gebhart/patrepeval huggingface dataset:
Developmental and Stage-Dependent Expression of Melanin-Concentrating Hormone in Mammalian Germ Cells1 (1996)

Melanin-concentrating hormone (MCH) is a cyclic peptide predominantly expressed in the hypothalamus of mammals. This peptide modulates the stress response and regulates many goal-oriented behaviors in the rat brain. MCH mRNA and peptides generated from the precursor, namely MCH and neuropeptide (N) glutamic acid (E) isoleucine (I) amide (NEI), were also found in rodent peripheral tissues including those in adult testis. In the present study, we first examined the cellular distribution and content of MCH gene products and peptide in the testes of adult rats. Using reverse-transcription polymerase chain reaction with MCH gene primers and in situ hybridization with specific 33P-labeled oligoprobes, we characterized the MCH RNA species. Pro-MCH products were revealed through use of immunoperoxidase detection and an RIA with specific MCH and NEI antisera. Both MCH gene transcripts and MCH peptide were found within germ cells at the periphery of some of the seminiferous tubules of adult rats. We further investigated temporal expression of MCH in 7-microns sections of testes from adult rats and mice. MCH was predominantly found in nuclei of spermatogonia at stages II-IV of spermatogenesis and in nuclei of leptotene and zygotene spermatocytes (at stages IX- XIII). MCH was markedly absent in preleptotene spermatocytes at the stage VII-VIII, and MCH immunoreactivity was no longer detectable as spermatocytes underwent the pachytene step. MCH immunoreactivity was also found in some peritubular cells, mainly at stages II-IV. Finally, we studied MCH expression during puberty in the rat, in sterile mutant mice, and in one adult man. We found predominant staining with MCH antiserum over nuclei of immature germ cells as early as 10 days postpartum in the rat and further confirmed the absence of staining except for that in spermatogonia and early spermatocytes during rat postnatal development. MCH distribution was found to be similar in normal and sterile mutant mice, suggesting that MCH expression is not dependent upon the early steps of spermiogenesis. MCH immunoreactivity was found to be confined to the nuclei of spermatogonia and early spermatocytes in the adult man. Our results indicate that MCH is present predominantly within nuclei of spermatogonia and primary spermatocytes in three mammalian species and that its expression is under strong stage-specific and developmental regulation. This peptide may play a role during stem cell renewal and/or differentiation of early spermatocytes.
Synthesis and Applications of a New Poly(ethylene glycol) Derivative for the Crosslinking of Amines with Thiols (1995)

A heterobifunctional crosslinker was synthesized from a diamine derivative of poly(ethylene glycol) (PEG, average molecular weight 800 Da), with the functional groups 2-(pyridyldithio)propionyl (PDP) and N-hydroxysuccinimide ester (NHS). The crosslinker can be used for linkage of two different proteins for which a suitable protocol is presented, explified by crosslinking of two antibodies with 50% yield. In a second application the crosslinker is used to generate immunoliposomes. The NHS group was reacted with an aminolipid for liposome anchorage, and antibodies were bound to the PDP group via disulfide bonds. Loading of liposomes with antibodies was easily adjustable, even down to only a few per liposome. This crosslinker with its particular length appears especially suited for the flexible anchorage of biomembranes, opening new perspectives in membrane research as discussed.
Detection of Somatic TP53 Mutations in Tampons of Patients With High-Grade Serous Ovarian Cancer (2014)

In this pilot study, DNA derived from tumor was detected in the vaginas of 60% of patients with ovarian cancer with intact fallopian tubes. With further development, this approach may hold promise for the early detection of this deadly disease.
Scatter estimation for a digital radiographic system using convolution filtering (1987)

The use of a convolution-filtering method to estimate the scatter distribution in images acquired with a digital subtraction angiography (DSA) imaging system has been studied. Investigation of more than 175 convolution kernels applied to images of anthropomorphic head, chest, and pelvic phantoms using 15-, 25-, and 36-cm fields of view (digitized onto a 512 X 512 pixel image matrix) showed that two-dimensional exponential kernels with a full width at half maximum (FWHM) of 50-150 pixels best reproduced the scatter fields within these images with a root-mean-square percentage error from 4% to 8%. A two-dimensional exponential kernal with a FWHM of 75 pixels in each dimension applied to ten different anatomic presentations and fields of view, resulted in an average root-mean-square percentage error of 6.6% for the ten cases studied. The method should be implementable using an array of small lead beam stops placed in the field of only a single mask image and the above described convolution kernel applied to both mask and postopacification images. The mask beam-stop data are used to scale both mask and postopacification convolution-filtered images. This scaled, convolution-filtered image is then subtracted from the original image to produce a largely scatter-corrected image.
Co-occurring Genomic Alterations Define Major Subsets of KRAS -Mutant Lung Adenocarcinoma with Distinct Biology, Immune Profiles, and Therapeutic Vulnerabilities (2015)

Co-occurring genetic alterations in STK11/LKB1, TP53, and CDKN2A/B-the latter coupled with low TTF1 expression-define three major subgroups of KRAS-mutant lung adenocarcinoma with distinct biology, patterns of immune-system engagement, and therapeutic vulnerabilities.
A model for the separation of large DNA molecules by crossed field gel electrophoresis (1987)

The idea that large DNA molecules adopt a stretched conformation as they pass through gels suggests a simple mechanism for the separation of DNA by crossed field electrophoresis: at each change in field direction a DNA molecule takes off in the new direction of the field by a movement which is led by what was formerly its back end. The effect of this ratcheting motion is to subtract from the DNA molecule's forward movement, at each step, an amount which is proportional to its length. We find that this model explains most of the features of the separation, and we describe experiments, using a novel electrophoresis apparatus, which support the model. The apparatus turns the gel between two preset orientations in a uniform electric field at preset time intervals. This separation method has the practical advantage over some others that the DNA molecules follow straight tracks. A further advantage is that the parameters which determine the separation are readily predicted from the simple theory describing their motion.
Line Generalization by Waterlining And Medial-Axis Transformation. Successes and Issues in an Implementation of Perkal's Proposal (2000)

The hydrography of Cat Island, a rather small, albeit interesting feature in the Gulf of Mexico, is the subject of six generalizations executed with a procedure that replicates and extends Julian Perkal's proposal for an objective generalization. The automated procedure, based on the two operations known as waterlining and Medial-Axis Transformation, is shown to lead to results that should be similar to those achieved by a trained cartographer working with the traditional manual method. Three aspects of generalization are covered by the procedure: line simplification in general, and dropping and aggregation of features of simple configurations. As regards Perkal's original objective, this presentation proves that it can be achieved by a combination of waterlining operations. The Medial-Axis Transformation, a concept developed within Pattern Recognition, is proposed as the best choice for spanning Perkal's boundary zones. The six generalizations are offered as evidence that the method preserves the general shape of features for lower scale factors and yields simple and compact shapes for larger factors. However, two problems were encountered that suggest that the method still needs further development in order to maintain its fully automated character, Or, alternatively, the method may need to be interlaced with the occasional use of interactive aids. The first of those two problems is encountered in attempting to bridge boundary zones of complex configurations. The second problem arises from the specifications for an autonomous feature dropping procedure and with the need to invoke it. Both problems are considered in some depth.
Trans-skull ultrasound therapy: the feasibility of using image-derived skull thickness information to correct the phase distortion (1999)

Recent papers have shown that focused ultrasound therapy may be feasible in the brain through an intact human skull by using phased arrays to correct the phase distortion induced by the skull bone. The hypothesis of this study is that the required phase shifts for the phased array can be calculated from the skull shape and thickness provided by modern imaging techniques. The shape and thickness of a piece of human skull was traced from the serial images and used in a theoretical model to calculate the phase distribution for a phased array. A 76-element phased array was manufactured and used in the tests. The piece of skull and the transducer array were positioned in a waterbath, and the ultrasound field distributions were mapped with and without the phase correction. The image-derived phase correction produced a sharp focus through the skull. These results showed that ultrasound brain therapy may be executed completely noninvasively through an intact skull by using a phased array and the skull thickness information derived from MRI scans.
Metabolic Complementarity and Genomics of the Dual Bacterial Symbiosis of Sharpshooters (2006)

Mutualistic intracellular symbiosis between bacteria and insects is a widespread phenomenon that has contributed to the global success of insects. The symbionts, by provisioning nutrients lacking from diets, allow various insects to occupy or dominate ecological niches that might otherwise be unavailable. One such insect is the glassy-winged sharpshooter (Homalodisca coagulata), which feeds on xylem fluid, a diet exceptionally poor in organic nutrients. Phylogenetic studies based on rRNA have shown two types of bacterial symbionts to be coevolving with sharpshooters: the gamma-proteobacterium Baumannia cicadellinicola and the Bacteroidetes species Sulcia muelleri. We report here the sequencing and analysis of the 686,192-base pair genome of B. cicadellinicola and approximately 150 kilobase pairs of the small genome of S. muelleri, both isolated from H. coagulata. Our study, which to our knowledge is the first genomic analysis of an obligate symbiosis involving multiple partners, suggests striking complementarity in the biosynthetic capabilities of the two symbionts: B. cicadellinicola devotes a substantial portion of its genome to the biosynthesis of vitamins and cofactors required by animals and lacks most amino acid biosynthetic pathways, whereas S. muelleri apparently produces most or all of the essential amino acids needed by its host. This finding, along with other results of our genome analysis, suggests the existence of metabolic codependency among the two unrelated endosymbionts and their insect host. This dual symbiosis provides a model case for studying correlated genome evolution and genome reduction involving multiple organisms in an intimate, obligate mutualistic relationship. In addition, our analysis provides insight for the first time into the differences in symbionts between insects (e.g., aphids) that feed on phloem versus those like H. coagulata that feed on xylem. Finally, the genomes of these two symbionts provide potential targets for controlling plant pathogens such as Xylella fastidiosa, a major agroeconomic problem, for which H. coagulata and other sharpshooters serve as vectors of transmission.
Eight-Year Follow-Up Study of a Patient with Central Alveolar Hypoventilation Treated with Diaphragm Pacing (1998)

We had treated a 17-year-old girl with central alveolar hypoventilation with diaphragm pacing at home for the past 8 years. Nocturnal diaphragm pacing with an open tracheostomy was effective in maintaining an adequate ventilation after 4 months of undergoing training of the diaphragm on the pacemaker implantation. However, the diaphragm pacemaker failed to maintain it mostly in the presence of respiratory tract infection, when she was treated with intermittent positive-pressure ventilation. Pulse oximetry was used at home for monitoring the adequacy of respiratory support. We conclude that the respiratory assistance by the diaphragm pacemaker or the use of a mechanical ventilator as a backup was highly useful for the home care of a patient with central alveolar hypoventilation.
Balancing Thymocyte Adhesion and Motility:A Functional Linkage Between β1 Lntegrinsand The Motility Receptor RHAMM (2000)

Thymocyte differentiation involves several processes that occur in different anatomic sites within the thymus. Therefore, thymocytes must have the ability to respond to signals received from stromal cells and adopt either adhesive or motile behavior. We will discuss our data indicating human thymocytes use alpha4beta1 integrin, alpha5beta1 integrin and RHAMM to mediate these activities. Immature multinegative (MN; CD3-4-8-19-) thymocytes use alpha4beta1 and alpha5beta1 integrins to mediate weak and strong adhesion. This subset also uses alpha4beta1 integrin to mediate motility. As thymocytes differentiate, they begin to express and use RHAMM to mediate motility in conjunction with alpha4beta1 and alpha5beta1 integrins. Motile thymocytes use beta1 integrins to maintain weakly adhesive contacts with substrate to provide traction for locomoting cells, thus weak adhesion is a requirement of motile behavior. Hyaluronan (HA) is also required by thymocytes to mediate motility. HA binding to cell surface RHAMM redistributes intracellular RHAMM to the cell surface where it functions to mediate motility. We propose that the decision to maintain adhesive or motile behavior is based on the balance between low and high avidity binding conformations of beta1 integrins on thymocytes and that RHAMM:HA interactions decrease high avidity binding conformations of integrins pushing the balance toward motile behavior.
Neuronal and Glial Apoptosis after Traumatic Spinal Cord Injury (1997)

Cell death was examined by studying the spinal cords of rats subjected to traumatic insults of mild to moderate severity. Within minutes after mild weight drop impact (a 10 gm weight falling 6.25 mm), neurons in the immediate impact area showed a loss of cytoplasmic Nissl substances. Over the next 7 d, this lesion area expanded and cavitated. Terminal deoxynucleotidyl transferase (TdT)-mediated deoxyuridine triphosphate-biotin nick end labeling (TUNEL)-positive neurons were noted primarily restricted to the gross lesion area 4-24 hr after injury, with a maximum presence at 8 hr after injury. TUNEL-positive glia were present at all stages studied between 4 hr and 14 d, with a maximum presence within the lesion area 24 hr after injury. However 7 d after injury, a second wave of TUNEL-positive glial cells was noted in the white matter peripheral to the lesion and extending at least several millimeters away from the lesion center. The suggestion of apoptosis was supported by electron microscopy, as well as by nuclear staining with Hoechst 33342 dye, and by examination of DNA prepared from the lesion site. Furthermore, repeated intraperitoneal injections of cycloheximide, beginning immediately after a 12.5 mm weight drop insult, produced a substantial reduction in histological evidence of cord damage and in motor dysfunction assessed 4 weeks later. Present data support the hypothesis that apoptosis dependent on active protein synthesis contributes to the neuronal and glial cell death, as well as to the neurological dysfunction, induced by mild-to-moderate severity traumatic insults to the rat spinal cord.
Multiple Eccrine Hidrocystomas: A New Therapeutic Option With Botulinum Toxin (2003)

The benefits of BTX-A treatment for multiple eccrine hidrocystomas include ease of application, no risk of scarring, and a good postoperative course. Because of the blockage produced by BTX-A on cholinergic terminals of the parasympathetic system that governs sweat glands secretion, it is suggested that periodic doses of BTX-A are injected in the superficial epidermis in order to treat multiple eccrine hidrocystomas.
First steps in using machine learning on fMRI data to predict intrusive memories of traumatic film footage (2014)

After psychological trauma, why do some only some parts of the traumatic event return as intrusive memories while others do not? Intrusive memories are key to cognitive behavioural treatment for post-traumatic stress disorder, and an aetiological understanding is warranted. We present here analyses using multivariate pattern analysis (MVPA) and a machine learning classifier to investigate whether peri-traumatic brain activation was able to predict later intrusive memories (i.e. before they had happened). To provide a methodological basis for understanding the context of the current results, we first show how functional magnetic resonance imaging (fMRI) during an experimental analogue of trauma (a trauma film) via a prospective event-related design was able to capture an individual's later intrusive memories. Results showed widespread increases in brain activation at encoding when viewing a scene in the scanner that would later return as an intrusive memory in the real world. These fMRI results were replicated in a second study. While traditional mass univariate regression analysis highlighted an association between brain processing and symptomatology, this is not the same as prediction. Using MVPA and a machine learning classifier, it was possible to predict later intrusive memories across participants with 68% accuracy, and within a participant with 97% accuracy; i.e. the classifier could identify out of multiple scenes those that would later return as an intrusive memory. We also report here brain networks key in intrusive memory prediction. MVPA opens the possibility of decoding brain activity to reconstruct idiosyncratic cognitive events with relevance to understanding and predicting mental health symptoms.
Quantitation of telomerase components and hTERT mRNA splicing patterns in immortal human cells (2001)

Telomerase is a reverse transcriptase that adds telomeric repeats to chromosomal ends. In most normal human somatic cells, telomerase is repressed and telomeres progressively shorten, leading to limited proliferative life-span. Telomerase reactivation is associated with cellular immortalization and is a frequent event during tumorigenesis. The telomerase ribonucleoprotein complex consists of two essential components, a catalytic protein subunit [human telomerase reverse transcriptase (hTERT)] and a template RNA (hTR). hTR is constitutively expressed, while hTERT is almost universally absent in telomerase-negative cells. Although repression of telomerase is transcriptional in telomerase-negative cells, post-transcriptional and assembly processes are likely to play important roles in regulating telomerase activity in those that are telomerase-positive. The telomerase transcript can also be alternatively spliced into a variety of non-functional forms. To establish the quantitative relationships between telomerase activity and its various components, we determined the numbers of molecules of hTR and hTERT mRNA, and the levels of alternatively spliced hTERT mRNA variants in normal, in vitro immortalized and cancer cell lines. We report here that there is surprisingly little variation in the proportion of alternatively spliced forms of hTERT in different cell lines. The only variation observed occurred when a change in splicing to non-functional forms appeared in response to conditions that repress telomerase activity in IDH4 cells. We also found that most telomerase-positive cell lines only contain a few molecules of potentially functional hTERT mRNA, and there is a correlation between telomerase activity and the levels of both hTR and hTERT +alpha+beta mRNA.
A psychophysical approach to assessing the quality of antialiased images (1988)

The assumption that antialiasing destroys useful visual information about object features is challenged in three experiments that examine the effects of antialiasing on the visual information for object location and motion. The results show that proper antialiasing eliminates the spurious visual information produced by sampling processes in image synthesis and allows the viewer's visual system to produce a precise representation of object location and a continuous representation of object motion. This suggests that in designing imagery systems, simply increasing the spatial and temporal addressability and resolution beyond limits set by the human visual system will have a negligible impact on image quality, but that effective use of antialiasing techniques could allow visual information about object features to be presented with great fidelity.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A novel heparin-dependent processing pathway for human tryptase. Autocatalysis followed by activation with dipeptidyl peptidase I. (1996)

Tryptase is the major protein constituent of human mast cells, where it is stored within the secretory granules as a fully active tetramer. Two tryptase genes (alpha and beta) are expressed by human mast cells at the level of mRNA and protein, each with a 30 amino acid leader sequence. Recombinant precursor forms of human alpha- and beta-tryptase were produced in a baculovirus system, purified, and used to study their processing. Monomeric beta-protryptase first is shown to be intermolecularly autoprocessed to monomeric beta-pro'tryptase at acid pH in the presence of heparin by cleavage between Arg-3 and Val-2 in the leader peptide. The precursor of alpha-tryptase has an Arg-3 to Gln-3 mutation that precludes autoprocessing. this may explain why alpha-tryptase is not stored in secretory granules, but instead is constitutively secreted by mast cells and is the predominant form of tryptase found in blood in both healthy subjects and those with systemic mastocytosis under nonacute conditions. Second, the NH2-terminal activation dipeptide on beta-pro'tryptase is removed by dipeptidyl peptidase I at acid pH in the absence of heparin to yield an inactive monomeric form of tryptase. Conversion of the catalytic portion of beta-tryptase to the active homotetramer at acid pH requires heparin. Thus, beta-tryptase homotetramers probably account for active enzyme detected in vivo. Also, processing of tryptase to an active form should occur optimally only in cells that coexpress heparin proteoglycan, restricting this pathway to a mast cell lineage.