gebhart/patrepeval huggingface dataset:
Induction of Circularly Polarized Electroluminescence from an Achiral Light‐Emitting Polymer via a Chiral Small‐Molecule Dopant (2013)

By simply doping the conventional light-emitting polymer F8BT with a helically chiral aromatic molecule, it is shown that substantial levels of CP-electroluminescence can be generated directly. Both photoluminescent and electroluminescent emission from the polymer are observed to become circularly polarized, with the sign of the CP emission directly determined by the handedness of the dopant.
v-rel oncoproteins in the nucleus and in the cytoplasm transform chicken spleen cells (1988)

The transforming protein encoded by the v-rel oncogene of the highly oncogenic avian retrovirus reticuloendotheliosis virus strain T (Rev-T) is a 59,000-dalton protein, p59v-rel. The mechanism by which p59v-rel induces transformation of early lymphoid cells is unknown. As a step towards understanding the mechanism of v-rel-induced transformation, we sought to establish the subcellular site of action of p59v-rel. In this report, we show that p59v-rel contains sequences that are necessary for its efficient localization in the nucleus of infected chicken embryo fibroblasts. These v-rel sequences when added to the normally cytoplasmic protein, beta-galactosidase, directed that protein to the nucleus. A mutation in the v-rel nuclear-localizing sequence did not affect the transforming function, although it did alter the nuclear-localizing function. The addition of a supplemental nuclear-localizing sequence from simian virus 40 large T-antigen to v-rel resulted in the expression of a transforming rel protein which was located exclusively in the nucleus of transformed spleen cells, in contrast to wild-type p59v-rel, which was largely cytoplasmic in transformed spleen cells. Our results support the hypothesis that v-rel encodes a protein which can act either in the nucleus or in the cytoplasm to transform spleen cells.
Specific anti-tumor immune response with photodynamic therapy mediated by benzoporphyrin derivative and chlorin(e6) (2003)

The purpose of this study was to investigate the induction of anti-tumor immunity by photodynamic therapy (PDT). We used EMT-6 mammary sarcoma, a moderately immunogenic tumor, with 10(6) cells injected s.c. in thighs of immunocompetent Balb/c mice. Mice were treated 10 days later when tumors were 6-mm diameter. Two PDT regimens were equally effective in curing tumors: 1-mg/kg of liposomal benzoporphyrin derivative (BPD) followed after 15 min by 150 J/cm<sup>2</sup> 690 nm light or 10-mg/kg chlorin(e6) (ce6) followed after 6 hours by 150 J/cm<sup>2</sup> 665 nm light. BPD-PDT produced a black eschar 24-48 hours after treatment with no visible tumor, followed by healing of the lesion. By contrast ce6-PDT showed no black eschar, but a slow disappearance of tumor over 5-7 days. When cured mice were rechallenged with 10(6) EMT-6 cells in the opposite thigh, all ce6-PDT cured mice rejected the challenge, but BPD-PDT cured mice grew tumors in a proportion of cases. When mice were cured by amputation of the tumor bearing leg, all mice subsequently grew tumors upon rechallenge. Mice were given two EMT6 tumors (1 in each leg) and the mouse was injected with ce6 or BPD but only one tumor was treated with light. Both tumors (PDT-treated and contralateral) regressed at an equal rate until they became undetectable, but in some mice the untreated tumor recurred. Those mice cured of both tumors rejected a subsequent EMT6 rechallenge. Amputation of the tumor bearing leg did not lead to regression of the contralateral tumor. Mice that rejected an EMT6 rechallenge failed to reject a subsequent cross-challenge with J774 reticulum cell sarcoma (an alternative Balb/c murine tumor). These data show that PDT generates a tumor-specific memory immune response, and in addition an active tumoricidal immune response capable of destroying distant established tumors. We hypothesize that ce6-PDT is more effective than BPD-PDT due to more necrotic rather than apoptotic cell death and/or generation of heat-shock proteins that are known for efficient presentation of tumor antigens via dendritic cells to cytotoxic T-cells. PDT could be used to treat a locally advanced tumor while at the same time destroying distant metastases via an induced immune response.
Removing near-neighbour redundancy from large protein sequence collections. (1998)

holm@embl-ebi.ac.uk
Tumor invasion and metastasis: an imbalance of positive and negative regulation. (1991)

A group of coordinated cellular processes, not just one gene product, is responsible for invasion and metastasis, the most life-threatening aspect of cancer. It is now recognized that negative factors may be just as important as positive elements. Genetic changes causing an imbalance of growth regulation lead to uncontrolled proliferation necessary for both primary tumor and metastasis expansion. However, unrestrained growth does not, by itself, cause invasion and metastasis. This phenotype may require additional genetic changes. Thus, tumorigenicity and metastatic potential have both overlapping and separate features. Invasion and metastasis can be facilitated by proteins which stimulate tumor cell attachment to host cellular or extracellular matrix determinants, tumor cell proteolysis of host barriers, such as the basement membrane, tumor cell locomotion, and tumor cell colony formation in the target organ for metastasis. Facilitory proteins may act at many levels both intracellularly or extracellularly but are counterbalanced by factors which can block their production, regulation, or action. A common theme has emerged. In addition to loss of growth control, an imbalanced regulation of motility and proteolysis appears to be required for invasion and metastasis.
THE HUMAN METAPHOR (1992)

The need to Induce a feeling of naturalness is a critical issue in user interface design. Workstations have improved the level of interaction with the user to the event level, so that computers are now more responsive. Non-keyboard interfaces—pen-based computers and systems that recognize voice, handwriting, and gestures that substitute for keystroke commands—will make computers more transparent to users and even more accessible to larger groups of users.
Reading without saccadic eye movements (1992)

To assess the limitation on reading speed imposed by saccadic eye movements, we measured reading speed in 13 normally-sighted observers using two modes of text presentations: PAGE text which presents an entire passage conventionally in static, paragraph format, and rapid serial visual presentation (RSVP) which presents text sequentially, one word at a time at the same location in the visual field. In Expt 1, subjects read PAGE and RSVP text orally across a wide range of letter sizes (2X to 32X single-letter acuity) and reading speed was computed from the number of correct words read per minute. Reading speeds were consistently faster for RSVP compared to PAGE text at all letter sizes tested. The average speeds for text of an intermediate letter size (8X acuity) were 1171 words/min for RSVP and 303 words/min for PAGE text. In Expt 2 subjects read PAGE and RSVP text silently and a multiple-choice comprehension test was administered after each passage. All subjects continued to read RSVP text faster, and 6 subjects read at the maximum testable rate (1652 words/min) with at least 75% correct on the comprehension tests. Experiment 3 assessed the minimum word exposure time required for decoding text using RSVP to minimize potential delays due to saccadic eye movement control. Successive words were presented for a fixed duration (word duration) with a blank interval (ISI) between words. The minimum word duration required for accurate oral reading averaged 69.4 msec and was not reduced by increasing ISI. We interpret these results as an indication that the programming and execution of saccadic eye movements impose an upper limit on conventional reading speed.
Distinct physicochemical characteristics of human mannose binding protein expressed by individuals of differing genotype. (1995)

Mannose binding protein (MBP) is a serum collectin (collagenous lectin) believed to be of importance in innate immunity. Three point mutations, in codons 52, 54 and 57 of exon 1 of the human MBP gene, have been predicted to affect the tertiary structure of the collagenous region of the protein, and are known to be associated with low serum concentrations of MBP. However, other groups working with recombinant mutant proteins have claimed that the proteins are expressed and assembled normally. The aim of the present investigation was to characterize the effects of these mutations on the physicochemical nature of MBP that is present in the circulation in vivo, and for this we used polyacrylamide gel electrophoresis, gel filtration and sucrose density gradient centrifugation, followed by immunoblotting and enhanced chemiluminescence. The circulating wild-type MBP appeared to comprise a mixture of polymers formed from two to eight subunits (each based on three identical 32,000 MW polypeptide chains) of apparent molecular weights 200,000-700,000, with dimers and trimers constituting the predominant forms. Individuals homozygous for the codon 54 or 57 mutation had dramatically reduced concentrations of serum MBP, mainly comprising material of an apparent molecular weight of 120,000-130,000. Heterozygous individuals showed characteristics of both phenotypes. In contrast to the results obtained with artificial expression systems, our data suggest that individuals homozygous for the MBP mutations have very little circulating protein and that this comprises mainly low molecular weight material.
Gene Therapy in a Humanized Mouse Model of Familial Hypercholesterolemia Leads to Marked Regression of Atherosclerosis (2010)

Collectively, the results presented herein suggest that AAV8-based gene therapy for FH may be feasible and support further development of this approach. The pre-clinical data from these studies will enable for the effective translation of gene therapy into the clinic for treatment of FH.
LEVERAGING SOCIAL CAPITAL AND ABSORPTIVE CAPACITY FOR KNOWLEDGE INTEGRATION: A CASE STUDY OF A CROSS-ORGANIZATION IT PROJECT (2012)

Based on an in-depth case study, this article studies a collaborative IT project (one IT service vendor and three clients) involving intensive knowledge integration activity. It explains how social capital (e.g. relational, cognitive, structural), absorptive capacity (e.g. exploratory, exploitative, transformative) interact with each other with the support of organizational culture (e.g. collective, cooperative, compatible) to ensure the success of cross-organization knowledge integration information system project. Dividing the project process into three phases, we discuss in detail that in initiation phase, relational social capital initiates the exploratory absorptive capacity while exploratory absorptive capacity enhances the relational social capital in return; in implementation phase, cognitive social capital and exploitative absorptive capacity are utilized and synthesized to keep the smoothness of the implementation process; and in assimilation phase, transformative absorptive capacity leads to the reconfiguration of structural social capital while the reconfigured structural social capital in turn reinforces the transformative absorptive capacity. Within these three phases, we identified the different roles that culture plays as norm, facilitator and harmonizer. Key Words: knowledge integration, social capital, absorptive capacity, organizational culture.
Anti-Submarine Warfare visual analysis tool geospatially enabling Four Dimensional METOC data (2009)

This research proposes methods and develops an open source based prototype for enabling Four-Dimensional (4-D) METOC data in support of the Navy Anti-Submarine Warfare directorate's visual analysis requirements. Useful 4-D METOC data is currently produced and stored in netCDF format. The data is then used to create, for each depth and time, a static JPEG image that becomes available for dissemination to the fleet. Current Command and Control (C2) systems use Open Geospatial Consortium (OGC) compliant GIS maps to display the common operational picture (COP) but the large collection of JPEG images cannot be introduced as map layers on the COP to fused decision support.
Transduction by adeno-associated virus vectors in the rabbit airway: efficiency, persistence, and readministration (1997)

The ability of recombinant adeno-associated virus (AAV) vectors to integrate into the host genome and to transduce nondividing cells makes them attractive as vehicles for gene delivery. In this study, we assessed the ability of several AAV vectors to transduce airway cells in rabbits by measuring marker gene expression. AAV vectors that transferred either a beta-galactosidase (beta-gal) or a human placental alkaline phosphatase (AP) gene were delivered to one lobe of the rabbit lung by use of a balloon catheter placed under fluoroscopic guidance. We observed vector-encoded beta-gal or AP staining almost exclusively in the epithelial and smooth muscle cells in the bronchus at the region of balloon placement. The overall efficiency of transduction in the balloon-treated bronchial epithelium was low but reached 20% in some areas. The majority of the staining was in ciliated cells but was also observed in basal cells and airway smooth muscle cells. We observed an 80-fold decrease in marker-positive epithelial cells during the 60-day period after vector infusion, whereas the number of marker-positive smooth muscle cells stayed constant. Although treatment with the topoisomerase inhibitor etoposide dramatically enhanced AAV transduction in primary airway epithelial cells in culture, treatment of rabbits did not improve transduction rates in the airway. Vector readministration failed to produce additional transduction events, which correlated with the appearance of neutralizing antibodies. These results indicate that both readministration and immune modulation will be required in the use of AAV vectors for gene therapy to the airway epithelium.
The Effect of Fruit and Vegetable Intake on Risk for Coronary Heart Disease (2001)

Consumption of fruits and vegetables, particularly green leafy vegetables and vitamin C-rich fruits and vegetables, appears to have a protective effect against coronary heart disease.
Unsupervised Feature Learning via Non-Parametric Instance-level Discrimination (2018)

Neural net classifiers trained on data with annotated class labels can also capture apparent visual similarity among categories without being directed to do so. We study whether this observation can be extended beyond the conventional domain of supervised learning: Can we learn a good feature representation that captures apparent similarity among instances, instead of classes, by merely asking the feature to be discriminative of individual instances? We formulate this intuition as a non-parametric classification problem at the instance-level, and use noise-contrastive estimation to tackle the computational challenges imposed by the large number of instance classes. Our experimental results demonstrate that, under unsupervised learning settings, our method surpasses the state-of-the-art on ImageNet classification by a large margin. Our method is also remarkable for consistently improving test performance with more training data and better network architectures. By fine-tuning the learned feature, we further obtain competitive results for semi-supervised learning and object detection tasks. Our non-parametric model is highly compact: With 128 features per image, our method requires only 600MB storage for a million images, enabling fast nearest neighbour retrieval at the run time.
Expression of Human Growth Hormone Fusion Genes in Cultured Lung Endothelial Cells and in the Lungs of Mice (1993)

We sought to develop genetic therapy for acute lung diseases by introducing genes into lung cells in vivo that were only transiently expressed. To that end, we introduced a gene encoding a physiologically relevant secreted human protein into bovine lung endothelial cells in culture and into the lungs of mice using the technique of lipofection. We exposed cultured endothelial cells to a plasmid containing the coding region for human growth hormone (hGH) driven by a metallothionein (MT) promoter. In cells lipofected with the plasmid containing the MT promoter, expression of the hGH gene in medium was low (peak = 30 ng hGH/24 h/60-mm dish), but expression was markedly increased by addition of either dexamethasone (peak = 91) or cadmium (peak = 120). Lipofection with the same construct except a thymidine kinase promoter showed no cadmium response. We gave mice 5,000 ppm ZnSO4 in their drinking water and 24 h later injected intravenously plasmid containing the MT promoter complexed to liposomes. Mice were killed 1, 3, and 5 days after injection, and hGH production by minced lung, liver, and kidneys was determined in vitro. Neither kidneys nor liver produced detectable hGH. However, hGH was produced by the lungs, beginning on day 1, peaking on day 3 (approximately 1.0 ng hGH/24 h/g tissue), and declining by day 5. Lungs from mice injected either with DNA alone or with liposome alone did not produce hGH. mRNA specific for hGH was demonstrated in the lungs by polymerase chain reaction amplification of cDNA followed by agarose gel electrophoreses.(ABSTRACT TRUNCATED AT 250 WORDS)
Connexin 43-mediated modulation of polarized cell movement and the directional migration of cardiac neural crest cells (2006)

Connexin 43 knockout (Cx43alpha1KO) mice have conotruncal heart defects that are associated with a reduction in the abundance of cardiac neural crest cells (CNCs) targeted to the heart. In this study, we show CNCs can respond to changing fibronectin matrix density by adjusting their migratory behavior, with directionality increasing and speed decreasing with increasing fibronectin density. However, compared with wild-type CNCs, Cx43alpha1KO CNCs show reduced directionality and speed, while CNCs overexpressing Cx43alpha1 from the CMV43 transgenic mice show increased directionality and speed. Altered integrin signaling was indicated by changes in the distribution of vinculin containing focal contacts, and altered temporal response of Cx43alpha1KO and CMV43 CNCs to beta1 integrin function blocking antibody treatment. High resolution motion analysis showed Cx43alpha1KO CNCs have increased cell protrusive activity accompanied by the loss of polarized cell movement. They exhibited an unusual polygonal arrangement of actin stress fibers that indicated a profound change in cytoskeletal organization. Semaphorin 3A, a chemorepellent known to inhibit integrin activation, was found to inhibit CNC motility, but in the Cx43alpha1KO and CMV43 CNCs, cell processes failed to retract with semaphorin 3A treatment. Immunohistochemical and biochemical analyses suggested close interactions between Cx43alpha1, vinculin and other actin-binding proteins. However, dye coupling analysis showed no correlation between gap junction communication level and fibronectin plating density. Overall, these findings indicate Cx43alpha1 may have a novel function in mediating crosstalk with cell signaling pathways that regulate polarized cell movement essential for the directional migration of CNCs.
Hepatic cirrhosis: magnetic resonance imaging. (1984)

The effect of periportal collagen deposition on magnetic resonance images and T1 and T2 relaxation times was studied in the rat. Hepatic cirrhosis was induced in 29 rats by chronic intraperitoneal thioacetamide injections. Another 14 rats in which liver abnormalities did not develop were used as controls. The rats were imaged using a small-bore resistive magnet. Histologic correlations and hydroxyproline measurements were performed to document the changes in periportal collagen deposition. The T1 and T2 relaxation times, determined both in vivo and in vitro with spectroscopy, were compared between the normal group and the group with moderate to severe histologic evidence of cirrhosis. The deposition of two to four times the normal amount of collagen in the liver did not affect the T1 or T2 relaxation time. Relatively pure periportal collagen fibrosis does not appear to affect the magnetic resonance image or T1 or T2 relaxation times of the rat liver.
Magic Moments for Structured Output Prediction (2008)

Most approaches to structured output prediction rely on a hypothesis space of prediction functions that compute their output by maximizing a linear scoring function. In this paper we present two novel learning algorithms for this hypothesis class, and a statistical analysis of their performance. The methods rely on efficiently computing the first two moments of the scoring function over the output space, and using them to create convex objective functions for training. We report extensive experimental results for sequence alignment, named entity recognition, and RNA secondary structure prediction.
Molecular Identification of a Novel Candidate Sorting Receptor Purified from Human Brain by Receptor-associated Protein Affinity Chromatography (1997)

Receptor-associated protein (RAP) is an endoplasmic reticulum/Golgi protein involved in the processing of receptors of the low density lipoprotein receptor family. A approximately 95-kDa membrane glycoprotein, designated gp95/sortilin, was purified from human brain extracts by RAP affinity chromatography and cloned in a human cDNA library. The gene maps to chromosome 1p and encodes an 833-amino acid type I receptor containing an N-terminal furin cleavage site immediately preceding the N terminus determined in the purified protein. Gp95/sortilin is expressed in several tissues including brain, spinal cord, and testis. Gp95/sortilin is not related to the low density lipoprotein receptor family but shows intriguing homologies to established sorting receptors: a 140-amino acid lumenal segment of sortilin representing a hitherto unrecognized type of extracellular module shows extensive homology to corresponding segments in each of the two lumenal domains of yeast Vps10p, and the extreme C terminus of the cytoplasmic tail of sortilin contains the casein kinase phosphorylation consensus site and an adjacent dileucine sorting motif that mediate assembly protein-1 binding and lysosomal sorting of the mannose-6-phosphate receptors. Expression of a chimeric receptor containing the cytoplasmic tail of gp95/sortilin demonstrates evidence that the tail conveys colocalization with the cation-independent mannose6-phosphate receptor in endosomes and the Golgi compartment.