gebhart/patrepeval huggingface dataset:
Processing of the T-DNA of Agrobacterium tumefaciens generates border nicks and linear, single-stranded T-DNA (1987)

Transfer and integration of a defined region (T-DNA) of the tumor-inducing (Ti) plasmid of Agrobacterium tumefaciens is essential for tumor formation. We used a physical assay to study structural changes induced in Agrobacterium T-DNA by cocultivation with plant cells. We show that nicks are introduced at unique, identical locations in each of the 24-base-pair imperfect direct repeats which flank the T-DNA and present evidence that a linear, single-stranded molecule is generated. We propose that these changes result from processing of the T-DNA for transfer and that they occur by a mechanism similar to DNA processing during conjugative DNA transfer between bacteria.
Combining Patterned Self‐Assembled Monolayers of Alkanethiolates on Gold with Anisotropic Etching of Silicon to Generate Controlled Surface Morphologies (1995)

Self‐assembled monolayers (SAMs) of hexadecanethiolate were patterned onto gold films supported on titanium‐primed silicon wafers using microcontact printing (μCP). Wet etching of the gold, and subsequently of the silicon, using three systems of resists based on these patterned SAMs, denoted by the shorthand labels Au/SAM, Ni/Au/SAM, and Au/SAM/polymer, produced features in silicon having dimensions in the 1 to 10 μm scale. In the Au/SAM system, the SAM acted as a resist to protect gold from etching by , and the resulting, patterned gold protected silicon from etching by (25% by volume) at 60°C. In the Ni/Au/SAM system, the pattern in the gold layer was transferred to an underlying nickel layer by etching in a bath consisting of conc , 30% , conc , and 30% aqueous solution of (5:5:1:4 by volume) at 35–40°C; in turn, the nickel acted as a resist to protect the silicon from etching. In the Au/SAM/polymer, a prepolymer of epoxy resin or polyurethane was self‐assembled onto hydrophilic SAMs on the surface that was patterned into regions of different interfacial free‐energy and wettability; after curing, the polymer served as the resist during etching gold by aqua regia, and etching silicon by . All three resists were compatible with etchants for silicon, and they masked the underlying silicon effectively.
Bottom-up histogenesis of colorectal adenomas: origin in the monocryptal adenoma and initial expansion by crypt fission. (2003)

The adenoma:carcinoma sequence is well established. Understanding the molecular pathology of the adenoma is therefore important. There is great controversy within the field. The Vogelstein group champions the "top-down" theory (colorectal adenomas arise and grow across the mucosal surface and down into the crypts), whereas other studies, including our own, propose "bottom-up" spread. Serial sections of 40 small (<3 mm) sporadic colorectal adenomas were stained with H&E, MIB-1, and for beta-catenin. 10 early adenomas were Feulgen-stained and microdissected. We also examined the flat mucosa of three patients who had undergone colectomies for familial adenomatous polyposis (FAP) and specimens from a XO/XY individual with FAP, the latter using in situ hybridization for the Y chromosome. In the earliest sporadic adenomas, there were crypts entirely filled with adenomatous epithelium, which showed proliferative activity and nuclear localization of beta-catenin. There was a sharp cutoff between crypt epithelial cells showing nuclear beta-catenin and surface cells with membrane staining. In slightly larger lesions, adenomatous spread from above was seen. Microdissected adenomas showed multiple fission events, with proliferation distributed equally throughout. In FAP tissue, numerous isolated monocryptal adenomas, which were clonal in origin, were seen. Examination of adenomas in the XO/XY individual showed no instances of XY or XO adenomatous epithelium growing down into crypts of the other genotype. Both sporadic and FAP adenomas start as a unicryptal adenomas and grow initially by crypt fission--a bottom-up pattern. Later, in sporadic adenomas, there is evidence of growth down into adjacent crypts (top-down).
Polymeric Scavenger Reagents in Organic Synthesis (2001)

Recent advances in polymeric supported reagents have led to the development of a new synthetic technique. The use of polymeric supports in solid phase synthesis has led to the design and synthesis of ionic and covalent polymeric scavengers. In this Microreview, we discuss the concept of this strategy and comment on the efficiency and versatility of this new purification procedure.
Normal cardiovascular development in mice deficient for 16 genes in 550 kb of the velocardiofacial/ DiGeorge syndrome region (2000)

Hemizygous interstitial deletions in human chromosome 22q11 are associated with velocardiofacial syndrome and DiGeorge syndrome and lead to multiple congenital abnormalities, including cardiovascular defects. The gene(s) responsible for these disorders is thought to reside in a 1.5-Mb region of 22q11 in which 27 genes have been identified. We have used Cre-mediated recombination of LoxP sites in embryonic stem cells and mice to generate a 550-kb deletion encompassing 16 of these genes in the corresponding region on mouse chromosome 16. Mice heterozygous for this deletion are normal and do not exhibit cardiovascular abnormalities. Because mice with a larger deletion on mouse chromosome 16 do have heart defects, the results allow us to exclude these 16 genes as being solely, or in combination among themselves, responsible for the cardiovascular abnormalities in velocardiofacial/DiGeorge syndrome. We also generated mice with a duplication of the 16 genes that may help dissect the genetic basis of "cat eye" and derivative 22 syndromes that are characterized by extra copies of portions of 22q11, including these 16 genes. We also describe a strategy for selecting cell lines with defined chromosomal rearrangements. The method is based on reconstitution of a dominant selection marker after Cre-mediated recombination of LoxP sites. Therefore it should be widely applicable to many cell lines.
Initiation of replication of the human hepatitis delta virus genome from cloned DNA: role of delta antigen (1989)

Beginning with three partial cDNA clones of the RNA genome of human hepatitis delta virus (HDV), we assembled the complete 1,679-base sequence on a single molecule and then inserted a trimer of this into plasmid pSLV, a simian virus 40-based eucaryotic expression vector. This construct was used to transfect both monkey kidney (COS7) and human hepatocellular carcinoma (HuH7) cell lines. In this way we obtained replication of the HDV RNA genome and the appearance, in the nucleoli, of the delta antigen, the only known virus-coded protein. This proved both that the HDV genome could replicate in nonliver as well as liver cells and that there was no requirement for the presence of hepatitis B virus sequences or proteins. When the pSVL construct was made with a dimer of an HDV sequence with a 2-base-pair deletion in the open reading frame, genome replication was reduced at least 40-fold. However, when we cotransfected with a plasmid that expressed the correct delta antigen, the mutated dimer achieved a level of genome replication comparable to that of the nonmutated sequence. We thus conclude that the delta antigen can act in trans and is essential for replication of the HDV genome.
Microencapsulation of probiotic bacteria: technology and potential applications. (2002)

In the recent past, there has been an explosion of probiotic health-based products. Many reports indicated that there is poor survival of probiotic bacteria in these products. Further, the survival of these bacteria in the human gastro-intestinal system is questionable. Providing probiotic living cells with a physical barrier against adverse environmental conditions is therefore an approach currently receiving considerable interest. The technology of micro-encapsulation of probiotic bacterial cells evolved from the immobilised cell culture technology used in the biotechnological industry. Several methods of micro-encapsulation of probiotic bacteria have been reported and include spray drying, extrusion, emulsion and phase separation. None of these reported methods however, has resulted in the large numbers of shelf-stable, viable probiotic bacterial cells necessary for use in industry for development of new probiotic products. The most commonly reported micro-encapsulation procedure is based on the calcium-alginate gel capsule formation. Kappa-carrageenan, gellan gum, gelatin and starch are also used as excipients for the micro-encapsulation of probiotic bacteria. The currently available equipment for micro-encapsulation is not able to generate large quantities of uniform sized micro or nano capsules. There is a need to design and develop equipment that will be able to generate precise and uniform micro or nano capsules in large quantities for industrial applications. The reported food vehicles for delivery of encapsulated probiotic bacteria are yoghurt, cheese, ice cream and mayonnaise. Studies need to be done on the application of micro-encapsulation of probiotic bacteria in other food systems. The number of probiotic supplements will increase in the future. More studies, however, need to be conducted on the efficacy of micro-encapsulation to deliver probiotic bacteria and their controlled or targeted release in the gastrointestinal tract.
The influence of cotinine on the non-small-cell lung cancer line A549. (2009)

The aim of this investigation was to determine the influence of cotinine on the non-small-cell lung cancer line A549. The material for the study was the A549 cell line. The cells were subjected to 24-h incubation with cotinine at doses of 18 and 36 ng/ml. Control cells were incubated under analogous conditions without the addition of cotinine. Cell viability was determined and the cells were Mayer hematoxylin stained, embedded in epon, and observed under an electron microscope. A fluorescent method was used to evaluate F-actin. Cotinine's action resulted in alteration of the cytoskeleton, with changes in the organization of F-actin. Also observed was A549 cell death, presumably due to the activation of apoptotic and mitotic catastrophe pathways. Moreover, the results at the ultrastructural level suggest that cotinine influences not only the nucleus and cell shape by acting on the actin cytoskeleton, but also plays a crucial role in changes which include the remaining cellular organelles. Until now, research has been focused on determining the action of constituents of cigarette smoke, mainly nicotine. From this point of view, studies on cotinine seem justified. Results of the study allow us to suppose that cotinine, through F-actin, can influence the size and shape of non-small-cell lung cancer cells. There are some suggestions that cells of the A549 cell line can undergo death through apoptotic and mitotic catastrophe pathways as a result of cotinine's action.
Wnt7A is a putative prognostic and chemosensitivity marker in human malignant pleural mesothelioma (2015)

Malignant pleural mesothelioma (MPM) is a highly aggressive tumor that has a poor prognosis, limited treatment options, and a worldwide incidence that is expected to increase in the next decade. We evaluated Wnt7A expression in 50 surgically resected tumor specimens using quantitative PCR. The expression values, were assessed by clinicopathological factors and K-M and Cox's regression with OS. The mean level of Wnt7A expression had a significant correlation with International Mesothelioma Interest Group (IMIG) stage (P<0.034), gender, smoking history and ethnicity, respectively (P=0.020, P=0.014, P=0.039). In the univariate analysis, low Wnt7A expression was a significant negative factor for overall survival (P=0.043, HR=2.30). However, multivariate Cox's regression revealed no significant factors for overall survival (low Wnt7A: P=0.051, HR=2.283; non-epithelioid subtype: P=0.050, HR=2.898). In patients with epithelioid tumors, those with low Wnt7A expression had significantly worse prognosis (P=0.019, HR=2.98). In patients with epithelioid tumors, females had significantly better prognosis than males (P=0.035). In patients who did not have neoadjuvant chemotherapy, prognosis was significantly more favorable for patients with high Wnt7A expression than for those with low Wnt7A expression (P=0.031). Among the patients with low Wnt7A-expressing tumors, those who received neoadjuvant chemotherapy had better prognosis than those who did not (P=0.024). The results of our study suggest that Wnt7A expression is a putative prognostic factor and a predictor of chemosensitivity.
Human Eukaryotic Release Factor 3a Depletion Causes Cell Cycle Arrest at G1 Phase through Inhibition of the mTOR Pathway (2007)

Eukaryotic release factor 3 (eRF3) is a GTPase associated with eRF1 in a complex that mediates translation termination in eukaryotes. Studies have related eRF3 with cell cycle regulation, cytoskeleton organization, and tumorigenesis. In mammals, two genes encode two distinct forms of eRF3, eRF3a and eRF3b, which differ in their N-terminal domains. eRF3a is the major factor acting in translation termination, and its expression level controls termination complex formation. Here, we investigate the role of eRF3a in cell cycle progression using short interfering RNAs and flow cytometry. We show that eRF3a depletion induces a G1 arrest and that eRF3a GTP-binding activity, but not the eRF3a N-terminal domain, is required to restore G1-to-S-phase progression. We also show that eRF3a depletion decreases the global translation rate and reduces the polysome charge of mRNA. Finally, we show that two substrates of the mammalian TOR (mTOR) kinase, 4E-BP1 and protein kinase S6K1, are hypophosphorylated in eRF3a-depleted cells. These results strongly suggest that the G1 arrest and the decrease in translation induced by eRF3a depletion are due to the inhibition of mTOR activity and hence that eRF3a belongs to the regulatory pathway of mTOR activity.
Efficient model-based 3D tracking of hand articulations using Kinect (2011)

We present a novel solution to the problem of recovering and tracking the 3D position, orientation and full articulation of a human hand from markerless visual observations obtained by a Kinect sensor. We treat this as an optimization problem, seeking for the hand model parameters that minimize the discrepancy between the appearance and 3D structure of hypothesized instances of a hand model and actual hand observations. This optimization problem is effectively solved using a variant of Particle Swarm Optimization (PSO). The proposed method does not require special markers and/or a complex image acquisition setup. Being model based, it provides continuous solutions to the problem of tracking hand articulations. Extensive experiments with a prototype GPU-based implementation of the proposed method demonstrate that accurate and robust 3D tracking of hand articulations can be achieved in near real-time (15Hz).
Origin and evolution of pathogenic coronaviruses (2018)

Severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV) are two highly transmissible and pathogenic viruses that emerged in humans at the beginning of the 21st century. Both viruses likely originated in bats, and genetically diverse coronaviruses that are related to SARS-CoV and MERS-CoV were discovered in bats worldwide. In this Review, we summarize the current knowledge on the origin and evolution of these two pathogenic coronaviruses and discuss their receptor usage; we also highlight the diversity and potential of spillover of bat-borne coronaviruses, as evidenced by the recent spillover of swine acute diarrhoea syndrome coronavirus (SADS-CoV) to pigs.
Expression of a translationally regulated, dominant-negative CCAAT/enhancer-binding protein beta isoform and up-regulation of the eukaryotic translation initiation factor 2alpha are correlated with neoplastic transformation of mammary epithelial cells. (1996)

A translationally regulated, dominant-negative isoform of CCAAT/enhancer-binding protein beta is expressed in transplantable and primary mouse mammary tumors of different etiologies but is not expressed in preneoplastic mammary hyperplasias or in primary prostate, lung, lens, ovary or lymphoid tumors. The eukaryotic initiation factor 2alpha protein is also expressed at significantly higher levels (69.8 +/- 7.2%) in these mammary tumors compared with normal and hyperplastic tissues. Thus, misregulation of eukaryotic initiation factor 2alpha may promote the expression of a dominant-negative CCAAT/enhancer-binding protein beta isoform, which may inhibit terminal differentiation and facilitate uncontrolled proliferation of mammary epithelial cells.
DNA-Templated Polymerization of Side-Chain-Functionalized Peptide Nucleic Acid Aldehydes (2008)

The DNA-templated polymerization of synthetic building blocks provides a potential route to the laboratory evolution of sequence-defined polymers with structures and properties not necessarily limited to those of natural biopolymers. We previously reported the efficient and sequence-specific DNA-templated polymerization of peptide nucleic acid (PNA) aldehydes. Here, we report the enzyme-free, DNA-templated polymerization of side-chain-functionalized PNA tetramer and pentamer aldehydes. We observed that polymerization of tetramer and pentamer PNA building blocks with a single lysine-based side chain at various positions in the building block could proceed efficiently and sequence specifically. In addition, DNA-templated polymerization also proceeded efficiently and in a sequence-specific manner with pentamer PNA aldehydes containing two or three lysine side chains in a single building block to generate more densely functionalized polymers. To further our understanding of side-chain compatibility and expand the capabilities of this system, we also examined the polymerization efficiencies of 20 pentamer building blocks each containing one of five different side-chain groups and four different side-chain regio- and stereochemistries. Polymerization reactions were efficient for all five different side-chain groups and for three of the four combinations of side-chain regio- and stereochemistries. Differences in the efficiency and initial rate of polymerization correlate with the apparent melting temperature of each building block, which is dependent on side-chain regio- and stereochemistry but relatively insensitive to side-chain structure among the substrates tested. Our findings represent a significant step toward the evolution of sequence-defined synthetic polymers and also demonstrate that enzyme-free nucleic acid-templated polymerization can occur efficiently using substrates with a wide range of side-chain structures, functionalization positions within each building block, and functionalization densities.
Dorsalization of the neural tube by the non-neural ectoderm (1995)

The patterning of cell types along the dorsoventral axis of the spinal cord requires a complex set of inductive signals. While the chordamesoderm is a well-known source of ventralizing signals, relatively little is known about the cues that induce dorsal cell types, including neural crest. Here, we demonstrate that juxtaposition of the non-neural and neural ectoderm is sufficient to induce the expression of dorsal markers, Wnt-1, Wnt-3a and Slug, as well as the formation of neural crest cells. In addition, the competence of neural plate to express Wnt-1 and Wnt-3a appears to be stage dependent, occurring only when neural tissue is taken from stage 8-10 embryos but not from stage 4 embryos, regardless of the age of the non-neural ectoderm. In contrast to the induction of Wnt gene expression, neural crest cell formation and Slug expression can be induced when either stage 4 or stage 8-10 neural plates are placed in contact with the non-neural ectoderm. These data suggest that the non-neural ectoderm provides a signal (or signals) that specifies dorsal cell types within the neural tube, and that the response is dependent on the competence of the neural tissue.
<title>Issues and solutions for authenticating MPEG video</title> (1999)

Video authentication techniques are used to prove the originality of received video content and to detect malicious tampering. Existing authentication techniques protect every single bit of the video content and do not allow any form of manipulation. In real applications, this may not be practical. In several situations, compressed videos need to be further processed to accommodate various application requirements. Examples include bitrate scaling, transcoding, and frame rate conversion. The concept of asking each intermediate processing stage to add authentication codes is flawed in practical cases. In this paper, we extend our prior work on JPEG- surviving image authentication techniques to video. We first discuss issues of authenticating MPEG videos under various transcoding situations, including dynamic rate shaping, requantization, frame type conversion, and re-encoding. Different situations pose different technical challenges in developing robust authentication techniques. In the second part of this paper, we propose a robust video authentication system which accepts some MPEG transcoding processes but is able to detect malicious manipulations. It is based on unique invariant properties of the transcoding processes. Digital signature techniques as well as public key methods are used in our robust video authentication system.
Depth-Map-Based Scene Analysis for Active Navigation in Virtual Angioscopy (2004)

This paper presents a new approach dealing with virtual exploratory navigation inside vascular structures. It is based on the notion of active vision in which only visual perception drives the motion of the virtual angioscope. The proposed fly-through approach does not require a premodeling of the volume dataset or an interactive control of the virtual sensor during the fly-through. Active navigation combines the on-line computation of the scene view and its analysis, to automatically define the three-dimensional sensor path. The navigation environment and the camera-like model are first sketched. The basic stages of the active navigation framework are then described: the virtual image computation (based on ray casting), the scene analysis process (using depth map), the navigation strategy, and the virtual path estimation. Experimental results obtained from phantom model and patient computed tomography data are finally reported.
Influenza virus RNA replication in vitro: synthesis of viral template RNAs and virion RNAs in the absence of an added primer (1988)

The two steps in influenza virus RNA replication are (i) the synthesis of template RNAs, i.e., full-length copies of the virion RNAs, and (ii) the copying of these template RNAs into new virion RNAs. We prepared nuclear extracts from infected HeLa cells that catalyzed both template RNA and virion RNA synthesis in vitro in the absence of an added primer. Antibody depletion experiments implicated nucleocapsid protein molecules not associated with nucleocapsids in template RNA synthesis for antitermination at the polyadenylation site used during viral mRNA synthesis. Experiments with the WSN influenza virus temperature-sensitive mutant ts56 containing a defect in the nucleocapsid protein proved that the nucleocapsid protein was indeed required for template RNA synthesis both in vivo and in vitro. Nuclear extracts prepared from mutant virus-infected cells synthesized template RNA at the permissive temperature but not at the nonpermissive temperature, whereas the synthesis of mRNA-size transcripts was not decreased at the nonpermissive temperature. Antibody depletion experiments showed that nucleocapsid protein molecules not associated with nucleocapsids were also required for the copying of template RNA into virion RNA. In contrast to the situation with the synthesis of transcripts complementary to virion RNA, no discrete termination product(s) were made during virion RNA synthesis in vitro in the absence of nucleocapsid protein molecules.