-ordered AAO nanoarrays, guided AAO self-assembly is of great interest since it can offer highly ordered, vertically aligned nanoporous templates which are suitable for various materials synthesis and alignment of nanosized structures. Moreover, structural modification of AAO nanoarrays by controlling fabrication process parameters are reviewed which can be applicable for advanced micro- and nanosystems. In this aspect, potential applications using AAO will be revealed in the aspects of self-ordered AAO, guided self-assembly of AAO, and biomedical and magnetic applications.
Copy detection mechanisms for digital documents (1995)

In a digital library system, documents are available in digital form and therefore are more easily copied and their copyrights are more easily violated. This is a very serious problem, as it discourages owners of valuable information from sharing it with authorized users. There are two main philosophies for addressing this problem: prevention and detection. The former actually makes unauthorized use of documents difficult or impossible while the latter makes it easier to discover such activity.In this paper we propose a system for registering documents and then detecting copies, either complete copies or partial copies. We describe algorithms for such detection, and metrics required for evaluating detection mechanisms (covering accuracy, efficiency, and security). We also describe a working prototype, called COPS, describe implementation issues, and present experimental results that suggest the proper settings for copy detection parameters.
Characterization of the enhancer region for germline transcription of the gamma 3 constant region gene of human immunoglobulin (1991)

A constant region gene (C) of the immunoglobulin heavy chain can be transcribed as germline transcripts from a promoter located upstream of a switch region. We have studied the structure and function of the human C gamma 3 promoter region. When the human IgM-producing cell line SSK41 is stimulated with interleukin 4 (IL-4) in the presence of phorbol myristate acetate (PMA) or Staphylococcus aureus Cowan I, expression of germline C gamma 3 transcripts was specifically augmented within 4 h. Upstream DNA fragments flanking the I gamma 3 exon were fused with a reporter gene and tested for IL-4-induced promoter/enhancer activity by transfection of SSK41 cells. The DNA fragment between 450 and 250 bp upstream of the transcription initiation site of the C gamma 3 gene was shown to be required for transcriptional up-regulation by PMA and IL-4. The upstream 514 bp fragment of the I gamma 3 flanking region was shown to contain an enhancer activity in response to PMA and IL-4.
Analysis of submicron carbon nanotube field-effect transistors (2000)

A theoretical analysis of carbon nanotube based field-effect transistors fabricated by two different groups [Tans et al., Nature (London) 393, 49 (1998); Martel et al., Appl. Phys. Lett. 73, 2447 (1998)] is presented. The metal (electrode)-semiconductor (nanotube) contact influences subthreshold channel conductance versus gate voltage VG, such that the occurrence of a kink depends on the transport mechanism across this contact. Saturation in the turn-on drain current ID vs VG seen in experiments reflects the nanotube state density. Saturationless ID versus drain voltage VD indicates transport in the weak-localization regime in the absence of carrier–carrier scattering so that pinch-off cannot occur. To compensate for saturationless ID(VD) in digital applications, nanotube transistors need to be designed to maximize their transconductance.
Internet search engine freshness by Web server help (2002)

We study how to keep the Internet search engines up-to-date with the changes occurring at the various Web servers in the Internet. Currently, Web search engines poll the Web servers on a per-URL basis for obtaining update information. We advocate an approach in which Web servers themselves track the changes happening to their content files for propagating updates to search engines. We propose an algorithm which uses both freshness and popularity of data at the Web servers for deciding the discrepancy between a Web site and a search engine. This algorithm batches the push of updates from the Web server to the search engine. We prove that this algorithm is competitive with an optimal algorithm.
The Neural Cell Adhesion Molecule (NCAM) as a Regulator of Cell-Cell Interactions (1988)

The neural cell adhesion molecule (NCAM) can influence a number of diverse intercellular events, including junctional communication, the association of axons with pathways and targets, and signals that alter levels of neurotransmitter enzymes. These pleiotropic effects appear to reflect the ability of NCAM to regulate membrane-membrane contact required to initiate specific interactions between other molecules. Such regulation can occur through changes in either NCAM expression or the molecule's content of polysialic acid (PSA). When NCAM with a low PSA content is expressed, adhesion is increased and contact-dependent events are triggered. In contrast, the large excluded volume of NCAM PSA can inhibit cell-cell interactions through hindrance of overall membrane apposition.
Theoretical aspects of antibiotic diffusion into microbial biofilms (1996)

Antibiotic penetration into microbial biofilm was investigated theoretically by the solution of mathematical equations describing various combinations of the processes of diffusion, sorption, and reaction. Unsteady material balances on the antibiotic and on a reactive or sorptive biomass constituent, along with associated boundary and initial conditions, constitute the mathematical formulations. Five cases were examined: diffusion of a noninteracting solute; diffusion of a reversibly sorbing, nonreacting solute; diffusion of an irreversibly sorbing, nonreacting solute; diffusion of a stoichiometrically reacting solute; and diffusion of a catalytically reacting solute. A noninteracting solute was predicted to penetrate biofilms of up to 1 mm in thickness relatively quickly, within a matter of seconds or minutes. In the case of a solute that does not sorb or react in the biofilm, therefore, the diffusion barrier is not nearly large enough to account for the reduced susceptibility of biofilms to antibiotics. Reversible and irreversible sorption retards antibiotic penetration. On the basis of data available in the literature at this point, the extent of retardation of antibiotic diffusion due to sorption does not appear to be sufficient to account for reduced biofilm susceptibility. A catalytic (e.g., enzymatic) reaction, provided it is sufficiently rapid, can lead to severe antibiotic penetration failure. For example, calculation of beta-lactam penetration indicated that the reaction-diffusion mechanism may be a viable explanation for failure of certain of these agents to control biofilm infections. The theory presented in this study provides a framework for the design and analysis of experiments to test these mechanisms of reduced biofilm susceptibility to antibiotics.