gebhart/patrepeval huggingface dataset:
Measurement of liver volume and hepatic functional reserve as a guide to decision-making in resectional surgery for hepatic tumors (1997)

The respective volumes of hepatic tumors and nontumorous parenchyma of 50 patients requiring hepatectomy of more than one segment of Healey for tumor removal were measured using computed tomography (Vol-CT). The volume estimated by Vol-CT was found to correlate with the real weight resected (P < .0001) with a mean absolute error of 64.9 mL. The ratio of the nontumorous parenchymal volume of the resected liver to that of the whole liver (R2) in 15 patients who underwent right or extended right hepatic lobectomy was 43% +/- 15%. Eight of 15 patients with R2s < 60% underwent the procedures without right portal vein embolization (PE). The other seven with R2s exceeding 60% or an indocyanine green retention rate after 15 minutes (ICG15) of 10% to 20% underwent PE: in six of seven, the nontumorous parenchyma of the right hepatic lobe became atrophic and in all seven, the volume of the remaining left hepatic lobe increased with a decrease in the mean R2 from 62% +/- 14% to 55% +/- 8% (P = .0006). In the remaining 35 who underwent other hepatectomy procedures, R2s also remained <60%. Overall, at surgery, in 27 with normal liver function (ICG15 < 10%), R2s exceeded 60% in one, remained at 50% to 60% in five, and <50% in 21, whereas 23 patients except for one with an ICG15 exceeding 10%, had R2s of <50%. The postoperative serum total bilirubin levels in 84% of the patients remained within the normal range and there was no surgery-related mortality. In conclusion, 1) Vol-CT can accurately assess the extent of liver resection, 2) individuals with normal liver function can undergo resection of up to 60% of the nontumorous parenchyma without the need for PE, and 3) PE can be used to reduce the size of the resected tissue and increase the volume of the remnant liver to approximate the target limits in individuals with large tumors or minimally abnormal liver function.
Chiropteran types I and II interferon genes inferred from genome sequencing traces by a statistical gene-family assembler (2010)

The statistical trace assembler described here provides a reliable method for extracting information from the many available and forthcoming partial or shallow genome sequencing projects, thereby facilitating the study of a wider variety of organisms with ecological and biomedical significance to humans than would otherwise be possible.
THE GENETICS OF <i>CAENORHABDITIS ELEGANS</i> (1974)

Methods are described for the isolation, complementation and mapping of mutants of Caenorhabditis elegans, a small free-living nematode worm. About 300 EMS-induced mutants affecting behavior and morphology have been characterized and about one hundred genes have been defined. Mutations in 77 of these alter the movement of the animal. Estimates of the induced mutation frequency of both the visible mutants and X chromosome lethals suggests that, just as in Drosophila, the genetic units in C. elegans are large.
[In vitro study of the directed inducing cartilage cells from rat bone mesenchymal stem cells on scaffolds]. (2005)

This study was conducted to assess the cell proliferation and cell cycle of the directed inducing cartilage cells from rat bone mesenchymal stem cells on collagen sponge and compare the results with those of the plane inducing cartilage cells. The MSCs were isolated from rat bone marrow by density gradient centrifuge and adhesive property, and then were induced into chondrogenic differentiation by adding transforming growth factor-beta1 (TGF-beta1), dexamethasone, transferring and insulin on collage sponge and plane condition. Immunohistochemistry was applied to detect the expression of collagen type II on the scaffolds and plane conditions. The cell proliferation and cell cycle on different conditions were detected with MTT automated colormetric microassay and flow cytometry. The differentiation of MSCs toward chondrogenic phenotype was verified by the positive result of collagen type II on the scaffolds and plane condition. The cell viability in scaffolds was better than that in plane conditions. The S phase and G2 phase were 30 percent in whole cell cycle on the scaffold, which was different from that of the control groups. The method of using the Using directed inducing cartilage from bone MSCs combined with collage sponge to construct tissue-engineered cartilage is feasible; it is better than the method of plane directed inducing.
Telomerase activity is required for bleomycin-induced pulmonary fibrosis in mice (2007)

In addition to its well-known expression in the germline and in cells of certain cancers, telomerase activity is induced in lung fibrosis, although its role in this process is unknown. To identify the pathogenetic importance of telomerase in lung fibrosis, we examined the effects of telomerase reverse transcriptase (TERT) deficiency in a murine model of pulmonary injury. TERT-deficient mice showed significantly reduced lung fibrosis following bleomycin (BLM) insult. This was accompanied by a significant reduction in expression of lung alpha-SMA, a marker of myofibroblast differentiation. Furthermore, lung fibroblasts isolated from BLM-treated TERT-deficient mice showed significantly decreased proliferation and increased apoptosis rates compared with cells isolated from control mice. Transplantation of WT BM into TERT-deficient mice restored BLM-induced lung telomerase activity and fibrosis to WT levels. Conversely, transplantation of BM from TERT-deficient mice into WT recipients resulted in reduced telomerase activity and fibrosis. These findings suggest that induction of telomerase in injured lungs may be caused by BM-derived cells, which appear to play an important role in pulmonary fibrosis. Moreover, TERT induction is associated with increased survival of lung fibroblasts, which favors the development of fibrosis instead of injury resolution.
Mini-batch Serialization: CNN Training with Inter-layer Data Reuse (2018)

Training convolutional neural networks (CNNs) requires intense computations and high memory bandwidth. We find that bandwidth today is over-provisioned because most memory accesses in CNN training can be eliminated by rearranging computation to better utilize on-chip buffers and avoid traffic resulting from large per-layer memory footprints. We introduce the MBS CNN training approach that significantly reduces memory traffic by partially serializing mini-batch processing across groups of layers. This optimizes reuse within on-chip buffers and balances both intra-layer and inter-layer reuse. We also introduce the WaveCore CNN training accelerator that effectively trains CNNs in the MBS approach with high functional-unit utilization. Combined, WaveCore and MBS reduce DRAM traffic by 75%, improve performance by 53%, and save 26% system energy for modern deep CNN training compared to conventional training mechanisms and accelerators.
Hyperglycemia Diverts Dividing Osteoblastic Precursor Cells to an Adipogenic Pathway and Induces Synthesis of a Hyaluronan Matrix That Is Adhesive for Monocytes (2014)

Isolated rat bone marrow stromal cells cultured in osteogenic medium in which the normal 5.6 mm glucose is changed to hyperglycemic 25.6 mm glucose greatly increase lipid formation between 21-31 days of culture that is associated with decreased biomineralization, up-regulate expression of cyclin D3 and two adipogenic markers (CCAAT/enhancer binding protein α and peroxisome proliferator-activated receptor γ) within 5 days of culture, increase neutral and polar lipid synthesis within 5 days of culture, and form a monocyte-adhesive hyaluronan matrix through an endoplasmic reticulum stress-induced autophagic mechanism. Evidence is also provided that, by 4 weeks after diabetes onset in the streptozotocin-induced diabetic rat model, there is a large loss of trabecular bone mineral density without apparent proportional changes in underlying collagen matrices, a large accumulation of a hyaluronan matrix within the trabecular bone marrow, and adipocytes and macrophages embedded in this hyaluronan matrix. These results support the hypothesis that hyperglycemia in bone marrow diverts dividing osteoblastic precursor cells (bone marrow stromal cells) to a metabolically stressed adipogenic pathway that induces synthesis of a hyaluronan matrix that recruits inflammatory cells and establishes a chronic inflammatory process that demineralizes trabecular cancellous bone.
IMG-ABC: new features for bacterial secondary metabolism analysis and targeted biosynthetic gene cluster discovery in thousands of microbial genomes (2016)

Secondary metabolites produced by microbes have diverse biological functions, which makes them a great potential source of biotechnologically relevant compounds with antimicrobial, anti-cancer and other activities. The proteins needed to synthesize these natural products are often encoded by clusters of co-located genes called biosynthetic gene clusters (BCs). In order to advance the exploration of microbial secondary metabolism, we developed the largest publically available database of experimentally verified and predicted BCs, the Integrated Microbial Genomes Atlas of Biosynthetic gene Clusters (IMG-ABC) (https://img.jgi.doe.gov/abc/). Here, we describe an update of IMG-ABC, which includes ClusterScout, a tool for targeted identification of custom biosynthetic gene clusters across 40 000 isolate microbial genomes, and a new search capability to query more than 700 000 BCs from isolate genomes for clusters with similar Pfam composition. Additional features enable fast exploration and analysis of BCs through two new interactive visualization features, a BC function heatmap and a BC similarity network graph. These new tools and features add to the value of IMG-ABC's vast body of BC data, facilitating their in-depth analysis and accelerating secondary metabolite discovery.
Marked increase of sulfur dioxide removal ability of poly(acrylonitrile)-based active carbon fiber by heat treatment at elevated temperatures (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMarked increase of sulfur dioxide removal ability of poly(acrylonitrile)-based active carbon fiber by heat treatment at elevated temperaturesIsao Mochida, Teruo Hirayama, Seiki Kisamori, Shizuo Kawano, and Hiroshi FujitsuCite this: Langmuir 1992, 8, 9, 2290–2294Publication Date (Print):September 1, 1992Publication History Published online1 May 2002Published inissue 1 September 1992https://pubs.acs.org/doi/10.1021/la00045a036https://doi.org/10.1021/la00045a036research-articleACS PublicationsRequest reuse permissionsArticle Views229Altmetric-Citations39LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
「RIP，426」：解析「大陸地區旅台學位生」的國族經驗 (2018)

In 2011, the Taiwanese government launched a new policy to open opportunities for students from mainland China (also known as ＂lusheng＂) to pursue higher education degrees in Taiwan. Many high officials and supporters optimistically expected that such a policy would advance mutual understandings between the younger generations across the Strait; some may even have thought that this policy would foster ＂Taiwan-friendly circles＂ that, in turn, would contribute to peace-building by reducing tensions across the Strait. Using data collected from in-depth interviews and participatory observations, this paper investigates mainland students' experiences regarding the ＂national question＂ through three levels: institutions, cognitive frames, and structures of feeling. It is found that ＂national experiences＂ of mainland students generate both ＂pushes＂ and ＂pulls＂ that further differentiate three types of students. Among them, two types of students have become more hostile to Taiwan and more supportive to the communist regime in China. Such a result seems to contradict the initial policy expectation. In conclusion, we explore the implications from this analysis for future reconciliation between the two sides across the Strait.
Characterization of a thiamin diphosphate‐dependent phenylpyruvate decarboxylase from <i>Saccharomyces cerevisiae</i> (2011)

The product of the ARO10 gene from Saccharomyces cerevisiae was initially identified as a thiamine diphosphate-dependent phenylpyruvate decarboxylase with a broad substrate specificity. It was suggested that the enzyme could be responsible for the catabolism of aromatic and branched-chain amino acids, as well as methionine. In the present study, we report the overexpression of the ARO10 gene product in Escherichia coli and the first detailed in vitro characterization of this enzyme. The enzyme is shown to be an efficient aromatic 2-keto acid decarboxylase, consistent with it playing a major in vivo role in phenylalanine, tryptophan and possibly also tyrosine catabolism. However, its substrate spectrum suggests that it is unlikely to play any significant role in the catabolism of the branched-chain amino acids or of methionine. A homology model was used to identify residues likely to be involved in substrate specificity. Site-directed mutagenesis on those residues confirmed previous studies indicating that mutation of single residues is unlikely to produce the immediate conversion of an aromatic into an aliphatic 2-keto acid decarboxylase. In addition, the enzyme was compared with the phenylpyruvate decarboxylase from Azospirillum brasilense and the indolepyruvate decarboxylase from Enterobacter cloacae. We show that the properties of the two phenylpyruvate decarboxylases are similar in some respects yet quite different in others, and that the properties of both are distinct from those of the indolepyruvate decarboxylase. Finally, we demonstrate that it is unlikely that replacement of a glutamic acid by leucine leads to discrimination between phenylpyruvate and indolepyruvate, although, in this case, it did lead to unexpected allosteric activation.
Spreading vectors for similarity search (2018)

Discretizing multi-dimensional data distributions is a fundamental step of\nmodern indexing methods. State-of-the-art techniques learn parameters of\nquantizers on training data for optimal performance, thus adapting quantizers\nto the data. In this work, we propose to reverse this paradigm and adapt the\ndata to the quantizer: we train a neural net which last layer forms a fixed\nparameter-free quantizer, such as pre-defined points of a hyper-sphere. As a\nproxy objective, we design and train a neural network that favors uniformity in\nthe spherical latent space, while preserving the neighborhood structure after\nthe mapping. We propose a new regularizer derived from the Kozachenko--Leonenko\ndifferential entropy estimator to enforce uniformity and combine it with a\nlocality-aware triplet loss. Experiments show that our end-to-end approach\noutperforms most learned quantization methods, and is competitive with the\nstate of the art on widely adopted benchmarks. Furthermore, we show that\ntraining without the quantization step results in almost no difference in\naccuracy, but yields a generic catalyzer that can be applied with any\nsubsequent quantizer.\n
Identification of microtubule-associated proteins in the centrosome, spindle, and kinetochore of the early Drosophila embryo. (1989)

We have developed affinity chromatography methods for the isolation of microtubule-associated proteins (MAPs) from soluble cytoplasmic extracts and have used them to analyze the cytoskeleton of the early Drosophila embryo. More than 50 Drosophila embryo proteins bind to microtubule affinity columns. To begin to characterize these proteins, we have generated individual mouse polyclonal antibodies that specifically recognize 24 of them. As judged by immunofluorescence, some of the antigens localize to the mitotic spindle in the early Drosophila embryo, while others are present in centrosomes, kinetochores, subsets of microtubules, or a combination of these structures. Since 20 of the 24 antibodies stain microtubule structures, it is likely that most of the proteins that bind to our columns are associated with microtubules in vivo. Very few MAPS seem to be identically localized in the cell, indicating that the microtubule cytoskeleton is remarkably complex.
Reactions of dialkylmagnesium-organolithium solutions with pyridine, quinoline, and cyclohexenone (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTReactions of dialkylmagnesium-organolithium solutions with pyridine, quinoline, and cyclohexenoneHerman G. Richey Jr. and Julius Farkas Jr.Cite this: Organometallics 1990, 9, 6, 1778–1784Publication Date (Print):June 1, 1990Publication History Published online1 May 2002Published inissue 1 June 1990https://pubs.acs.org/doi/10.1021/om00156a015https://doi.org/10.1021/om00156a015research-articleACS PublicationsRequest reuse permissionsArticle Views316Altmetric-Citations33LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Surgical Robot for Single-Incision Laparoscopic Surgery (2014)

This paper introduces a novel surgical robot for single-incision laparoscopic surgeries. The robot system includes the cone-type remote center-of-motion (RCM) mechanism and two articulated instruments having a flexible linkage-driven elbow. The RCM mechanism, which has two revolute joints and one prismatic joint, is designed to maintain a stationary point at the apex of the cone shape. By placing the stationary point on the incision area, the mechanism allows a surgical instrument to explore the abdominal area through a small incision point. The instruments have six articulated joints, including an elbow pitch joint, which make the triangulation position for the surgery possible inside of the abdominal area. The presented elbow pitch structure is similar to the slider-crank mechanism but the connecting rod is composed of a flexible leaf spring for high payload and small looseness error. We verified the payload of the robot is more than 10 N and described preliminary experiments on peg transfer and suture motion by using the proposed surgical robot.
Freehand spatial-angular compounding of photoacoustic images (2014)

Photoacoustic (PA) imaging is an emerging medical imaging modality that relies on the absorption of optical energy and the subsequent emission of acoustic waves that are detected with a conventional ultrasound probe. PA images are susceptible to background noise artifacts that reduce the signal-to-noise ratio (SNR) and contrast-to-noise ratio (CNR). We investigated spatial-angular compounding of PA images to enhance these image qualities. Spatial-angular compounding was implemented by averaging multiple PA images acquired as an ultrasound probe was rotated about the elevational axis with the laser beam and PA target fixed in the same location. An external tracking system was used to provide the position and orientation (i.e. pose) information of each PA image. Based on this pose information, frames in similar elevational planes were filtered from the acquired image data and compounded using one of two methods. One method registered overlapping signals between frames prior to compounding (using the pose information), while the second method omitted this spatial registration step. These two methods were applied to pre-beamformed RF, beamformed RF, and envelope-detected data, resulting in six different compounding pipelines. Compounded PA images with similar lateral resolution to a single reference image had factors of 1.1 - 1.6, 2.0 - 11.1, and 2.0 - 11.1 improvements in contrast, CNR, and SNR, respectively, when compared to the reference image. These improvements depended on the amount of relative motion between the reference image and the images that were compounded. The inclusion of spatial registration prior to compounding preserved lateral resolution and signal location when the relative rotations about the elevation axis were 3.5° or less for images that were within an elevational distance of 2.5 mm from the reference image, particularly when the method was applied to the enveloped-detected data. Results indicate that spatial-angular compounding has the potential to improve image quality for a variety of photoacoustic imaging applications.
Dendrite‐Free, High‐Rate, Long‐Life Lithium Metal Batteries with a 3D Cross‐Linked Network Polymer Electrolyte (2017)

A 3D network gel polymer electrolyte (3D-GPE) is designed for lithium metal batteries and prepared by an initiator-free one-pot ring-opening polymerization technique. This 3D-GPE exhibits an unprecedented combination of mechanical strength, ionic conductivity, and more importantly, effective suppression of Li dendrite growth. The produced lithium-based battery presents long life, high rate, and excellent safety.