gebhart/patrepeval huggingface dataset:
Pathomic Fusion: An Integrated Framework for Fusing Histopathology and Genomic Features for Cancer Diagnosis and Prognosis (2019)

Cancer diagnosis, prognosis, and therapeutic response predictions are based on morphological information from histology slides and molecular profiles from genomic data. However, most deep learning-based objective outcome prediction and grading paradigms are based on histology or genomics alone and do not make use of the complementary information in an intuitive manner. In this work, we propose Pathomic Fusion, an interpretable strategy for end-to-end multimodal fusion of histology image and genomic (mutations, CNV, RNA-Seq) features for survival outcome prediction. Our approach models pairwise feature interactions across modalities by taking the Kronecker product of unimodal feature representations and controls the expressiveness of each representation via a gating-based attention mechanism. Following supervised learning, we are able to interpret and saliently localize features across each modality, and understand how feature importance shifts when conditioning on multimodal input. We validate our approach using glioma and clear cell renal cell carcinoma datasets from the Cancer Genome Atlas (TCGA), which contains paired whole-slide image, genotype, and transcriptome data with ground truth survival and histologic grade labels. In a 15-fold cross-validation, our results demonstrate that the proposed multimodal fusion paradigm improves prognostic determinations from ground truth grading and molecular subtyping, as well as unimodal deep networks trained on histology and genomic data alone. The proposed method establishes insight and theory on how to train deep networks on multimodal biomedical data in an intuitive manner, which will be useful for other problems in medicine that seek to combine heterogeneous data streams for understanding diseases and predicting response and resistance to treatment.
Highly Efficient Assay of Circulating Tumor Cells by Selective Sedimentation with a Density Gradient Medium and Microfiltration from Whole Blood (2012)

Isolation of circulating tumor cells (CTCs) by size exclusion can yield poor purity and low recovery rates, due to large variations in size of CTCs, which may overlap with leukocytes and render size-based filtration methods unreliable. This report presents a very sensitive, selective, fast, and novel method for isolation and detection of CTCs. Our assay platform consists of three steps: (i) capturing CTCs with anti-EpCAM conjugated microbeads, (ii) removal of unwanted hematologic cells (e.g., leukocytes, erythrocytes, etc.) by selective sedimentation of CTCs within a density gradient medium, and (iii) simple microfiltration to collect these cells. To demonstrate the efficacy of this assay, MCF-7 breast cancer cells (average diameter, 24 μm) and DMS-79 small cell lung cancer cells (average diameter, 10 μm) were used to model CTCs. We investigated the relative sedimentation rates for various cells and/or particles, such as CTCs conjugated with different types of microbeads, leukocytes, and erythrocytes, in order to maximize differences in the physical properties. We observed that greater than 99% of leukocytes in whole blood were effectively removed at an optimal centrifugal force, due to differences in their sedimentation rates, yielding a much purer sample compared to other filter-based methods. We also investigated not only the effect of filtration conditions on recovery rates and sample purity but also the sensitivity of our assay platform. Our results showed a near perfect recovery rate (~99%) for MCF-7 cells and very high recovery rate (~89%) for DMS-79 cells, with minimal amounts of leukocytes present.
Circulating Tumor Cells: From Bench to Bedside (2012)

Circulating tumor cells (CTCs) represent a surrogate biomarker of hematogenous metastases. In recent years, their detection has gained increasing interest. There is ample evidence regarding the ability to detect CTCs and their prognostic relevance, but their demonstrated predictive value in therapeutic response monitoring is clinically even more meaningful. Many clinical trials in the early and metastatic cancer setting now include CTCs as a monitoring parameter, and numerous translational studies attempting their molecular characterization are under way. There has been great progress in defining the clinical importance of CTCs, and it now seems likely that we may expect wider implementation of CTCs as a diagnostic oncology tool to monitor therapeutic response in real time. Novel technologies may further facilitate molecular characterization of CTCs and development of novel therapeutic targets, possibly leading to more powerful treatment strategies for cancer patients. As the detection and evaluation of CTCs are becoming an increasingly important diagnostic and prognostic tool, the goal of this review is to communicate the knowledge obtained through analysis of primary tumors and CTCs to oncologists and medical specialists in managing patients with cancer.
Effect of Monensin and Lasalocid-Sodium on the Growth of Methanogenic and Rumen Saccharolytic Bacteria (1979)

It is thought that monensin increases the efficiency of feed utilization by cattle by altering the rumen fermentation. We studied the effect of monensin and the related ionophore antibiotic lasalocid-sodium (Hoffman-LaRoche) on the growth of methanogenic and rumen saccharolytic bacteria in a complex medium containing rumen fluid. Ruminococcus albus, Ruminococcus flavefaciens, and Butyrivibrio fibrisolvens were inhibited by 2.5 mug of monensin or lasalocid per ml. Growth of Bacteroides succinogenes and Bacteroides ruminicola was delayed by 2.5 mug of monensin or lasalocid per ml. Populations of B. succinogenes and B. ruminicola that were resistant to 20 mug of either drug per ml were rapidly selected by growth in the presence of each drug at 5.0 mug/ml. Selenomonas ruminantium was insensitive to 40 mug of monensin or lasalocid per ml. Either antibiotic (10 mug/ml) inhibited Methanobacterium MOH, Methanobacterium formicicum, and Methanosarcina barkeri MS. Methanobacterium ruminantium PS was insensitive to 40 mug of monensin or 20 mug of lasalocid per ml. The methanogenic strain 442 was insensitive to 40 mug of monensin but sensitive to 10 mug of lasalocid per ml. The results suggest that monensin or lasalocid acts in the rumen by selecting for succinate-forming Bacteroides and for S. ruminantium, a propionate producer that decarboxylates succinate to propionate. The selection could lead to an increase in rumen propionate formation. Selection against H(2) and formate producers, e.g. R. albus, R. flavefaciens, and B. fibrisolvens, could lead to a depression of methane production in the rumen.
Biotransformation of the antiestrogen clomiphene to chemically reactive metabolites in the immature female rat. (1987)

Novel metabolites of clomiphene (CLO), an antiestrogen effective in experimental breast cancer models, were characterized in studies using immature female rats. After i.p. administration, CLO was eliminated unchanged in feces and as two components which were chromatographically identical to synthetic CLO analogues bearing a m-methoxy-p-hydroxyphenyl (guaiacol) moiety in place of one or the other of its phenyl rings. These components were also found in liver tissue. In the presence of liver microsomal homogenate, CLO underwent p-hydroxylation of either of its phenyl rings, affording 4-hydroxy-CLO and 4'-hydroxy-CLO. These in turn underwent liver microsomal mediated conversion to the respective guaiacol metabolites. 4'-Hydroxy-CLO and its 3'-methoxy analogue, but not positional isomers of these, had arylating ability as shown by chemical and spectral studies, apparently due to spontaneous conversion to electrophilic allene-quinones. Reproductive tract abnormalities produced in neonatal rats by CLO were suggested not to be mediated via such metabolites, since similar such effects were caused by 4'-fluoro-CLO. However, the latent arylating potential of the 4'-hydroxylated metabolites of CLO suggests that these compounds may be useful in biochemical studies of breast cancer cell growth inhibition.
Environmental impact assessment (2002)

This environmental assessment for the PCF Xiaogushan Hydropower Project for China, which increases electric power transmission, anticipates negative environmental impacts and proposes measures to mitigate them. They are summarized here as follows: To effects on water quality, wastewater containing sand produced from the dam and power station will be treated using sedimentation method, oil-contained water will be treated using biochemicals. To reduce noise, use low-level construction equipment, shield and place noisy equipment outdoors, provide protective gear and equipment to workers, and ban noisy equipment near residential areas. To minimize air-polluting dust, adopt wet methods during construction and other dust-reducing equipment, spray water regularly, and use sealed containers during transport. To avoid water and soil losses, adopt appropriate engineering methods and replant. Protect vegetation and land animals. When cultural relics are occasionally discovered, suspend construction, protect the site, and report to the relevant authorities. Regularly clean and maintain roads, and plant trees along roads to offset dust pollution. Prohibit use of vehicle horns near residential and office areas. Treat and dispose of sewage and rubbish: either re-use it or bury it in a sanitary layer in the ground. Control the spread of disease and epidemics from the construction camps by regularly examining workers. During project operation, avoid a reduction in the water table and interference with aquaculture by guaranteeing water flow during the dry season. To offset land acquisition, plant trees.
Synthesis and Biological Evaluation of Novel Thiazolidinedione Analogues as 15-Hydroxyprostaglandin Dehydrogenase Inhibitors (2011)

Novel thiazolidinedione analogues as 15-hydroxyprostaglandin dehydrogenase (15-PGDH) inhibitors were synthesized. Compounds 2, 3, and 4 exhibited IC(50) of 25, 8, and 19 nM, respectively. They also significantly increased levels of PGE(2) in A549 cells. To assess the influence of 15-PGDH inhibitor on cochlear blood flow (CBF), 2 was applied intravenously to guinea pigs. It increased their CBFs. Scratch wounds were also analyzed in confluent monolayers of HaCaT cells. Cells exposed to 4 showed significantly improved wound healing with respect to a control.
Heterogeneous effects of IFN-gamma in adjuvant arthritis. (1989)

In an attempt to evaluate the role of IFN-gamma in autoimmune arthritis, we tested the effects of IFN-gamma and anti-IFN-gamma mAb (DB-1) in various phases of arthritis development in a rat model for rheumatoid arthritis; the adjuvant arthritis (AA) model, induced by immunization with CFA. In addition, the effects of IFN-gamma were tested in vitro on T cell clones derived from rats afflicted with AA. T cell clone A2b, which has been shown to be arthritogenic secreted low amounts of IFN-gamma and its Ag-specific proliferation was inhibited by IFN-gamma. In contrast, clone A2c, which can inhibit the development of AA, produced high amounts of IFN-gamma and its proliferation was increased by IFN-gamma. In vivo administration of IFN-gamma 24 h before CFA caused an enhancement of arthritis, whereas giving IFN-gamma 24 to 48 h after CFA suppressed the disease. Administration of IFN-gamma between day +4 to +12 or between day +12 to +24 increased the severity of the first phase of the disease, but had no effect later. Administration of DB-1 1 to 2 days before adjuvant or between day +4 to +8 substantially decreased the disease, whereas DB-1 given from day +12 to +24 significantly enhanced it. Taken together, these results illustrate the heterogeneity of IFN-gamma in autoimmune arthritis and suggest a rational explanation for the possibly conflicting reports regarding the role(s) and effects of IFN-gamma in autoimmune processes. The multistage nature of T cell-mediated autoimmune arthritis may be due to the predominance of distinct T cell populations at different stages of the disease. The differences in the biologic activities of these T cells may be due to their patterns of lymphokine production.
Hardware Trojan horse detection using gate-level characterization (2009)

Hardware Trojan horses (HTHs) are the malicious altering of hardware specification or implementation in such a way that its functionality is altered under a set of conditions defined by the attacker. There are numerous HTHs sources including untrusted foundries, synthesis tools and libraries, testing and verification tools, and configuration scripts. HTH attacks can greatly comprise security and privacy of hardware users either directly or through interaction with pertinent systems and application software or with data. However, while there has been a huge research and development effort for detecting software Trojan horses, surprisingly, HTHs are rarely addressed. HTH detection is a particularly difficult task in modern and pending deep submicron technologies due to intrinsic manufacturing variability.
C1q PRECIPITINS IN THE SERA OF PATIENTS WITH SYSTEMIC LUPUS ERYTHEMATOSUS AND OTHER HYPOCOMPLEMENTEMIC STATES: CHARACTERIZATION OF HIGH AND LOW MOLECULAR WEIGHT TYPES (1971)

Precipitin reactions of C1q in gel diffusion proved useful in detecting unknown complexes containing gamma-globulin in the sera of patients with SLE. Using this method low molecular weight C1q reactants also have been detected in a number of sera from patients with SLE as well as other diseases. Both the circulating complexes and the unidentified low molecular weight reactants are associated with disease activity and in vivo complement depression. In some sera from patients with SLE, circulating complexes as detectable by C1q precipitation were closely associated with cryoprecipitins and an active nephritic process. Evidence is presented that both rheumatoid factors and C1q interact with circulating complexes in these patients and that the interaction is related to cryoprecipitation. The demonstration of the same rheumatoid factors in the cryoprecipitates and in the renal glomerular deposits suggests that rheumatoid factors have a special significance in the presence of circulating complexes.
Pharmacokinetic Properties of Peptidic Radiopharmaceuticals: Reduced Uptake of (EH)3-Conjugates in Important Organs (2013)

The biodistribution data suggest that (EH)3 is able to improve the pharmacokinetic properties of peptidic radiopharmaceuticals, leading to reduced uptake in organs such as the liver, an important site of metastatic disease.
Transcatheter Electrocoagulation of Blood Vessels (1973)

Precise electrocoagulation of splanchnic blood vessels using direct currents applied by catheter-placed electrodes has proved feasible. This technique might prove feasible in controlling massive gastrointestinal bleeding or in the occlusion of arterial feeders to AV malformations. Electrocoagulation is well tolerated in the blood vessels supplying the stomach and duodenum of dogs. It produces infarction of the small bowel if branches of the superior mesenteric artery are coagulated. Arrythmias proved no problem provided care was taken to avoid current flow pathways through the region of the myocardium. A-C electrocoagulation was found to have serious intrinsic complications manifested by rupture of the blood vessel wall.
Oral fast-dissolving drug delivery membranes prepared from electrospun polyvinylpyrrolidone ultrafine fibers (2009)

Oral fast-dissolving drug delivery membranes (FDMs) for poorly water-soluble drugs were prepared via electrospinning technology with ibuprofen as the model drug and polyvinylpyrrolidone (PVP) K30 as the filament-forming polymer and drug carrier. Results from differential scanning calorimetry, x-ray diffraction, and morphological observations demonstrated that ibuprofen was distributed in the ultrafine fibers in the form of nanosolid dispersions and the physical status of drug was an amorphous or molecular form, different from that of the pure drug and a physical mixture of PVP and ibuprofen. Fourier-transform infrared spectroscopy results illustrated that the main interactions between PVP and ibuprofen were mediated through hydrogen bonding. Pharmacotechnical tests showed that FDMs with different drug contents had almost the same wetting and disintegrating times, about 15 and 8 s, respectively, but significantly different drug dissolution rates due to the different physical status of the drug and the different drug-release-controlled mechanisms. 84.9% and 58.7% of ibuprofen was released in the first 20 s for FDMs with a drug-to-PVP ratio of 1:4 and 1:2, respectively. Electrospun ultrafine fibers have the potential to be used as solid dispersions to improve the dissolution profiles of poorly water-soluble drugs or as oral fast disintegrating drug delivery systems.
Acetyl‐CoA:benzylalcohol acetyltransferase – an enzyme involved in floral scent production in Clarkia breweri (1998)

Volatile esters impart distinct characteristics to the floral scent of many plants, and are important in attracting insect pollinators. They are also important flavor compounds in fruits. The ester benzylacetate is a major constituent of the floral scent of Clarkia breweri, an annual plant native to California. The enzyme acetyl-CoA:benzylalcohol acetyltransferase (BEAT), which catalyzes the formation of benzylacetate, has been purified from C. breweri petals, and a cDNA encoding this enzyme has been isolated and characterized. The sequence of the 433-residue BEAT protein does not show high similarity to any previously characterized protein, but a 35-residue region from position 135-163 has significant similarity (42-56% identity) to several proteins known or suspected to use an acyl-CoA substrate. E. coli cells expressing C. breweri BEAT produced enzymatically active protein, and also synthesized benzylacetate and secreted it into the medium. Of the different parts of the C. breweri flower, petals contained the majority of BEAT transcripts, and no BEAT mRNA was detected in leaves. The levels of BEAT mRNA in the petals increased as the bud matured, and peaked at anthesis, paralleling changes in BEAT activity. However, three days after anthesis, mRNA levels began a steep decline, whereas BEAT activity remained high for the next two days, suggesting that the BEAT protein is relatively stable.
A Fault-Containing Self-Stabilizing Algorithm for 6-Coloring Planar Graphs (2010)

This paper presents the first fault-containing self-stabilizing algorithm which can 6-color any planar graph. Besides the capability to contain the fault in any single-fault situation, the proposed algorithm also has the capability to stabilize faster in single-fault situations. For single-fault situations, the worst-case stabilization time of the proposed algorithm is O (Δ), whereas the worst-case stabilization times of all the previous self-stabilizing algorithms for 6-coloring planar graphs are Ω (n), where Δ is the maximum node degree, and n is the number of nodes in the system.
Single-chain antibody streptavidin fusions: Tetrameric bifunctional scFv-complexes with biotin binding activity and enhanced affinity to antigen (1995)

To increase the avidity of single-chain antibodies (scFv) for their antigen, we have fused them to core-streptavidin. The chimeric protein, expressed by the vector pSTE (plasmid for streptavidin-tagged expression) from Escherichia coli, can form tetrameric complexes, binds its antigen and contains four biotin binding sites per tetrameric complex. An additional cysteine inserted near the carboxy terminus further stabilised the complex. The scFv fusion protein tetramers could be enriched by affinity chromatography using the biotin analog 2-iminobiotin from periplasmic inclusion bodies after refolding. We have also shown that the scFv fusion protein could be used for direct detection of its antigen in ELISA when stained with biotinylated horseradish peroxidase. The affinity of the scFv-antibody complex was substantially increased by avidity effects due to the tetrameric structure. The biotin binding sites may be used for coupling other antibodies and molecules to form bispecific and bifunctional reagents.
Single-to-balanced filters for mobile phones using coupled resonator BAW technology (2005)

The coupled resonator filter (CRF) is a new type of bulk-acoustic-wave (BAW) device in which two piezoresonators are stacked on top of each other in a way that a certain degree of acoustic interaction occurs. Experimental results of single-ended and mode-converting CRF for GSM applications also featuring impedance conversion, operating at 1.8 GHz and manufactured at Infineon Technologies are presented. For the balanced port, those results demonstrate excellent amplitude- and phase-imbalance, obtained by a very symmetrical design. Also, a method for suppression of spurious resonances is demonstrated. Moreover, the latest results confirm that unwanted passbands can be overcome by modification of the acoustic mirror. Furthermore, the temperature coefficient of frequency (TCF) has been measured. Due to the compensating effect of SiO/sub 2/ in the CRF stack the values obtained are exceptionally small.
Current topic: PACS (picture archiving and communication systems): filmless radiology (2000)

A picture archiving and communication system (PACS) is a computerised means of replacing the roles of conventional radiological film. This review describes the Hammersmith PACS, and discusses the advantages and disadvantages of PACS systems.
Use of multiple inflammatory marker tests in primary care: using Clinical Practice Research Datalink to evaluate accuracy (2019)

Testing multiple inflammatory markers simultaneously does not increase ability to rule out disease and should generally be avoided. CRP has marginally superior diagnostic accuracy for infections, and is equivalent for autoimmune conditions and cancers, so should generally be the first-line test.
Transgenic mouse models of lipoprotein metabolism and atherosclerosis. (1993)

Lipoprotein transport genes have either been added to the germ line of mice by transgenic techniques or knocked out by homologous recombination in embryonic stem cells. The resultant over- or underexpression of these genes has resulted in new insights about how these genes function in the body and their role in lipoprotein metabolism. Either singly or in combination, these genetic modifications can be used to engineer the mouse to make it a better model for human lipoprotein disorders and atherosclerosis.
Managing and Querying Distributed Multimedia Metadata (2009)

The authors propose an automatically constructed metadata resume to facilitate the retrieval of desired media information about content distributed across several servers.
Synthesis and DNA Binding Properties of DNA-PNA Chimeras (2003)

A systematic study to evaluate the ability of 5'-DNA-3'-p-(N)-PNA-(C) chimeras to form triple helix structures has been undertaken. Preliminary results carried out on a 16-mer chimera with three PNA monomers at the 3'-end showed the formation of a stable DNA-PNA/DNA/DNA triplex, having similar conformational behaviour to a canonical DNA/DNA/DNA triplex.