gebhart/patrepeval huggingface dataset:
A mutant neomycin phosphotransferase II gene reduces the resistance of transformants to antibiotic selection pressure. (1990)

The neo (neomycin-resistance) gene of transposon Tn5 encodes the enzyme neomycin phosphotransferase II (EC 2.7.1.95), which confers resistance to various aminoglycoside antibiotics, including kanamycin and G418. The gene is widely used as a selectable marker in the transformation of organisms as diverse as bacteria, yeast, plants, and animals. We found a mutation that involves a glutamic to aspartic acid conversion at residue 182 in the protein encoded by the chimeric neomycin phosphotransferase II genes of several commonly used transformation vectors. The mutation substantially reduces phosphotransferase activity but does not appear to affect the stability of the neomycin phosphotransferase II mRNA or protein. Plants and bacteria transformed with the mutant gene are less resistant to antibiotics than those transformed with the normal gene. A simple restriction endonuclease digestion distinguishes between the mutant and the normal gene.
Recognizing objects in adversarial clutter: breaking a visual CAPTCHA (2003)

In this paper we explore object recognition in clutter. We test our object recognition techniques on Gimpy and EZ-Gimpy, examples of visual CAPTCHAs. A CAPTCHA ("Completely Automated Public Turing test to Tell Computers and Humans Apart") is a program that can generate and grade tests that most humans can pass, yet current computer programs can't pass. EZ-Gimpy, currently used by Yahoo, and Gimpy are CAPTCHAs based on word recognition in the presence of clutter. These CAPTCHAs provide excellent test sets since the clutter they contain is adversarial; it is designed to confuse computer programs. We have developed efficient methods based on shape context matching that can identify the word in an EZ-Gimpy image with a success rate of 92%, and the requisite 3 words in a Gimpy image 33% of the time. The problem of identifying words in such severe clutter provides valuable insight into the more general problem of object recognition in scenes. The methods that we present are instances of a framework designed to tackle this general problem.
Sulfur doped indium phosphide on silicon substrate grown by epitaxial lateral overgrowth (2005)

The epitaxial lateral overgrowth (ELOG) of sulfur doped InP from ring shaped openings on SiN/sub x/ masked InP/Si substrate in low pressure hydride vapor phase epitaxy system was investigated. Octahedral shaped ELOG InP templates with smooth surface were formed and studied by cathodoluminescence (CL). High energy transition at 825 nm (1.52 eV) due to the band filling effect caused by high concentration sulfur atoms trapped in threading dislocations was observed in spectra at 80 K. The band edge transition at 875 nm (1.42 eV) in CL spectra has no red shift caused by thermal strain. As observed in panchromatic image, defect free area was surrounded by high density threading dislocations that were pined by sulfur atoms due to impurity hardening. The quality of the ELOG InP templates is promising for the integration of photonic active layer on Si substrate.
Effect of minimal amounts of thymidine on activity of trimethoprim-sulfamethoxazole against Staphylococcus epidermidis (1987)

The antibacterial activity of trimethoprim-sulfamethoxazole against 99 strains of Staphylococcus epidermidis was tested on media known to be low in thymidine content, as determined by screening with Streptococcus faecalis. Eighty-one percent of the isolates were susceptible by agar dilution. Trimethoprim-sulfamethoxazole was bactericidal against two strains of S. epidermidis when thymidine phosphorylase was added to the medium, indicating utilization of minimal amounts of thymidine that were undetected by screening. Because bacteria vary in their utilization of thymidine and body tissues vary in thymidine content, in vitro susceptibility tests may not correlate with in vivo bactericidal activity.
Specific cytotoxicity against autologous tumour and proliferative responses of human lymphocytes grown in interleukin 2 (1982)

Peripheral blood lymphocytes of cancer patients were sensitized in vitro to autologous tumour cells in mixed lymphocyte-tumour culture (MLTC). Blast cells were isolated on discontinuous Percoll gradients from MLTC which showed significant stimulation of [3H]-thymidine incorporation. Cultured T cells (CTC) were derived from these blasts by growth in conditioned medium containing interleukin-2 (IL-2) and maintained for up to 51 days by repeated feeding with IL-2 and in some cases by addition of irradiated allogeneic blood mononuclear cells as "fillers". These cultures showed specific cytotoxic reactivity against autologous tumour and in only a few cases was natural killing (NK) of K562 cells apparent. Restimulation of CTC with tumour was measured in primed lymphocyte test (PLT). Increased uptake of [3H]-thymidine was found upon stimulation by autologous tumour and allogeneic tumour of the same site and histology but there was no response to non-related tumours or to a panel of allogeneic lymphocytes. No sensitization to autologous HLA-D/DR could be detected by restimulation or cytotoxicity against monocytes in the majority of cases. These data suggest that, by careful selection of sensitised blasts from MLTC, it is possible to obtain CTC with both helper (proliferative) and cytotoxic T cells and that such CTC have specific reactivity against tumour cells. These cellular reagents will be useful in defining the antigenicity of human neoplasms and possibly in therapy.
Current status of pig liver xenotransplantation (2015)

The shortage of organs from deceased human donors is a major problem limiting the number of organs transplanted each year and results in the death of thousands of patients on the waiting list. Pigs are currently the preferred species for clinical organ xenotransplantation. Progress in genetically-engineered (GE) pig liver xenotransplantation increased graft and recipient survival from hours with unmodified pig livers to up to 9 days with normal to near-normal liver function. Deletion of genes such as GGTA1 (Gal-knockout pigs) or adding genes such as human complement regulatory proteins (hCD55, hCD46 expressing pigs) enabled hyperacute rejection to be overcome. Although survival up to 9 days was recorded, extended pig graft survival was not achieved due to lethal thrombocytopenia. The current status of GE pig liver xenotransplantation with world experience, potential factors causing thrombocytopenia, new targets on pig endothelial cells, and novel GE pigs with more genes deletion to avoid remaining antibody response, such as beta1,4-N-acetyl galactosaminyl transferase 2 (β4GalNT2), are discussed.
The three-dimensional organization of collagen fibrils in the human cornea and sclera. (1991)

The organization of collagen fibrils in the human cornea and sclera was studied by scanning electron microscopy, after digestion of cellular elements by sodium hydroxide, and by conventional transmission electron microscopy. The collagen fibrils in the cornea had a uniform diameter of about 25 nm. In Bowman's layer, individual collagen fibrils were interwoven densely to form a felt-like sheet. In the stroma, most of the collagen fibrils ran abreast in lamellae, with varying widths and thickness. These lamellae were arranged basically parallel to the corneal surface but often communicated with those of adjacent layers by interchanging their fibrils. In the innermost stromal region adjacent to Descemet's membrane, collagen fibrils were oriented in various directions and interlaced, forming loose fibrillar networks. The sclera, however, was composed of collagen fibrils with various diameters ranging from 25-230 nm. Although these collagen fibrils formed bundles, they were not parallel but were entangled in individual bundles. These collagen bundles varied in width and thickness, often gave off branches, and intertwined with each other.
A synthetic amphiphilic helical docosapeptide with the surface properties of plasma apolipoprotein A-I (1979)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA synthetic amphiphilic helical docosapeptide with the surface properties of plasma apolipoprotein A-IDaikichi Fukushima, Josh P. Kupferberg, Shinji Yokoyama, Daniel J. Kroon, E. T. Kaiser, and F. J. KezdyCite this: J. Am. Chem. Soc. 1979, 101, 13, 3703–3704Publication Date (Print):June 1, 1979Publication History Published online1 May 2002Published inissue 1 June 1979https://pubs.acs.org/doi/10.1021/ja00507a068https://doi.org/10.1021/ja00507a068research-articleACS PublicationsRequest reuse permissionsArticle Views75Altmetric-Citations64LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Effect of a Dipeptidyl Peptidase-IV Inhibitor, Des-Fluoro-Sitagliptin, on Neointimal Formation after Balloon Injury in Rats (2012)

Sitagliptin has protective properties against restenosis after carotid injury and therapeutic implications for treating macrovascular complications of diabetes.
The pharmacokinetics of sodium cromoglycate in man after intravenous and inhalation administration. (1986)

The pharmacokinetics of sodium cromoglycate in four healthy volunteers after slow intravenous infusion have been evaluated following measurement of plasma concentrations by radioimmunoassay. The results confirm earlier findings that sodium cromoglycate is rapidly eliminated from the body and that the data can be fitted to a two compartment open model. The pharmacokinetic parameters derived from the intravenous administration were used to evaluate the pharmacokinetics after inhalation administration via the Spinhaler. A model for absorption from the lungs is described which involves absorption at two different rates; this gives a better fit to the observed data than a single absorption rate. A fast absorption rate constant with a mean value of 0.54 min-1 and a slower rate constant with a mean value of 0.0097 min-1 were found. Of a mean total of 2.84 mg absorbed from a 20 mg inhaled dose, 0.68 +/- 0.15 (s.e. mean) mg were absorbed at the fast rate and 2.17 +/- 0.37 mg at the slower rate. These rates probably reflect absorption from different sites within the lungs. The results may have important implications for interpretation of clinical findings.
Microvascular Dysfunction in Chronic Total Coronary Occlusions (2001)

Microvascular dysfunction was observed in 55% of TCOs, independent of the impairment of regional myocardial function. Dysfunction was observed more often in patients with diabetes and hypertension. Neither CFVR or FFR alone is appropriate for assessing angioplasty results in patients with a TCO; CFVR should be combined with FFR to differentiate microvascular dysfunction from residual coronary stenosis or diffuse disease.
Review of the Chemistry of Cyclopropene Compounds (1964)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTReview of the Chemistry of Cyclopropene CompoundsFairie Lyn Carter and Vernon L. FramptonCite this: Chem. Rev. 1964, 64, 5, 497–525Publication Date (Print):October 1, 1964Publication History Published online1 May 2002Published inissue 1 October 1964https://pubs.acs.org/doi/10.1021/cr60231a001https://doi.org/10.1021/cr60231a001research-articleACS PublicationsRequest reuse permissionsArticle Views1557Altmetric-Citations132LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Type-Assisted Dynamic Buffer Overflow Detection (2002)

Programs written in C are inherently vulnerable to buffer overflow attacks. Functions are frequently passed pointers as parameters without any hint of their sizes. Since their sizes are unknown, most run time buffer overflow detection techniques instead rely on signatures of known attacks or loosely estimate the range of the referenced buffers. Although they are effective in detecting most attacks, they are not infallible. In this paper we present a buffer overflow detection technique that range checks the referenced buffers at run time. Our solution is a small extension to a generic C compiler that augments executable files with type information of automatic buffers (local variables and parameters of functions) and static buffers (global variables in data / bss section) in order to detect the actual occurrence of buffer overflow. It also maintains the sizes of allocated heap buffers. A simple implementation is described, with which we currently protect vulnerable copy functions in the C library.
[Histopathologic evaluation of death certificates in Soria in 1985]. (1991)

The aim of this paper is to evaluate the quality of the Death Certificates by means of the Death Statistics Bulletins, in their NEOPLASIC aspect in the year 1985 in the Province of Soria, determining the histopathologic confirmation of the deaths by means of the neoplasic patients' records in the two existing Pathology Services. An overall histologic verification of 80.76% is observed in the cases with an I.C. of +/- 4.79. In the case of BREAST, HEMATOLOGIC, OROPHARYNX, ENDOMETRIUM, ESOPHAGUS, OVARIAN, LARYNX and VULVA tumors, it is 100%. Whereas it is 14.3% in HEPATIC Tumors. Of the total of deaths registered in said year, the percentage of deaths caused by malignant neoplasias is over 26%, more than a fourth of which were Gastric. The preparation of the Death Certificates should be modified so that they can be objectively evaluated epidemiologically without bias or mistakes.
A monoclonal antibody inhibits adhesion to fibronectin and vitronectin of a colon carcinoma cell line and recognizes the integrins alpha v beta 3, alpha v beta 5, and alpha v beta 6. (1994)

Using whole viable human colon carcinoma HT29 cells as immunogen, we produced a monoclonal antibody (mAb) termed 69-6-5. The antibody was functionally selected on its anti-cell-spreading activity. By immunoprecipitation of surface radiolabeled cell lysates from HT29-D4 cells (an HT29 cell clone), mAb 69-6-5 recognized a molecular complex resembling integrin heterodimers. Sequential immunodepletions with mAb to the integrin alpha v subunit demonstrated that this complex was composed of alpha v-containing integrins. Accordingly, mAb 69-6-5 reacted with integrin alpha v beta 3 immunopurified from melanoma cells and integrins alpha v beta 5 and alpha v beta 6 immunopurified from pancreatic carcinoma cells. In cell adhesion assays, the 69-6-5 mAb was able to inhibit strongly in a dose-dependent manner arginine-glycine-aspartic acid-mediated adhesion of HT29-D4 cells to vitronectin, fibronectin, or ProNectin F but not to laminin or collagen. Immunoprecipitations with beta chain-specific antisera indicated that these cells express integrins alpha v beta 5 (receptor for vitronectin) and alpha v beta 6 (receptor for fibronectin) but neither alpha v beta 1 nor alpha v beta 3. In summary, these results indicated that mAb 69-6-5 reacts with several alpha v integrins and that it can effectively interfere with the adhesive functions of at least alpha v beta 5 and alpha v beta 6, which represent the major receptors on HT29-D4 cells responsible for their adhesion on vitronectin and fibronectin.
Challenges Associated with Post-Deployment Screening for Mild Traumatic Brain Injury in Military Personnel (2009)

There is ongoing debate regarding the epidemiology of mild traumatic brain injury (MTBI) in military personnel. Accurate and timely estimates of the incidence of brain injury and the prevalence of long-term problems associated with brain injuries among active duty service members and veterans are essential for (a) operational planning, and (b) to allocate sufficient resources for rehabilitation and ongoing services and supports. The purpose of this article is to discuss challenges associated with post-deployment screening for MTBI. Multiple screening methods have been used in military, Veterans Affairs, and independent studies, which complicate cross-study comparisons of the resulting epidemiological data. We believe that post-deployment screening is important and necessary--but no screening methodology will be flawless, and false positives and false negatives are inevitable. Additional research is necessary to refine the sequential screening methodology, with the goal of minimizing false negatives during initial post-deployment screening and minimizing false positives during follow-up evaluations.
New Insights on Human Polyomavirus JC and Pathogenesis of Progressive Multifocal Leukoencephalopathy (2013)

John Cunningham virus (JCV) is a member of the Polyomaviridae family. It was first isolated from the brain of a patient with Hodgkin disease in 1971, and since then the etiological agent of the progressive multifocal leukoencephalopathy (PML) was considered. Until the human immunodeficiency virus (HIV) pandemic, PML was rare: in fact HIV-induced immunodeficiency is the most common predisposing factor accounting for 85% of all instances of PML. This data led to intense research on JCV infection and resulted in better understanding of epidemiology and clinic-pathologic spectrum. Recently, cases of PML have been observed after the introduction of monoclonal antibodies, such as natalizumab, rituximab, efalizumab, and infliximab, in the treatment of autoimmune disease, underlining the important role of host immunity in PML pathogenesis. In this review current understanding of the JCV infection and the new findings relating to the pathogenesis of PML has been comprehensively revised, focusing our attention on the interaction between the cellular and viral molecular pathways implicated in the JCV infection and the modulating role of host immune surveillance in the viral reactivation from a latent state.
XREF coupling: capacitive coupling error checker (2002)

Capacitive coupling among critical nodes in a CMOS VLSI circuit can cause disastrous effects on the logical operation of the circuit. At present, the only simulation method that can accurately detect global capacitive coupling errors is the classical circuit simulation, which, due to its limited capacity, is not practical to apply to the entire design. A pattern-independent circuit verification tool, XREF, is presented which can detect and report all possible failures in a design due to capacitive coupling effects.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Joint multipath-Doppler diversity in mobile wireless communications (1999)

We introduce a new approach for achieving diversity in spread-spectrum communications over fast-fading multipath channels. The RAKE receiver used in existing systems suffers from significant performance degradation due to the rapid channel variations encountered under fast fading. We show that the Doppler spread induced by temporal channel variations in fact provides another means for diversity that can be further exploited to combat fading. We develop the concept of Doppler diversity and propose a framework that exploits joint multipath-Doppler diversity in an optimal fashion. Performance analysis shows that even the relatively small Doppler spreads encountered in practice can be leveraged into significant diversity gains via our approach. The framework is applicable in several mobile wireless multiple access systems and can provide substantial performance improvement over existing systems.
Generation of siRNA Nanosheets for Efficient RNA Interference (2016)

After the discovery of small interference RNA (siRNA), nanostructured siRNA delivery systems have been introduced to achieve an efficient regulation of the target gene expression. Here we report a new siRNA-generating two dimensional nanostructure in a formation of nanosized sheet. Inspired by tunable mechanical and functional properties of the previously reported RNA membrane, siRNA nanosized sheets (siRNA-NS) with multiple Dicer cleavage sites were prepared. The siRNA-NS has two dimensional structure, providing a large surface area for Dicer to cleave the siRNA-NS for the generation of functional siRNAs. Furthermore, downregulation of the cellular target gene expression was achieved by delivery of siRNA-NS without chemical modification of RNA strands or conjugation to other substances.
Cone Channel Optics (1985)

Abstract An expression is derived for the solid angle of acceptance for any point in the mouth of a condensing cone optic.
Modeling of reflectometric and ellipsometric spectra from the skin in the terahertz and submillimeter waves region (2011)

The human skin is modeled as a stack of homogeneous layers in the terahertz and submillimeter waves regions with some anisotropy due to the helical sweat glands and other elongated entities. A dielectric model for the skin is presented, valid for a wider frequency range (up to the terahertz region) taking into account the dispersive nature of the effective conductivity. Polarized reflectivity and generalized ellipsometric parameters are calculated versus angle and wavelength. Recent studies have claimed that the helical sweat ducts act as an array of low-Q helical antennae and are dominant in shaping the spectral response in the sub-terahertz region. We found that water absorption, dispersion and multiple interference effects play the major role in shaping the spectrum without the need for the assumption of the sweat ducts acting as low-Q helical antennae. High sensitivities to the water content are found particularly in the ellipsometric parameters at large incidence angles. Hence a new methodology is proposed to detect skin cancer using variable angle ellipsometry or polarized reflectometry. The parameter found with the highest sensitivity to water content is cos Δ(pp) with Δ(pp) being the phase of the on-diagonal reflection matrix ratio between p-to-p polarization.