gebhart/patrepeval huggingface dataset:
THE EFFECTS OF pH AND TEMPERATURE ON THE KINETICS OF THE PHOSPHORYLASE REACTION (1964)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Deep Convolutional Neural Networks Enable Discrimination of Heterogeneous Digital Pathology Images (2017)

Pathological evaluation of tumor tissue is pivotal for diagnosis in cancer patients and automated image analysis approaches have great potential to increase precision of diagnosis and help reduce human error. In this study, we utilize several computational methods based on convolutional neural networks (CNN) and build a stand-alone pipeline to effectively classify different histopathology images across different types of cancer. In particular, we demonstrate the utility of our pipeline to discriminate between two subtypes of lung cancer, four biomarkers of bladder cancer, and five biomarkers of breast cancer. In addition, we apply our pipeline to discriminate among four immunohistochemistry (IHC) staining scores of bladder and breast cancers. Our classification pipeline includes a basic CNN architecture, Google's Inceptions with three training strategies, and an ensemble of two state-of-the-art algorithms, Inception and ResNet. Training strategies include training the last layer of Google's Inceptions, training the network from scratch, and fine-tunning the parameters for our data using two pre-trained version of Google's Inception architectures, Inception-V1 and Inception-V3. We demonstrate the power of deep learning approaches for identifying cancer subtypes, and the robustness of Google's Inceptions even in presence of extensive tumor heterogeneity. On average, our pipeline achieved accuracies of 100%, 92%, 95%, and 69% for discrimination of various cancer tissues, subtypes, biomarkers, and scores, respectively. Our pipeline and related documentation is freely available at https://github.com/ih-_lab/CNN_Smoothie.
Characterization of Four Extensin Genes in Arabidopsis thaliana by Differential Gene Expression under Stress and Non-Stress Conditions (2001)

From Arabidopsis thaliana we isolated four different cDNAs that encode extensins, a family of cell-wall hydroxyproline-rich glycoproteins (HRGPs). Putative proteins (AtExt2-5) contained one open reading frame and characteristic Ser-(Pro)4 sequences organized in a high-order repetitive motif. AtExt2-5 genes were strongly expressed during rehydration after dehydration. They were also expressed after treatment with various amino acids. In particular, AtExt3 and five mRNAs were abundantly accumulated after treatment with L-Ser, Hyp, and L-Pro, which are major components of extensin proteins. The AtExt transcripts were strongly expressed in root tissues of both unbolted and bolted plants. The transcripts of AtExt2, 3, and 5 were also detected in the lower stem and flower buds, and that of AtExt4 was detected in bolted flowers. Therefore, we suggest that these four AtExt genes are novel extensin genes in A. thaliana, because the expression of atExt1, which has already been isolated from A. thaliana, was different from these.
Nutritional influences on illness (1987)

Folic acid nutriture has been shown to be directly related to gingival health, [none study, following 30 days during which patients with normal plasma folate levels ingested 2 mg folic acid twice daily or placebo under double-blind conditions, folate increased the resistance ot the gingiva to local irritants leading to a reduction in inflammation - even though plasma folate levels were unchanged.* Folate mouthwash is also effective, and may be even more effective than dietary supplements,* Vitamin A A deficiency of vitamin A is well known to predispose to periodontal disea.se. For example, a group of pregnant women was found to show maximal inflammatory changes of the periodontium in the 8th month when the mean physiologic level of vitamin A declined. Shortly after delivery, by contrast, vitamin A levels became markedly elevated and periodontal inflammation improved, raising the question of whether periodontitis of pregnancy is related to changes in the levels of the vitamin,' Vitamin C Ascorbic acid protects the oral mucosal epithelium against the infiltration of antigenic materials such as bacterial endotoxins, so it is not surprising that serum vitamin C levels have a significant (although weak) inverse association with periodoniitis,'' Dietary vitamin C intake shows a similar relationship, at least up to an intake of 180 mg daily,' Also. 500 mg daily ofthe vitamin for 90 days has been shown to reduce both dental plaque and stain,
A Configurable FPGA Implementation of PEG-based PS-LDPC Decoder (2010)

Low-density parity-check (LDPC) codes form an important subclass of error correcting coding techniques, and its implementation has been hot spot of domains such as signal process, magnetic recording or next generation communication for years. This paper proposes a configurable FPGA implementation of Partition-and-Shift LDPC decoder based on Min-Sum algorithm. An MPEG algorithm is introduced to reduce the complexity of searching for closed paths in shift matrix. And a routing paths switch concept is proposed to realize the expected configurability. Benefits of the proposed technique are demonstrated with FPGA design for differently configured PS-LDPC decoders which all achieve a Gbps throughput, low hardware cost and excellent BER performance at 16 iterations.
Translational control of mRNA expression during the early mitogenic response in Swiss mouse 3T3 cells: identification of specific proteins. (1986)

Addition of serum or epidermal growth factor to quiescent Swiss mouse 3T3 cells in culture leads to a number of specific changes in the pattern of protein synthesis. Earlier experiments with actinomycin D suggested that the altered expression of these proteins was controlled at either the pretranslational or translational level. Here we have identified and further characterized the regulation of mRNA expression for ten of these proteins, including protein synthesis elongation factor eEF-1 alpha, poly A binding protein, vimentin, the multiple forms of the actin protein family, and alpha- and beta-tubulin. Using an in vitro translation system, we determined the change in the level of mRNA encoding for each of these proteins after serum stimulation. The results showed that the amount of mRNA coding for eEF-1 alpha, poly A binding protein, vimentin, and alpha- and beta-tubulin remains unchanged during this time, whereas that of the actin family increases. Thus, with the exception of the actin family, the results argue that the expression of all the proteins identified is regulated at the translational level. The importance of this latter group of proteins in cell growth and the abundance of their cognate mRNAs should prove them useful tools in elucidating the mechanisms involved in the activation of translationally repressed mRNA during the mitogenic response.
Off-Flavor Problems in Two Reservoirs, Associated with Planktonic Pseudanabaena Species (1999)

In the summer of 1996, off-flavor episodes involving 2-methylisoborneol (MIB) occurred in two southern California reservoirs: San Vicente Reservoir, in the San Diego area, and Lake Skinner, in western Riverside County. These events resulted in many consumer complaints from the respective communities served. During the San Diego episode, moderate numbers of Pseudanabaena and other plankton were present in the water, and MIB was detected in one sample at 23 ng/l. Two strains of Pseudanabaena that produced MIB were isolated; cultures of this organism yielded 22 and 23 μg/l, respectively. Lake Skinner water also contained a moderate number of Pseudanabaena and other plankton when MIB levels began to rise, with MIB reaching 10 ng/l. Liquid and agar cultures derived from Lake Skinner water developed a strong MIB odor, and eventually three MIB-producing isolates were obtained. MIB levels in the cultures were all less than 1 μg/l. This was the first known MIB episode of planktonic origin in Lake Skinner, and it was the first off-flavor event in either reservoir in which Pseudanabaena was implicated. These two events underscore the potential importance of an organism not generally recognized as a cause of off-flavor in water supplies.
An empirical analysis of the optimization of deep network loss surfaces (2016)

The success of deep neural networks hinges on our ability to accurately and efficiently optimize high-dimensional, non-convex functions. In this paper, we empirically investigate the loss functions of state-of-the-art networks, and how commonly-used stochastic gradient descent variants optimize these loss functions. To do this, we visualize the loss function by projecting them down to low-dimensional spaces chosen based on the convergence points of different optimization algorithms. Our observations suggest that optimization algorithms encounter and choose different descent directions at many saddle points to find different final weights. Based on consistency we observe across re-runs of the same stochastic optimization algorithm, we hypothesize that each optimization algorithm makes characteristic choices at these saddle points.
THE EFFECT OF FATTY ACID BUFFER SYSTEMS ON THE APPARENT VISCOSITY OF THE <i>ARBACIA</i> EGG, WITH ESPECIAL REFERENCE TO THE QUESTION OF CELL PERMEABILITY TO IONS (1931)

The effects of the pH of the medium on the apparent viscosity of Arbacia eggs have been studied by means of an adaptation of the centrifuge method. It was found that the degree to which fatty acids decrease the protoplasmic viscosity can be altered by the presence of the salt of the acid, apparently by virtue of the influence of the salt on the intracellular hydrogen ion equilibria. Similar pH variations of the medium produced by mineral acids do not affect viscosity. These results offer confirmation, from a separate type of evidence, of Smith's observation that the salts of penetrating acids differ from other ionized compounds in apparently being able to penetrate the living cell much more easily. It is suggested that cell permeability to this type of salt could be explained as resulting from a cation exchange of external base for internal hydrogen ions from the penetrating acid, the entrance of the salt therefore being accomplished without the direct transfer of its anions.
A 70-GHz f/sub T/ low operating bias self-aligned p-type SiGe MODFET (1996)

A self-aligned process for the fabrication of SiGe p-type modulation-doped field-effect transistors (MODFETs) is described. Self-aligned devices with 0.1-μm gate-length have been fabricated and characterized. A maximum dc extrinsic transconductance of 258 mS/mm was obtained with a low turn-on resistance and very low knee voltage. Excellent high frequency performance with a unity current-gain cutoff frequency (f <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">T</sub> ) of 70 GHz was obtained. This excellent high frequency performance was exhibited even at drain bias as low as 0.5 V.
TGFβ-induced downregulation of E-cadherin-based cell-cell adhesion depends on PI3-kinase and PTEN (2005)

Transforming growth factor beta (TGFbeta) has profound growth-suppressive effects on normal epithelial cells, but supports metastasis formation in many tumour types. In most epithelial tumour cells TGFbeta(1) treatment results in epithelial dedifferentiation with reduced cell aggregation and enhanced cellular migration. Here we show that the epithelial dedifferentiation, accompanied by dissociation of the E-cadherin adhesion complex, induced by TGFbeta(1) depended on phosphatidylinositol 3-kinase (PI3-kinase) and the phosphatase PTEN as analysed in PANC-1 and Smad4-deficient BxPC-3 pancreatic carcinoma cells. TGFbeta(1) treatment enhanced tyrosine phosphorylation of alpha- and beta-catenin, which resulted in dissociation of the E-cadherin/catenin complex from the actin cytoskeleton and reduced cell-cell adhesion. The PI3-kinase and PTEN were found associated with the E-cadherin/catenin complex via beta-catenin. TGFbeta(1) treatment reduced the amount of PTEN bound to beta-catenin and markedly increased the tyrosine phosphorylation of beta-catenin. By contrast, forced expression of PTEN clearly reduced the TGFbeta(1)-induced phosphorylation of beta-catenin. The TGFbeta(1)-induced beta-catenin phosphorylation was also dependent on PI3-kinase and Ras activity. The described effects of TGFbeta(1) were independent of Smad4, which is homozygous deleted in BxPC-3 cells. Collectively, these data show that the TGFbeta(1)-induced destabilisation of E-cadherin-mediated cell-cell adhesion involves phosphorylation of beta-catenin, which is regulated by E-cadherin adhesion complex-associated PI3-kinase and PTEN.
Molecular Aspects of Renal Anionic Drug Transport (2002)

Multiple organic anion transporters in the proximal tubule of the kidney are involved in the secretion of drugs, toxic compounds, and their metabolites. Many of these compounds are potentially hazardous on accumulation, and it is therefore not surprising that the proximal tubule is also an important target for toxicity. In the past few years, considerable progress has been made in the cloning of these transporters and their functional characterization following heterologous expression. Members of the organic anion transporter (OAT), organic anion transporting polypeptide (OATP), multidrug resistance protein (MRP), sodium-phosphate transporter (NPT), and peptide transporter (PEPT) families have been identified in the kidney. In this review, we summarize our current knowledge on their localization, molecular and functional characteristics, and substrate and inhibitor specificity. A major challenge for the future will be to understand how these transporters work in concert to accomplish the renal secretion of specific anionic substrates.
Characteristics of p-type GaN Films Doped with Isoelectronic Indium Atoms (2002)

The method of isoelectronic doping, is employed to prepare p-type GaN films using metalorganic chemical vapor deposition. With the addition of In atoms, the film surface becomes much smoother, and the corresponding hole concentration and resistivity are also improved, to 8.7 £ 10^17 cm^(-3) and » 1 Ω-cm, respectively. More interestingly, it is found that an ohmic I-V characteristic can be obtained in such types of films without any dehydrogenation treatment.
l-Tartaric acid assisted binary organogel system: strongly enhanced fluorescence induced by supramolecular assembly (2005)

A new series of binary organogels, which showed good gelated capability and strongly enhanced fluorescence emission, were designed and prepared by simply mixing two components of L-tartaric acid and alkoxyl substituted stilbazoles. It was found that L-tartaric acid could not only introduce stilbazole with fluorescent property into the gel system, but also provided a main motif for the formation of the gel-phase via multiple hydrogen bonds. Meanwhile, pi-pi interactions between the complexes also played a key role in the gel formation. The decreased nonradiative process, suggested by the longer fluorescent lifetime of aggregates than that of monomers and the presence of the J-aggregation for the aggregated state, favored the enhanced fluorescence emission.
Palladium-Catalyzed Aryl C−H Bonds Activation/Acetoxylation Utilizing a Bidentate System (2009)

A palladium-catalyzed aryl C-H bonds activation/acetoxylation reaction utilizing a bidentate system has been explored. This transformation has been applied to a wide array of pyridine and 8-aminoquinoline derivatives and it exhibits excellent functional group tolerance.
Specificity of action of piperidylcholine derivatives as substrates of cholinesterases of various origin (2009)

The review deals with study of enzymologic properties of a novel highly specific acetylcholinesterase substrate iodomethylate N-beta-(acetoxyethyl)piperidinium ("piperidylcholine") and its 30 derivatives that were tested as effectors of cholinesterases of mammals and various species of Pacific squids. It was proven for the first time that responsible for specificity of action was structure of cyclic ammonium grouping of the alcohol part of molecule of the ester substrate. Analysis of specificity is performed based on enzymatic analysis parameters - activity of catalytic center of cholinesterases and bimolecular constant of the reaction rate that are determined at optimal and low substrate concentrations. Among the specially synthesized group of thioester compounds there is revealed one more highly specific acetylcholine esterase substrate - N-beta-(acetoxyethyl)piperidinium.
Characterization and autoprocessing of precursor and mature forms of human immunodeficiency virus type 1 (HIV 1) protease purified from <i>Escherichia coli</i> (1989)

A recombinant plasmid encompassing the human immunodeficiency virus type 1 (HIV 1) protease coding sequence and flanking regions (Ala-13 to Gly-185 of the pol open reading frame) has been expressed in two distinct strains of Escherichia coli, AR58 and AR68. In the first strain, AR58, the primary translation product, a 25 kilodalton (kDa) precursor protein, is short-lived and rapidly processes itself to the 11 kDa mature protease in vivo. In the second strain, AR68, the 25 kDa species is only partially processed, and it, a 13 kDa intermediate, and the mature 11 kDa enzyme accumulate at a ratio of 3:4.5:2.5, respectively. The 11 kDa mature protease from AR58 and the 25 kDa precursor from AR68 have been purified to homogeneity. The yield of 11 kDa enzyme from AR58 is approximately 0.02 mg/g wet weight of E. coli cell pellet. The protease has both the expected NH2- and COOH-terminal sequences. The yield of 25 kDa enzyme from AR68 is approximately 0.1 mg/g wet weight of E. coli cell pellet. In vitro, the 25 kDa precursor enzyme rapidly (t1/2 approximately equal to 9 min) processes itself into a species with a mass of approximately 13 kDa and a species with a mass of approximately 11 kDa. Both of these latter species can be separated by RP-HPLC, have the NH2-terminal sequence expected for the mature protease, and are active. The 11 kDa enzyme from AR58 comigrates with the 11 kDa enzyme from AR68 on RP-HPLC and SDS polyacrylamide gel electrophoresis. On extended incubation at 4 degrees C at either neutral or acidic pH all species of the protein exhibit further autodegradation at defined sequences. The availability of the mature, 11 kDa enzyme and the 25 kDa precursor will allow biochemical and physical studies on this critical viral enzyme.
The electromagnetic wave resistivity MWD tool (1983)

This paper is an overview of the development of a 2 MHz MWD (measurement while drilling) resistivity logging tool. This tool uses propagating electromagnetic waves rather than the pseudo static fields of its low frequency counterparts. The basic theory of operation is presented along with a discussion of factors affecting tool response and the tradeoffs which led to the specific embodiment. Field data are presented from which a comparison is made between this tool and wireline tools. It is seen that it is often possible to obtain a direct reading of R /SUB t/ using this tool.
Scalable Simple Random Sampling and Stratified Sampling (2013)

Analyzing data sets of billions of records has now become a regular task in many companies and institutions. In the statistical analysis of those massive data sets, sampling generally plays a very important role. In this work, we describe a scalable simple random sampling algorithm, named ScaSRS, which uses probabilistic thresholds to decide on the fly whether to accept, reject, or wait-list an item independently of others. We prove, with high probability, it succeeds and needs only O ( √ k) storage, where k is the sample size. ScaSRS extends naturally to a scalable stratified sampling algorithm, which is favorable for heterogeneous data sets. The proposed algorithms, when implemented in MapReduce, can effectively reduce the size of intermediate output and greatly improve load balancing. Empirical evaluation on large-scale data sets clearly demonstrates their superiority. 1
Exploring OpenStreetMap Capability for Road Perception (2018)

Drivable space detection or road perception is one of the most important tasks for autonomous driving. Sensorbased vision/laser systems may have limited performance in bad illumination/weather conditions, a prior knowledge of the road from the map data is expected to improve the effectiveness. This paper is to employ the map information extracted from the OpenStreetMap (OSM) data, and explore its capability for road perception. The OSM data can be used to render virtual street views, and further refined to provide the prior road mask. The OSM masks can be also combine with image processing and Lidar point clouding approaches to characterize the drivable space. Using a Fully Convolutional Neural Network (FCNN), the OSM availability for deep learning methods is also discussed.
Distribution and location of genetic effects for dairy traits (2009)

Genetic effects for many dairy traits and for total economic merit are evenly distributed across all chromosomes. A high-density scan using 38,416 single nucleotide polymorphism markers for 5,285 bulls confirmed 2 previously known major genes on Bos taurus autosomes (BTA) 6 and 14 but revealed few other large effects. Markers on BTA18 had the largest effects on calving ease, several conformation traits, longevity, and total merit. Prediction accuracy was highest using a heavy-tailed prior assuming that each marker had an effect on each trait, rather than assuming a normal distribution of effects as in a linear model, or that only some loci have nonzero effects. A prior model combining heavy tails with finite alleles produced results that were intermediate compared with the individual models. Differences between models were small (1 to 2%) for traits with no major genes and larger for heavy tails with traits having known quantitative trait loci (QTL; 6 to 8%). Analysis of bull recessive codes suggested that marker effects from genomic selection may be used to identify regions of chromosomes to search in detail for candidate genes, but individual single nucleotide polymorphisms were not tracking causative mutations with the exception of diacylglycerol O-acyltransferase 1. Additive genetic merits were constructed for each chromosome, and the distribution of BTA14-specific estimated breeding value (EBV) showed that selection primarily for milk yield has not changed the distribution of EBV for fat percentage even in the presence of a known QTL. Such chromosomal EBV also may be useful for identifying complementary mates in breeding programs. The QTL affecting dystocia, conformation, and economic merit on BTA18 appear to be related to calf size or birth weight and may be the result of longer gestation lengths. Results validate quantitative genetic assumptions that most traits are due to the contributions of a large number of genes of small additive effect, rather than support the finite locus model.
One-Third Resonance Extraction from INS AG Electron Synchrotron (1968)

Slow beam extraction from the INS-AG electron synchrotron was done by using a one-third resonance of the betatron oscillation. A current strip was used to change the number of the radial betatron oscillation per revolution from 2.25 to 7/3 and to enlarge the amplitude of the oscillation. The extracting beam orbit was analysed using an approximate Hamiltonian which has a separatrix represented by three straight lines and the result was in good agreement with that pursued by a computer. The properties of the extracted beam were as follows; The efficiency was 50% for electrons of 300 MeV up to 1 GeV. The maximum beam intensity was 4×10 11 electrons per second. The maximum duty cycle was 3%. Phase volumes for the horizontal and the vertical motions were 10 -3 rad cm and 0.75×10 -3 rad cm, respectively. The beam transport system and the radiation shielding system are also described.