gebhart/patrepeval huggingface dataset:
Normal and Friedreich Ataxia Cells Express Different Isoforms of Frataxin with Complementary Roles in Iron-Sulfur Cluster Assembly (2010)

Friedreich ataxia (FRDA) is an autosomal recessive degenerative disease caused by insufficient expression of frataxin (FXN), a mitochondrial iron-binding protein required for Fe-S cluster assembly. The development of treatments to increase FXN levels in FRDA requires elucidation of the steps involved in the biogenesis of functional FXN. The FXN mRNA is translated to a precursor polypeptide that is transported to the mitochondrial matrix and processed to at least two forms, FXN(42-210) and FXN(81-210). Previous reports suggested that FXN(42-210) is a transient processing intermediate, whereas FXN(81-210) represents the mature protein. However, we find that both FXN(42-210) and FXN(81-210) are present in control cell lines and tissues at steady-state, and that FXN(42-210) is consistently more depleted than FXN(81-210) in samples from FRDA patients. Moreover, FXN(42-210) and FXN(81-210) have strikingly different biochemical properties. A shorter N terminus correlates with monomeric configuration, labile iron binding, and dynamic contacts with components of the Fe-S cluster biosynthetic machinery, i.e. the sulfur donor complex NFS1·ISD11 and the scaffold ISCU. Conversely, a longer N terminus correlates with the ability to oligomerize, store iron, and form stable contacts with NFS1·ISD11 and ISCU. Monomeric FXN(81-210) donates Fe(2+) for Fe-S cluster assembly on ISCU, whereas oligomeric FXN(42-210) donates either Fe(2+) or Fe(3+). These functionally distinct FXN isoforms seem capable to ensure incremental rates of Fe-S cluster synthesis from different mitochondrial iron pools. We suggest that the levels of both isoforms are relevant to FRDA pathophysiology and that the FXN(81-210)/FXN(42-210) molar ratio should provide a useful parameter to optimize FXN augmentation and replacement therapies.
Quantum ensembles of quantum classifiers (2018)

Quantum machine learning witnesses an increasing amount of quantum algorithms for data-driven decision making, a problem with potential applications ranging from automated image recognition to medical diagnosis. Many of those algorithms are implementations of quantum classifiers, or models for the classification of data inputs with a quantum computer. Following the success of collective decision making with ensembles in classical machine learning, this paper introduces the concept of quantum ensembles of quantum classifiers. Creating the ensemble corresponds to a state preparation routine, after which the quantum classifiers are evaluated in parallel and their combined decision is accessed by a single-qubit measurement. This framework naturally allows for exponentially large ensembles in which - similar to Bayesian learning - the individual classifiers do not have to be trained. As an example, we analyse an exponentially large quantum ensemble in which each classifier is weighed according to its performance in classifying the training data, leading to new results for quantum as well as classical machine learning.
Skinny Hedgehog, an Acyltransferase Required for Palmitoylation and Activity of the Hedgehog Signal (2001)

One of the most dominant influences in the patterning of multicellular embryos is exerted by the Hedgehog (Hh) family of secreted signaling proteins. Here, we identify a segment polarity gene in Drosophila melanogaster, skinny hedgehog (ski), and show that its product is required in Hh-expressing cells for production of appropriate signaling activity in embryos and in the imaginal precursors of adult tissues. The ski gene encodes an apparent acyltransferase, and we provide genetic and biochemical evidence that Hh proteins from ski mutant cells retain carboxyl-terminal cholesterol modification but lack amino-terminal palmitate modification. Our results suggest that ski encodes an enzyme that acts within the secretory pathway to catalyze amino-terminal palmitoylation of Hh, and further demonstrate that this lipid modification is required for the embryonic and larval patterning activities of the Hh signal.
Oxidative Aliphatic C-H Fluorination with Fluoride Ion Catalyzed by a Manganese Porphyrin (2012)

Despite the growing importance of fluorinated organic compounds in drug development, there are no direct protocols for the fluorination of aliphatic C-H bonds using conveniently handled fluoride salts. We have discovered that a manganese porphyrin complex catalyzes alkyl fluorination by fluoride ion under mild conditions in conjunction with stoichiometric oxidation by iodosylbenzene. Simple alkanes, terpenoids, and even steroids were selectively fluorinated at otherwise inaccessible sites in 50 to 60% yield. Decalin was fluorinated predominantly at the C2 and C3 methylene positions. Bornyl acetate was converted to exo-5-fluoro-bornyl acetate, and 5α-androstan-17-one was fluorinated selectively in the A ring. Mechanistic analysis suggests that the regioselectivity for C-H bond cleavage is directed by an oxomanganese(V) catalytic intermediate followed by F delivery via an unusual manganese(IV) fluoride that has been isolated and structurally characterized.
Noncontact transscleral Nd:YAG cyclophotocoagulation: a long-term follow-up of 500 patients. (1994)

Long-term experience with transscleral cyclophotocoagulation in 500 patients suggests that this operation is the cyclodestructive procedure of choice. It offers a reasonable surgical option in the high-risk glaucoma population, which includes patients with neovascular glaucoma, glaucomas with active uveitis, glaucomas in aphakia or pseudophakia, and other cases in which filtering surgery has failed or is felt to have a low chance for success. Satisfactory intraocular pressure reduction was achieved in 62% of the patients with one treatment session. After one or more repeated procedures in 21% of the study group, the final intraocular pressure was below baseline in 94%, with a mean final reduction of 24 mm Hg, which was judged to be adequate for 87% of the patients. However, visual loss remains a significant postoperative complication, with some degree of reduced vision occurring in 39% of the study population. Patients with neovascular glaucoma had the greatest percentage of visual loss at 46%, compared with 34% and 38% for patients with glaucomas in pseudophakia and aphakia, respectively. While it is hard to know how many of these cases of visual loss were a direct result of the cyclophotocoagulation, the procedure should be used with caution in eyes with a potential for good central vision. Further study is needed to determine the relative indications for transcleral cyclophotocoagulation and the various operations to increase aqueous outflow in the management of patients in the high-risk glaucoma population.
Interleukin-6 gene amplification and shortened survival in glioblastoma patients (2007)

Interleukin-6 (IL-6) is known to promote tumour growth and survival. We evaluated IL-6 gene amplification in tumours from 53 glioma patients using fluorescence in situ hybridisation. Amplification events were detected only in glioblastomas (15 out of 36 cases), the most malignant tumours, and were significantly associated with decreased patient survival.
Spontaneous Orofacial Dyskinesia and Dopaminergic Function in Rats After 6 Months of Neuroleptic Treatment (1983)

A syndrome of spontaneous orofacial dyskinesia was identified in groups of rats treated for 6 months with a wide range of neuroleptic drugs. Phenothiazines, thioxanthenes, and substituted benzamides were particularly likely to induce the syndrome. It was observed in the presence of a functional blockade of dopamine receptors and endured for at least 2.5 months after drug withdrawal. There was no relation between the syndrome and changes in striatal dopamine receptors, as indexed by the binding of tritiated spiperone and tritiated cis(Z)-flupenthixol. The syndrome parallels several of the features of clinical tardive dyskinesia, whose pathophysiology thus may not involve changes in the characteristics of striatal dopamine receptors.
Fiber Field‐Effect Device Via In Situ Channel Crystallization (2010)

The in situ crystallization of the incorporated amorphous semiconductor within the multimaterial fiber device yields a large decrease in defect density and a concomitant five-order-of-magnitude decrease in resistivity of the novel metal-insulator-crystalline semiconductor structure. Using a post-drawing crystallization process, the first tens-of-meters-long single-fiber field-effect device is demonstrated. This work opens significant opportunities for incorporating higher functionality in functional fibers and fabrics.
19.7% Efficient All-Screen-Printed Back-Contact Back-Junction Silicon Solar Cell With Aluminum-Alloyed Emitter (2011)

A back-contact back-junction solar cell on n-type silicon with an aluminum-alloyed emitter is introduced, where both structuring and metallization are realized by screen-printing. The process sequence for realizing the cell with a pitch of 2 mm is displayed and described. The cell parameters are shown for three different emitter coverages on the rear side (45%, 58%, and 72%). An analysis of the saturation current density J <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">ο</sub> of the different areas was carried out on lifetime samples, and the calculated V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">oc</sub> is compared to the measured one. The potentially critical edge of the Al finger is analyzed in a scanning electron microscopy cross section. No damaging of the aluminum paste to the passivation layer and a homogenous p+-layer over the whole finger width is observed. A conversion efficiency of 19.7% is presented for a cell with an aperture area of 16.65 cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> that was exclusively processed in Fraunhofer ISE PV-TEC, which is an industrial-like fabrication environment.
Genome-Wide Analysis of the ERF Gene Family in Arabidopsis and Rice (2006)

Genes in the ERF family encode transcriptional regulators with a variety of functions involved in the developmental and physiological processes in plants. In this study, a comprehensive computational analysis identified 122 and 139 ERF family genes in Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa L. subsp. japonica), respectively. A complete overview of this gene family in Arabidopsis is presented, including the gene structures, phylogeny, chromosome locations, and conserved motifs. In addition, a comparative analysis between these genes in Arabidopsis and rice was performed. As a result of these analyses, the ERF families in Arabidopsis and rice were divided into 12 and 15 groups, respectively, and several of these groups were further divided into subgroups. Based on the observation that 11 of these groups were present in both Arabidopsis and rice, it was concluded that the major functional diversification within the ERF family predated the monocot/dicot divergence. In contrast, some groups/subgroups are species specific. We discuss the relationship between the structure and function of the ERF family proteins based on these results and published information. It was further concluded that the expansion of the ERF family in plants might have been due to chromosomal/segmental duplication and tandem duplication, as well as more ancient transposition and homing. These results will be useful for future functional analyses of the ERF family genes.
Real-Time Image Subtraction Using A Liquid Crystal Light Valve (1986)

A technique for subtracting images in real time utilizing a single liquid crystal light valve (LCLV) is described. The two images are projected in registration on the LCLV through a common grating. The projections are chosen such that the grating's image due to one beam is complementary to that displayed by the second beam, thus generating an interlacing effect. The readout light beam is optically filtered, so that only different features in the two images are revealed. Experimental results are presented.
Gene-Expression Profile Changes Correlated with Tumor Progression and Lymph Node Metastasis in Esophageal Cancer (2004)

We suggest that these characteristic genes will provide useful information for understanding the malignant nature of ESCC as well as information useful for personalizing the treatments.
Inheriting and articulating a community (2012)

In a recent Companion to Ancient History (Erskine 2009), little mention is made of Cyrene. Such absence is not unusual: the volume on Greeks beyond the Aegean (Karageorghis 2002), for example, contains nothing on Cyrene at all. But where it is mentioned most in Erskine (2009) is instructive: not in the chapter on North Africa, but in the chapter on concepts of citizenship. A quick look through the surviving ancient literature and modern scholarship on Cyrene shows an overwhelming interest in the story of its foundation, the celebration of its ruling kings, the arrangement of its later democratic constitution and the intrigue of its political place and stance within the Hellenistic and Roman worlds. Running through all these approaches is a common thread: that Cyrene is, from the standpoint of the literary sources, most often a creation of other writers, times and places.
Antiproinflammatory Effects of Iodixanol (OptiPrep)-Based Density Gradient Purification on Human Islet Preparations (2010)

Islet isolation and purification using a continuous density gradient may reduce the volume of tissue necessary for implantation into patients, therefore minimizing the risks associated with intraportal infusion in islet transplantation. On the other hand, the purification procedure might result in a decreased number of islets recovered due to various stresses such as exposure to cytokine/chemokine. While a Ficoll-based density gradient has been widely used in purification for clinical trials, purification with iodixanol (OptiPrep) has been recently reported in islet transplant series with successful clinical outcomes. The aim of the current study was to compare the effects of the purification method using OptiPrep-based and Ficoll-based density gradients. Human islet isolations were performed using a modified automated method. After the digestion phase, pre-purification digests were divided into two groups and purified using a semiautomated cell processor with either a continuous Ficoll- or OptiPrep-based density gradient. The quantity, purity, viability, and cellular composition of islet preparations from each group were assessed. Cytokine/chemokine and tissue factor production from islet preparations after 48-h culture were also measured. Although islet purity, post-purification IEQ, islet recovery rate, FDA/PI, and fractional β-cell viability were comparable, β-cell mass after 48-h culture significantly improved in the OptiPrep group when compared to the Ficoll group. The production of cytokine/chemokine including IL-1β, TNF-α, IFN-γ, IL-6, IL-8, MIP-1β, MCP-1, and RANTES but not tissue factor from the OptiPrep group was significantly lower during 48-h culture after isolation. Each preparation contained the similar number of ductal cells and macrophages. Endotoxin level in both gradient medium was also comparable. The purification method using OptiPrep gradient media significantly reduced cytokine/chemokine production but not tissue factor from human islet preparations and improved β-cell survival during pretransplant culture. Our results suggest that the purification method using OptiPrep gradient media may be of assistance in increasing successful islet transplantation.
Isolation and characterization of permanent cell lines from inner cell mass cells of bovine blastocysts (1995)

Inner cell masses (ICM) from in vitro produced day 8 or 9 bovine blastocysts were isolated by immunosurgery and cultured under different conditions in order to establish which of two feeder cell types and culture media were most efficient in supporting attachment and outgrowth of the bovine ICM cells. The efficiency of attachment and outgrowth of the ICM cells could be markedly improved when STO feeder cells were used instead of bovine uterus epithelial cells, and by using charcoal-stripped serum instead of normal serum to supplement the culture medium. More than 20 stable cell lines were obtained. Some of these lines were examined by immunofluorescence for developmentally regulated markers. From these results we conclude that the cell lines resemble epithelial cells, rather than pluripotent ICM cells. The developmental potential of cells of one of the lines was tested in the nuclear transfer assay. The cell line could support the initial development of enucleated oocytes, but none of the reconstructed embryos passed the eight-cell block.
Small scale sediment removal from beaches in Northern Ireland: environmental impact, community perception and conservation management (1992)

Abstract 1. Small scale sand removal (loads of 0.5 to 10 tonnes) is a persistent environmental problem on beaches within Areas of Outstanding Natural Beauty in Northern Ireland. 2. This study provides the first objective assessment of the problem in the British Isles, examining both the physical and biological impacts on the beach and the cultural background. These approaches are combined to indicate possible management strategies. 3. About 5000 to 6000 tonnes of sediment (sand and gravel) was ‘drawn’ from the eleven beaches in the study area during 1990. The rate and magnitude of sediment removal varied between and within sites, by day of the week and by season. 4. There are two direct impacts to the shoreline environment. First, over a long period, the amount of sediment removed is enough to cause serious erosion on some smaller beaches. Up to 80% of shoreline recession can be explained by sand lost through extraction. Second, extraction appears to lead to an impoverished beach fauna. More indirect impacts include the loss of aesthetic quality (important in an area reliant on tourism), disturbance of wildlife, damage to and possible reduction of access provision, and impairing the ability of the shoreline to develop foredunes. 5. The views of the coastal community are quite polarized. One group (about 55%) wish to see sand removal cease, while the remainder (45%) do not. Interviews with people actually taking sand suggest that they do not see their actions as damaging the environment. 6. Several options for future management are discussed. It would appear that a management prescription for each site, backed by legislation, might relieve the problem.
Cardiac Progenitor Cells and Biotinylated Insulin-Like Growth Factor-1 Nanofibers Improve Endogenous and Exogenous Myocardial Regeneration After Infarction (2009)

The addition of nanofiber-mediated IGF-1 delivery to CPC therapy improved in part the recovery of myocardial structure and function after infarction.
The Chloroplast Triggers Developmental Reprogramming When MUTS HOMOLOG1 Is Suppressed in Plants (2012)

Multicellular eukaryotes demonstrate nongenetic, heritable phenotypic versatility in their adaptation to environmental changes. This inclusive inheritance is composed of interacting epigenetic, maternal, and environmental factors. Yet-unidentified maternal effects can have a pronounced influence on plant phenotypic adaptation to changing environmental conditions. To explore the control of phenotypy in higher plants, we examined the effect of a single plant nuclear gene on the expression and transmission of phenotypic variability in Arabidopsis (Arabidopsis thaliana). MutS HOMOLOG1 (MSH1) is a plant-specific nuclear gene product that functions in both mitochondria and plastids to maintain genome stability. RNA interference suppression of the gene elicits strikingly similar programmed changes in plant growth pattern in six different plant species, changes subsequently heritable independent of the RNA interference transgene. The altered phenotypes reflect multiple pathways that are known to participate in adaptation, including altered phytohormone effects for dwarfed growth and reduced internode elongation, enhanced branching, reduced stomatal density, altered leaf morphology, delayed flowering, and extended juvenility, with conversion to perennial growth pattern in short days. Some of these effects are partially reversed with the application of gibberellic acid. Genetic hemicomplementation experiments show that this phenotypic plasticity derives from changes in chloroplast state. Our results suggest that suppression of MSH1, which occurs under several forms of abiotic stress, triggers a plastidial response process that involves nongenetic inheritance.
Virus-specific cellular immune correlates of survival in vaccinated monkeys after SIV challenge (2006)

Understanding the characteristics of the virus-specific T lymphocyte response that will confer optimal protection against the clinical progression of AIDS will inform the development of an effective cellular immune-based HIV vaccine. We have recently shown that survival in plasmid DNA-primed/recombinant adenovirus-boosted rhesus monkeys that are challenged with SIVmac251 is associated with the preservation post-challenge of central memory CD4+ T lymphocytes and robust IFN-g-producing SIV-specific CD8+ and CD4+ T lymphocyte responses. Further studies were initiated to extend these observations to determine which virus-specific T lymphocyte subpopulations play a primary role in controlling disease progression and characterize the functional repertoire of these cells. We show that the preservation of the SIV-specific central memory CD8+ T lymphocyte population and a linked SIV-specific CD4+ T lymphocyte response are associated with prolonged survival in vaccinated monkeys following challenge. Further, we demonstrate that SIV-specific IFN-g, TNF-a, and IL-2 producing T lymphocytes are all comparably associated with protection against disease progression. These findings underscore the contribution of virus-specific central memory T lymphocytes in controlling clinical progression in vaccinated individuals following a primate immunodeficiency virus infection.
BiSeNet: Bilateral Segmentation Network for Real-time Semantic Segmentation (2018)

Semantic segmentation requires both rich spatial information and sizeable receptive field. However, modern approaches usually compromise spatial resolution to achieve real-time inference speed, which leads to poor performance. In this paper, we address this dilemma with a novel Bilateral Segmentation Network (BiSeNet). We first design a Spatial Path with a small stride to preserve the spatial information and generate high-resolution features. Meanwhile, a Context Path with a fast downsampling strategy is employed to obtain sufficient receptive field. On top of the two paths, we introduce a new Feature Fusion Module to combine features efficiently. The proposed architecture makes a right balance between the speed and segmentation performance on Cityscapes, CamVid, and COCO-Stuff datasets. Specifically, for a 2048x1024 input, we achieve 68.4% Mean IOU on the Cityscapes test dataset with speed of 105 FPS on one NVIDIA Titan XP card, which is significantly faster than the existing methods with comparable performance.