gebhart/patrepeval huggingface dataset:
Amino acid sequence of human pregnancy-associated plasma protein A derived from cloned cDNA (1994)

The amino acid sequence of human pregnancy-associated plasma protein-A (PAPP-A), a component of the circulating complex with the proform of eosinophil major basic protein (proMBP), has been determined from partial protein sequencing and from sequencing of cloned cDNA. The PAPP-A monomer contains 1547 amino acid residues, but is derived from a larger precursor of placental origin. PAPP-A contains 82 Cys residues, which are all bridged, 14 putative sites for N-glycosylation, and 7 putative sites for attachment of glycosaminoglycan groups. The C-terminal part of PAPP-A contains 5 approximately 60-residue motifs related to the short consensus repeats of complement proteins and selectins. The SCRs presently known can be grouped into three classes: complement-type, class I; selectin-type, class II; PAPP-A-type, class III. PAPP-A further contains three approximately 26-residue motifs, related to the lin-notch motifs of proteins regulating early tissue differentiation, and, in addition, a putative Zn2+ binding site similar to that found in many metalloproteinases has been identified. Apart from these features, the PAPP-A sequence is not related to other known protein sequences.
High Macrophage Infiltration along the Tumor Front Correlates with Improved Survival in Colon Cancer (2007)

In conclusion, our data indicate that a dense macrophage infiltration at the tumor front positively influences prognosis in colon cancer and that the degree of cell-to-cell contact may influence the balance between protumorigenic and antitumorigenic properties of macrophages.
Electromagnetic Wave Interaction With Stratified Negative Isotropic Media - Abstract (2001)

In this paper we provide a general formulation for the electromagnetic wave interaction with stratified media and then specialize to slabs of negative isotropic media. The field solutions are obtained in all regions of the stratified medium. The characteristic waves in negative isotropic media are backward waves. We derive the field solutions and show that a Gaussian beam is laterally shifted by a negative isotropic slab. The amount of beam center shift is calculated for both cases of transmission and reflection. Guided waves in stratified media are studied. Placing a linear antenna and all types of Hertzian dipole antennas in a stratified medium, we obtained solutions in all regions. We demonstrate and locate the positions of the perfect images of the antenna sources in the presence of negative isotropic slabs.
Tissue Culture and Applications of Dendrobium (2008)

Research advances on tissue culture methods of Dendrobium candidum,Dendrobium huoshanense,Dendrobium chrysotoxum and other plants of Dendrobium genus and applications are reviewed in this paper.Some problems existed are pointed out,and it is very important for the enrichment of the resources and comprehensive utilization of Dendrobium.
Anti-parasitic Peptides from Arthropods and their Application in Drug Therapy (2016)

Africa, Asia, and Latin America are regions highly affected by endemic diseases, such as Leishmaniasis, Malaria, and Chagas' disease. They are responsible for the death of 1000s of patients every year, as there is not yet a cure for them and the drugs used are inefficient against the pathogenic parasites. During the life cycle of some parasitic protozoa, insects become the most important host and disseminator of the diseases triggered by these microorganisms. As infected insects do not develop nocive symptoms, they can carry the parasites for long time inside their body, enabling their multiplication and life cycle completion. Eventually, parasites infect human beings after insect's transmission through their saliva and/or feces. Hence, host insects and general arthropods, which developed a way to coexist with such parasites, are a promising source for the prospection of anti-parasitic compounds, as alternative methods for the treatment of protozoa-related diseases. Among the molecules already isolated and investigated, there are proteins and peptides with high activity against parasites, able to inhibit parasite activity in different stages of development. Although, studies are still taking their first steps, initial results show new perspectives on the treatment of parasitic diseases. Therefore, in this report, we describe about peptides from host insect sources with activity against the three most endemic parasites: Leishmania sp., Plasmodium sp., and Trypanosomes. Moreover, we discuss the future application insect peptides as anti-parasitic drugs and the use of non-hosts insect transcriptomes on the prospection of novel molecules for the treatment of parasitic neglected diseases.
Transgenerational Homophobia in the Family (1995)

Journal entries, personal correspondence, and family memories are used to reconstruct the author's experience growing up in a family with a gay father, her own coming out, and her father's death six years ago from AIDS. The memoir illustrates how both internalized and institutional homophobia shape self-definition and family relationships over three generations, in living and in dying.
CCL5 evokes calcium signals in microglia through a kinase‐, phosphoinositide‐, and nucleotide‐dependent mechanism (2006)

Microglia, the resident macrophages of the CNS, are responsible for the innate immune response in the brain and participate in the pathogenesis of certain neurodegenerative disorders. Chemokines initiate activation and migration of microglia. The beta-chemokine CCL5 induces an elevation in intracellular calcium concentration ([Ca(2+)](i)) in human microglia. Here, we examined the signal transduction pathway linking activation of chemokine receptor CCR5 to an elevation in [Ca(2+)](i) in cultured microglia by using pharmacological approaches in combination with Fura-2-based digital imaging. The CCL5-induced response required Janus kinase (Jak) activity and the stimulation of an inhibitory G protein. Multiple downstream signaling pathways were involved, including phosphatidylinositol 3-kinase (PI3K), Bruton's tyrosine kinase (Btk), and phospholipase C (PLC)-mediated release of Ca(2+) from inositol 1,4,5-trisphosphate (IP(3))-sensitive stores. Activation of both the kinase and the lipase pathways was required for eliciting the Ca(2+) response. However, the majority of the [Ca(2+)](i) increase was derived from sources activated by NAD metabolites. Cyclic ADP-ribose (cADPR) evoked Ca(2+) release from intracellular stores, and ADPR evoked Ca(2+) influx via a nimodipine-sensitive channel. Thus, a multistep cascade couples CCR5 activation to Ca(2+) increases in human microglia. Because changes in [Ca(2+)](i) affect chemotaxis, secretion, and gene expression, pharmacologic modulation of this pathway may alter inflammatory and degenerative processes in the CNS.
The plasmid replicator AMA1 in Aspergillus nidulans is an inverted duplication of a low‐copy‐number dispersed genomic repeat (1996)

The AMA1 sequence was isolated from a genomic library of Aspergillus nidulans on the basis of its ability to enhance transformation frequency and generate phenotypically unstable transformants in this fungus. These properties were previously shown to be the result of extrachromosomal replication of AMA1-bearing plasmids. Here we demonstrate that AMA1 is an inverted duplication of a sequence which has other isolated genomic copies. These sequences (mobile Aspergillus transformation enhancers, or MATEs) share a high degree of sequence similarity and exhibit some features characteristic of mobile elements, including a potential Met-tRNA priming site, similar to that found in retrotransposons of the Ty-copia group. The nucleotide sequence does not encode any extended polypeptides but contains ARS-consensus matches and a multiply repeated 'Spe' motif, which may be described as a symmetrically duplicated topoisomerase I recognition site. This motif was shown to be a target for illegitimate recombination events. The mobility of members of the MATE family is inferred from the observation that their chromosomal locations are highly variable between wild Aspergillus isolates. The inverted duplication AMA1 is present in laboratory strains derived from the Glasgow isolate but not in other wild isolates tested. This indicates that the inverted duplication AMA1 is of recent evolutionary origin and probably does not exert any conserved function in the chromosome. We discuss possible connections between structural features of AMA1 and its ability to promote extrachromosomal plasmid replication.
Surface‐Attached Polyhistidine‐Tag Proteins Characterized by FTIR Difference Spectroscopy (2012)

A universal label-free method for the spectroscopic investigation of polyhistidine-tagged proteins is presented. A solid supported lipid bilayer (SSLB, picture) containing nitrilotriacetic-acid-modified lipids is attached on top of a germanium attenuated total reflection crystal by hydrophilic interactions. Any His tag-modified protein can be immobilized and investigated by FTIR spectroscopy.
Visual tracking using learned linear subspaces (2004)

This paper presents a simple but robust visual tracking algorithm based on representing the appearances of objects using affine warps of learned linear subspaces of the image space. The tracker adaptively updates this subspace while tracking by finding a linear subspace that best approximates the observations made in the previous frames. Instead of the traditional L/sup 2/-reconstruction error norm which leads to subspace estimation using PCA or SVD, we argue that a variant of it, the uniform L/sup 2/-reconstruction error norm, is the right one for tracking. Under this framework we provide a simple and a computationally inexpensive algorithm for finding a subspace whose uniform L/sup 2/-reconstruction error norm for a given collection of data samples is below some threshold, and a simple tracking algorithm is an immediate consequence. We show experimental results on a variety of image sequences of people and man-made objects moving under challenging imaging conditions, which include drastic illumination variation, partial occlusion and extreme pose variation.
Behavioral Deficits and Axonal Injury Persistence after Rotational Head Injury Are Direction Dependent (2012)

Pigs continue to grow in importance as a tool in neuroscience. However, behavioral tests that have been validated in the rodent model do not translate well to pigs because of their very different responses to behavioral stimuli. We refined metrics for assessing porcine open field behavior to detect a wide spectrum of clinically relevant behaviors in the piglet post-traumatic brain injury (TBI). Female neonatal piglets underwent a rapid non-impact head rotation in the sagittal plane (n=8 evaluable) or were instrumented shams (n=7 evaluable). Open field testing was conducted 1 day prior to injury (day -1) in order to establish an individual baseline for analysis, and at days +1 and +4 after injury. Animals were then killed on day +6 after injury for neuropathological assessment of axonal injury. Injured piglets were less interested in interacting with environmental stimuli and had a lower activity level than did shams. These data were compared with previously published data for axial rotational injuries in neonatal piglets. Acute behavioral outcomes post-TBI showed a dependence on the rotational plane of the brain injury, with animals with sagittal injuries demonstrating a greater level of inactivity and less random usage of the open field space than those with axial injuries. The persistence of axonal injury is also dependent on the rotational plane, with sagittal rotations causing more prolonged injuries than axial rotations. These results are consistent with animal studies, finite element models, and studies of concussions in football, which have all demonstrated differences in injury severity depending upon the direction of head impact rotation.
Mobilization of Peripheral Blood Progenitor Cells by Betafectin® PGG‐Glucan Alone and in Combination with Granulocyte Colony‐Stimulating Factor (1998)

Betafectin PGG-Glucan, a novel beta-(1,6) branched beta-(1,3) glucan purified from the cell walls of Saccharomyces cerevisiae, has been shown to synergize with myeloid growth factors in vitro and to enhance hematopoietic recovery in myelosuppressed mice and primates. Here we report that PGG-Glucan is also capable of mobilizing peripheral blood progenitor cells (PBPC). PGG-Glucan (0.5 mg/kg to 16 mg/kg) was administered intravenously to C3H/HeN male mice and blood collected at times ranging from 30 min to seven days after injection. Based on granulocyte-macrophage colony-forming cell (GM-CFC) levels, peak mobilization occurred 30 min after a 2 mg/kg PGG-Glucan dose. At this time GM-CFC numbers in PGG-Glucan-treated mice were approximately fourfold greater than in saline-treated control mice. A second, smaller wave of GM-CFC mobilization (approximately twofold increase) also occurred on days 4 and 5 after PGG-Glucan treatment. Mobilization was not associated with the induction of alpha-chemokines, which have recently been reported to induce rapid progenitor cell mobilization. Competitive repopulation experiments performed in irradiated female C3H/HeN mice revealed that, at three months after transplantation, more male DNA was present in bone marrow, splenic, and thymic tissues from animals transplanted with cells obtained from mice 30 min after a 2 mg/kg PGG-Glucan dose than in tissues from animals transplanted with cells obtained from saline-treated mice. Additional experiments evaluated the mobilization effects of PGG-Glucan (2 mg/kg) administered to mice which had been pretreated for three consecutive days with G-CSF (125 microg/kg/day). When blood was collected 30 min after PGG-Glucan treatment, the number of GM-CFC mobilized in combination-treated mice was additive between the number mobilized in mice treated with G-CSF alone and the number mobilized in mice treated with PGG-Glucan alone. These studies demonstrate that: A) PGG-Glucan can rapidly mobilize PBPC; B) the kinetic pattern of PGG-Glucan-induced mobilization is different from that of the CSFs; C) the reconstitutional potential of PGG-Glucan mobilized cells is greater than that of steady-state PBPC, and D) PGG-Glucan can enhance G-CSF-mediated PBPC mobilization.
A Highly Scalable Peptide-Based Assay System for Proteomics (2012)

We report a scalable and cost-effective technology for generating and screening high-complexity customizable peptide sets. The peptides are made as peptide-cDNA fusions by in vitro transcription/translation from pools of DNA templates generated by microarray-based synthesis. This approach enables large custom sets of peptides to be designed in silico, manufactured cost-effectively in parallel, and assayed efficiently in a multiplexed fashion. The utility of our peptide-cDNA fusion pools was demonstrated in two activity-based assays designed to discover protease and kinase substrates. In the protease assay, cleaved peptide substrates were separated from uncleaved and identified by digital sequencing of their cognate cDNAs. We screened the 3,011 amino acid HCV proteome for susceptibility to cleavage by the HCV NS3/4A protease and identified all 3 known trans cleavage sites with high specificity. In the kinase assay, peptide substrates phosphorylated by tyrosine kinases were captured and identified by sequencing of their cDNAs. We screened a pool of 3,243 peptides against Abl kinase and showed that phosphorylation events detected were specific and consistent with the known substrate preferences of Abl kinase. Our approach is scalable and adaptable to other protein-based assays.
Heterocycles. VI. Syntheses of 4H-s-Triazolo [4, 3-a] [1, 4] benzodiazepines, Novel Tricyclic Psychosedatives (1973)

A variety of 4H-s-triazolo [4, 3-a] [1, 4] benzodiazepines (VII) which are highly active in central nervous system depression was synthesized with the aim of investigating structure-activity relationships.
Scalable feedback control for multicast video distribution in the Internet (1994)

We describe a mechanism for scalable control of multicast continuous media streams. The mechanism uses a novel probing mechanism to solicit feedback information in a scalable manner and to estimate the number of receivers. In addition, it separates the congestion signal from the congestion control algorithm, so as to cope with heterogeneous networks. This mechanism has been implemented in the IVS video conference system using options within RTP to elicit information about the quality of the video delivered to the receivers. The H.261 coder of IVS then uses this information to adjust its output rate, the goal being to maximize the perceptual quality of the image received at the destinations while minimizing the bandwidth used by the video transmission. We find that our prototype control mechanism is well suited to the Internet environment. Furthermore, it prevents video sources from creating congestion in the Internet. Experiments are underway to investigate how the scalable proving mechanism can be used to facilitate multicast video distribution to large number of participants.
Skeleton-based Hierarchical Shape Segmentation (2007)

We present an effective framework for segmenting 3D shapes into meaningful components using the curve skeleton. Our algorithm identifies a number of critical points on the curve skeleton, either fully automatically as the junctions of the curve skeleton, or based on user input. We use these points to construct a partitioning of the object surface using geodesies. Because it is based on the curve skeleton, our segmentation intrinsically reflects the shape symmetry and topology. By using geodesies we obtain segments that have smooth, minimally twisting borders. Finally, we present a hierarchical segmentation of shapes which reflects the hierarchical structure of the curve skeleton. We describe a voxel-based implementation of our method which is robust and noise resistant, computationally efficient, able to handle shapes of complex topology, and which delivers level- of-detail segmentations. We demonstrate the framework on various real-world 3D shapes.
Advances in Uterine Leiomyoma Research: The Progesterone Hypothesis (2000)

Uterine leiomyomas are monoclonal tumors. However, the factors involved in their initiation and growth remain poorly understood. The neoplastic transformation of myometrium to leiomyoma likely involves somatic mutations of normal myometrium and the complex interactions of sex steroids and local growth factors. Traditionally, estrogen has been considered the major promoter of myoma growth. The purpose of this review is to highlight the biochemical, histologic, and clinical evidence that supports an equally important role for progesterone in the growth of uterine myomas. Biochemical studies suggest that progesterone, progestins, and the progesterone receptor modulate myoma mitotic activity. A hypothesis to explain the pathogenesis of myomas is presented.
Solid-State Diode-like Chemiluminescence Based on Serial, Immobilized Concentration Gradients in Mixed-Valent Poly[Ru(vbpy)3](PF6)2 Films (1996)

The electronic conductivity and electrogenerated chemiluminescence (ECL) of thin, electropolymerized films of the fixed-site redox polymer poly[Ru(vbpy)3](PF6)2 (vbpy = 4-vinyl-4‘-methyl-2,2‘-bipyridine) on Pt interdigitated array electrodes were examined for both solvent-swollen and dry films. In both cases emission arose from *Ru2+ produced via the electron-transfer reaction between Ru3+ and Ru1+ states within the film (Ru = Ru(vbpy)3). Dry films contained fixed concentration gradients of Ru3+, Ru2+, and Ru1+ states which were first introduced in an acetonitrile-swollen film via the constant potential oxidation and reduction of Ru2+ at opposing IDA fingers. The gradients were then immbolized by drying and cooling the film while retaining the inter-electrode bias (2.6 V). The resulting dried and cooled films responded rapidly to changes in voltage bias and exhibited diode-like characteristics, conducting and emitting light at biases ≥2.6 V and undergoing a reverse bias breakdown current, unassociated with light emission, at ca. −5.5 V. At 0 °C the optimum quantum efficiency of solid-state ECL emission (φECL) was similar to that in solvent-swollen films: 0.0003 photon/electron. In contrast to the dry films, solvent-swollen films were slow to respond to changes in voltage bias and did not exhibit diode-like behavior.
Tumor Metabolism of Lactate: The Influence and Therapeutic Potential for MCT and CD147 Regulation (2009)

Tumor metabolism consists of complex interactions between oxygenation states, metabolites, ions, the vascular network and signaling cascades. Accumulation of lactate within tumors has been correlated with poor clinical outcomes. While its production has negative implications, potentially contributing to tumor progression, the implications of the ability of tumors to utilize lactate can offer new therapeutic targets for the future. Monocarboxylate transporters (MCTs) of the SLC16A gene family influence substrate availability, the metabolic path of lactate and pH balance within the tumor. CD147, a chaperone to some MCT subtypes, contributes to tumor progression and metastasis. The implications and consequences of lactate utilization by tumors are currently unknown; therefore future research is needed on the intricacies of tumor metabolism. The possibility of metabolic modification of the tumor microenvironment via regulation or manipulation of MCT1 and CD147 may prove to be promising avenues of therapeutic options.
Identification of a Pituitary Growth Hormone-Releasing Peptide (GHRP) Receptor Subtype by Photoaffinity Labeling (1998)

Hexarelin, an analogue of GHRP-6, in which D-Tryptophan has been replaced by its 2-methyl derivative, is known to release growth hormone (GH) in vivo and in vitro by direct action on receptors present in anterior pituitary cells. Measurement of second messengers (c-AMP, Ca++, IP3) upon somatotrophs stimulation, suggests the existence of more than one GHRP receptor subtype. In order to document such an hypothesis, we have used a new photoactivatable derivative of Hexarelin, Tyr-Bpa-Ala-Hexarelin. This derivative was shown to be fully active in the release of GH in vivo with neonate rats. Using this photoactivatable ligand, we have specifically labeled a protein with an apparent Mr of 57 000 in human, bovine and porcine anterior pituitary membranes. Hexarelin and the spiroindoline sulfonamide MK-0677 displaced the Mr −57 000 photolabeled band with an apparent ED50 of 6×10−7 M and 2×10−5 M respectively. Taking into account the high efficiency (>60%) of covalent incorporation of the Bpa residue, this photoactivatable Hexarelin derivative has allowed the identification of a pituitary GHRP receptor subtype, which is apparently distinct from the recently cloned GH secretagogue receptor.