gebhart/patrepeval huggingface dataset:
The History Began from AlexNet: A Comprehensive Survey on Deep Learning Approaches (2018)

Deep learning has demonstrated tremendous success in variety of application domains in the past few years. This new field of machine learning has been growing rapidly and applied in most of the application domains with some new modalities of applications, which helps to open new opportunity. There are different methods have been proposed on different category of learning approaches, which includes supervised, semi-supervised and un-supervised learning. The experimental results show state-of-the-art performance of deep learning over traditional machine learning approaches in the field of Image Processing, Computer Vision, Speech Recognition, Machine Translation, Art, Medical imaging, Medical information processing, Robotics and control, Bio-informatics, Natural Language Processing (NLP), Cyber security, and many more. This report presents a brief survey on development of DL approaches, including Deep Neural Network (DNN), Convolutional Neural Network (CNN), Recurrent Neural Network (RNN) including Long Short Term Memory (LSTM) and Gated Recurrent Units (GRU), Auto-Encoder (AE), Deep Belief Network (DBN), Generative Adversarial Network (GAN), and Deep Reinforcement Learning (DRL). In addition, we have included recent development of proposed advanced variant DL techniques based on the mentioned DL approaches. Furthermore, DL approaches have explored and evaluated in different application domains are also included in this survey. We have also comprised recently developed frameworks, SDKs, and benchmark datasets that are used for implementing and evaluating deep learning approaches. There are some surveys have published on Deep Learning in Neural Networks [1, 38] and a survey on RL [234]. However, those papers have not discussed the individual advanced techniques for training large scale deep learning models and the recently developed method of generative models [1].
The detection of d-dimer in plasma by enzyme immunoassay (1994)

Most commercial D-dimer enzyme immunoassays employ two antibodies, a fibrin specific capture monoclonal and a less specific antibody cross-reacting with epitopes present on fibrinogen. Two different ELISA systems were compared to test whether this cross-reaction can lead to overestimation of the true levels of cross-linked fibrin derivatives. Both assays used the same D-dimer specific antibody for capture, DD-3B6/22, but utilized signalling antibodies which differed in fibrinogen reactivity. The assays gave low results for 210 normal samples (conventional ELISA, 39 +/- 45 ng/ml; non-fibrinogen reactive ELISA, 23 +/- 20 ng/ml) with a high degree of elevation for 53 patients with active thrombosis (conventional ELISA, 901 +/- 649 ng/ml; non-fibrinogen reactive ELISA, 1,906 +/- 1,725 ng/ml). However, a dramatic difference between results was seen when fibrinogenolysis was induced by treatment of 20 normal plasmas with high levels of t-PA and plasminogen. The D-dimer levels estimated with the conventional fibrinogen-reactive signal antibody rose 25-fold (normal, 36 +/- 27 ng/ml; treated, 833 +/- 272 ng/ml), whereas no increase was obtained with the non-fibrinogen reactive ELISA (normal, 24 +/- 21 ng/ml; treated, 27 +/- 22 ng/ml). These results suggest that a more accurate estimation of D-dimer levels in samples containing high levels of fibrinogen derivatives is achieved in assays incorporating non-fibrinogen reactive antibodies.
Heterogeneous expression of the SSX cancer/testis antigens in human melanoma lesions and cell lines. (2000)

The SSX genes, located on the X chromosome, encode a family of highly homologous nuclear proteins. The SSX1 and SSX2 genes were initially identified as fusion partners of the SYT gene in t(X;18)-positive synovial sarcomas. Recently, however, it was found that these two genes, as well as the highly homologous SSX4 and SSX5 genes, are aberrantly expressed in different types of cancers, including melanomas. Because normal SSX expression has been detected only in the testis and, at very low levels, the thyroid, these proteins are considered as new members of the still growing family of cancer/testis antigens. These antigens are presently considered as targets for the development of cancer immunotherapy protocols. In the present study, we developed a monoclonal antibody found to recognize SSX2, SSX3, and SSX4 proteins expressed in formaldehyde-fixed and paraffin-embedded tissues. This antibody was used to investigate SSX expression in normal testis and thyroid, benign melanocytic lesions, melanoma lesions, and melanoma cell lines. SSX nuclear expression in the testis was found to be restricted to spermatogenic cells, mainly spermatogonia. Of 18 melanoma cell lines analyzed, 9 showed SSX RNA and protein expression, although heterogeneously and at variable levels. Treatment of an SSX-negative cell line with 5-aza-2'-deoxycytidine, a demethylating agent, led to SSX RNA and protein expression, indicating a role for methylation in transcription regulation. Thirty-four of 101 primary and metastatic melanoma cases and 2 of 24 common nevocellular and atypical nevus cases showed SSX nuclear staining. Again, SSX expression was heterogeneous, ranging from widespread to scarce. Our findings stress the importance of assessing the a priori SSX expression status of melanoma cases that may be selected for immunotherapeutic trials.
Analysis conditions for proteomic profiling of mammalian tissue and cell extracts with antibody microarrays (2010)

Antibody microarrays are a developing tool for global proteomic profiling. A protocol was established that permits robust analyses of protein extracts from mammalian tissues and cells rather than body fluids. The factors optimized were buffer composition for surface blocking, blocking duration, protein handling and processing, labeling parameters like type of dye, molar ratio of label versus protein, and dye removal, as well as incubation parameters such as duration, temperature, buffer, and sample agitation.
ChemInform Abstract: A Stacked Capacitor Cell with a Fully Self‐Aligned Contact Process for High‐Density Dynamic Random Access Memories (DRAM). (1992)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Generation and characterization of phase and amplitude shaped femtosecond mid-IR pulses (2006)

A germanium acousto-optic modulator was recently reported (Shim et al., Optics Letters, 31, 838, 2006) that is capable of generating phase and amplitude shaped femtosecond pulses directly in the mid-infrared. In this paper, the design, implementation and performance of this novel mid-IR shaper is described in detail as is the sub-50 fs optical parametric amplifier that provides large bandwidth for generation of complex pulse shapes. These details include the acoustic power and wavelength dependence of the deflection efficiency, the phase stability of the shaper, the synchronization of electronics, and a study on how the mid-IR bandwidth of the optical parametric amplifier depends on its optical configuration. With these details quantified, the accuracy of the device is tested by creating a series of shaped pulses that are characterized by cross-correlation with well-known mid-IR reference pulses and by simulations. Test waveforms include optimally compressed, phase-chirped and amplitude-modulated mid-IR pulses. The shaped pulses are of sufficient quality that they will enable new experiments in 2D IR spectroscopy and in the coherent control of vibrations in ground electronic states.
Bacterial Distribution of Glycolaldehyde Dehydrogenase in Relation to Vitamin B6Biosynthesis (1979)

Journal Article Bacterial Distribution of Glycolaldehyde Dehydrogenase in Relation to Vitamin B6 Biosynthesis Get access Hiroshi Morita, Hiroshi Morita Department of Agricultural Chemistry, Kyoto University, Kyoto 606, Japan Present address: Kyoto College of Nutritional Sciences, 18 Tenryujisetogawacho, Saga, Ukyo-ku, Kyoto 616, Japan. Search for other works by this author on: Oxford Academic Google Scholar Tetsujiro Nishimura, Tetsujiro Nishimura Department of Agricultural Chemistry, Kyoto University, Kyoto 606, Japan Search for other works by this author on: Oxford Academic Google Scholar Yoshiki Tani, Yoshiki Tani Department of Agricultural Chemistry, Kyoto University, Kyoto 606, Japan Search for other works by this author on: Oxford Academic Google Scholar Koichi Ogata, Koichi Ogata Department of Agricultural Chemistry, Kyoto University, Kyoto 606, Japan Deceased. Search for other works by this author on: Oxford Academic Google Scholar Hideaki Yamada Hideaki Yamada Department of Agricultural Chemistry, Kyoto University, Kyoto 606, Japan Search for other works by this author on: Oxford Academic Google Scholar Agricultural and Biological Chemistry, Volume 43, Issue 1, 1 January 1979, Pages 185–186, https://doi.org/10.1080/00021369.1979.10863421 Published: 01 January 1979 Article history Received: 24 July 1978 Published: 01 January 1979
Pexelizumab Alexion. (2002)

Alexion and Procter & Gamble (P&G) are developing pexelizumab (h5G1.1-SC), a short-acting, recombinant complement C5 inhibitor for the potential treatment of complications of cardiovascular surgery, such as complement activation during cardiopulmonary bypass (CPB) procedures, for which it has completed phase II trials [275707]. By November 2001, the companies were also conducting two phase II trials for the treatment of acute myocardial infarction (MI) and by March 2002, patient accrual in the first of these MI trials (COMPLY) had been completed [429171], [443067]. In April 2002, accrual in the second MI trial (COMMA) was also completed [446377]. Results from the MI trials had been expected in the first half of 2002 [435888]. By January 2002, pivotal phase III trials had been initiated in patients undergoing coronary artery bypass graft (CABG) with CPB [435058]. The compound may also have potential in the treatment of stroke [188595]. In September 2000, the US FDA granted Alexion Fast Track status for pexelizumab for CPB patients [381531]. The company is collaborating with P&G to develop and commercialize this inhibitor drug for patients undergoing CPB during CABG [313015]. In December 2001, the terms of the collaboration were altered and as a result Alexion was to play an increased role in the development and marketing of pexelizumab in the US [433296]. Alexion licensed the complement protein C5 technology from Enzon Inc, developed during Enzon's short chain antigen binding (SCA) proteins program, in May 1996 [352743]. Analysts at US Bancorp Piper Jaffray predicted in January 2002 that pexelizumab has potential peak sales of US $350 million. At this time, approval for the CPB indication was expected in the US in the second half of 2004, and sales in 2005 were expected to reach US $50 million, rising to US $227 million in 2008. In the rest of the world, CPB approvals were expected to begin in the second half of 2005. Sales in 2006 were expected to reach US $35 million, rising to US $110 million in 2008 [438051].
Application of neural networks to the classification of giant cell arteritis (1994)

Neural networks are a potentially useful method for developing diagnostic classification rules from clinical data.
Search for Chlamydia pneumoniae genes and their expression in atherosclerotic plaques of carotid arteries (2001)

Samples of atherosclerotic tissue from 58 patients undergoing carotid surgery were analysed by tissue culture and PCR for Chlamydia pneumoniae; PCR was performed to detect Omp1, 16S rRNA and HSP-70 genes. To understand the active pathogenic role of C. pneumoniae, a reverse transcriptase-PCR (RT-PCR) assay was applied to detect the specific RNAs expressed either in the replicative form, or in the cryptic form found in chronic infection. The C. pneumoniae omp1 gene, encoding the major outer-membrane protein (MOMP), was detected in 13 of 58 samples. Among these, the result was confirmed in 11 samples after amplification of a further target, the 16S rRNA, and the presence of the HSP-70 gene, encoding heat-shock protein 70, was revealed in only five cases. All the samples were negative for evidence of specific RNAs by RT-PCR. The presence of genomic DNA and absence of specific RNAs in atherosclerotic tissue samples suggests a lack of an active metabolic or persistent infective role for C. pneumoniae. Thus, traces of C. pneumoniae DNA in these samples could be due to a degradative pathway of the host defensive cellular and biochemical mechanisms.
p300/CBP is required for transcriptional induction by interleukin-4 and interacts with Stat6 (1999)

Interleukin-4 (IL-4) induces tyrosine phosphorylation of the latent transcription factor Stat6, which mediates the transcriptional responses of IL-4. The transactivation domain of Stat6 has recently been mapped to the C-terminal region of Stat6. We have investigated the mechanism by which Stat6, through its transactivation domain, induces transcription. Previous studies have shown that diverse regulated transcription factors interact with coactivators such as p300 and CBP. We report that Stat6 used the interaction with p300/CBP to exert its stimulatory effects. Overexpression of p300/CBP increased IL-4-induced transcription of Stat6 activated reporter genes. The requirement of p300/CBP for Stat6-mediated transactivation is shown by coexpression of the adenovirus E1A protein. E1A repressed the IL-4-induced reporter gene activity, while mutants of E1A, which do not interact with p300/CBP, failed to block the IL-4-induced response. In addition, we found that the minimal transactivation domain of Stat6, when fused to the GAL4 DNA-binding domain, was repressed by E1A, whereas the fusion protein p300-VP16 increased the transcriptional activity. In two-hybrid protein interaction assays in mammalian cells, we mapped the interaction domain of CBP to a C-terminal region between amino acids 1850 and 2176, a region distinct from the interaction domain of CBP with Stat1, Stat2 or Stat5. Finally, we show that antibodies raised against p300 coimmunoprecipitated Stat6 and p300 from transfected COS7 cells and antibodies against Stat6 coimmunprecipitated endogenous Stat6 and CBP from Ba/F3 cells. Our data suggest that the transactivation domain of Stat6 makes contact with the basal transcription machinery by binding to p300/CBP.
Rate Capabilities of Nanostructured LiMn[sub 2]O[sub 4] Electrodes in Aqueous Electrolyte (2000)

Nanostructured electrodes consisting of nanotubules that protrude from a current collector surface like the bristles of a brush were prepared using the template method. The rate capabilities of these nanostructured electrodes were investigated at the 4 V (vs. ) potential plateau in aqueous electrolyte. Rate capability improved with decreasing wall thickness of the tubules which formed the electrode. This result is in agreement with our prior investigations of template‐synthesized electrode materials which showed that rate capabilities improve with decreasing distance for transport in the solid state. The rate capabilities of electrodes prepared from the smallest‐wall‐thickness tubules are extraordinary; these electrodes can be cycled at C rates as high as 109 C. In addition, these investigations suggest that the poor cycling performance observed in prior studies of this electrode/electrolyte system results from unwanted oxidation of water during the charging process. By controlling the charge rate and the dimensions of the nanotubules making up the template‐synthesized cathodes, this unwanted side reaction can be eliminated and good cycle life is observed. These data show that the nanostructured electrodes offer a unique advantage to this particular electrode/electrolyte system. © 2000 The Electrochemical Society. All rights reserved.
Antibody Responses in Invasive Group B Streptococcal Infection in Adults (1998)

Nonpregnant adults with group B streptococcus bacteremia were identified by active surveillance in three hospitals. Serum samples collected within 2 days of the time of blood culture were assayed for IgG antibodies to the capsular polysaccharide of the infecting strain: serotype Ia (3 isolates), III (5 isolates), or V (4 isolates). In 7 of 12 bacteremia episodes, the serum level of IgG to the infecting isolate was > or = 3.5 microg/mL, higher than the 1-2 microg/mL level thought to be protective in neonates. Among selected acute-phase sera, 4 of 5 that contained > or = 3.5 microg/mL specific IgG mediated efficient opsonophagocytic killing of the corresponding group B streptococcus isolate in vitro. High levels of specific antibodies during the acute phase of invasive group B streptococcus infection in nonpregnant adults may reflect a rapid antibody response to infection or, in some cases, may indicate that susceptibility is due to defects in other immune effectors.
Ventilatory Responses to Sustained Eucapnic Hypoxia in Healthy Males During Wakefulness and NREM Sleep (1997)

The effects of sustained eucapnic hypoxia (SEH, 20 minutes SaO2, approximately 80%) on ventilation and supraglottic airflow resistance (Rua) plus genioglossal (gg) and diaphragmatic (di) electromyograms (EMGs) were compared during wakefulness and nonrapid eye movement (NREM) sleep in six healthy normal male subjects. Early augmentation of ventilation was followed by decline or roll-off in both states. The augmentation of ventilation was less in sleep than wakefulness (e.g., after 5 minutes hypoxia, 140% and 167% of baseline, respectively, p < 0.05). This appeared to be due to three factors: 1) sleep-related increases in Rua [the ventilatory responses to SEH (sleep vs. awake) were inversely related to changes in Rua (sleep vs. awake) (p < 0.05)], 2. reduced central neural drive (inspiratory phasic EMG di after 5 minutes SEH, 111% and 121% of baseline, p < 0.05), and 3) failure to increase respiratory frequency during SEH sleep. There was also a nonsignificant trend to a biphasic response in EMG gg and a small increase in Rua during SEH.
Prediction of Sensitivity to STI571 among Chronic Myeloid Leukemia Patients by Genome‐wide cDNA Microarray Analysis (2002)

One of the most critical issues to be solved in regard to cancer chemotherapy is the establishment of ways to predict the efficacy of anti-cancer drugs for individual patients. To develop a prediction system based on expression of specific genes, we analyzed expression profiles of mononuclear cells from 18 chronic myeloid leukemia (CML) patients who were treated with the tyrosine kinase inhibitor STI571. cDNA microarrays representing 23 040 genes identified 79 genes that were expressed differentially between responders and non-responders to STI571. On the basis of the expression patterns of 15 or 30 of these genes among the patients, we developed a "Prediction Score" system that could clearly separate the responder group from the non-responder group. Verification of this system using four additional ("test") cases succeeded in predicting the response of each of those four patients to the drug. These results provide the first evidence that gene-expression profiles can predict sensitivity of CML cells to STI571, and may eventually lead to the achievement of "personalized therapy" for this disease.
Cloning of extracellular DNase and construction of a DNase-negative strain of Vibrio cholerae (1985)

The structural gene xds for extracellular DNase of Vibrio cholerae was cloned and inactivated by insertion of the transposon Tn5. The inactivated gene was introduced into the chromosome of V. cholerae by recombination to construct an extracellular DNase-negative strain. Tn5-mediated transposon-facilitated recombination was used to establish the position of xds between the pro-1 and ile-201 markers on the genetic map of V. cholerae. The extracellular DNase-negative strain described here should be useful for investigating the role of the xds-encoded DNase in the physiology of V. cholerae and its plasmids as well as for characterizing other DNases in this organism.
Subsets of migrating intestinal dendritic cells (2010)

Dendritic cells (DCs) in the intestine are heterogeneous. Phenotypically different populations of conventional DCs have been identified in the intestinal lamina propria, Peyer's patches, and in the draining mesenteric lymph nodes, to which these DCs constitutively migrate. Markers used to identify these populations include major histocompatibility complex class II, CD11c, CD8 alpha, CD11b, and CD103. Extensive studies in rats, summarized here, which involved collection of migrating DCs by thoracic duct cannulation after mesenteric lymphadenectomy, have clearly demonstrated that the subsets of migrating intestinal lymph DCs have different functional properties. The subsets might play different roles in the induction of oral tolerance and in driving systemic immune responses after vaccination or intestinal stimulation with Toll-like receptor ligands. The use of these surgical techniques allows investigation of the functions of purified subsets of migrating DCs. However, in the rat, these studies are limited by the range of available reagents and are difficult to compare with data from other species in this fast-moving field. Recent refinements have enabled the collection of migrating intestinal DCs from mice; our initial results are described here. We believe that these studies will generate exciting data and have the potential to resolve important questions about the functions of migrating intestinal DC subsets.
Amyloid plaque imaging agent [C-11]-6-OH-BTA-1: biodistribution and radiation dosimetry in baboon (2005)

Background The amyloid neuritic plaque is considered to be a toxic collection of amyloid-ß protein found in brain tissue in Alzheimer's disease. A neutral analogue of the amyloid-binding thioflavin-T (BTA), has been radiolabeled as [C-11]-6-OH-BTA-1. It crosses the blood brain barrier, and is a promising tracer for imaging plaques in vivo using positron emission tomography. We now report the biodistribution and dosimetry of [C-11]-6-OH-BTA-1 in baboons. Methods Four 2-hour whole body studies were acquired in an ECAT ACCEL camera in two baboons after the bolus injection of [C-11]-6-OH-BTA-1. After 3.5 minute transmission scans performed per bed position prior to injection, emission scans were collected in 2-D mode over five bed positions. Regions of interest (ROI) were drawn around the brain, left and right lungs, heart, liver, gall bladder, left and right kidneys, spleen and urinary bladder. Since no fluid was removed from the baboons, total body radioactivity was calculated using the injected dose and a calibration factor determined from a cylinder phantom. The area under the curve (AUC) for each ROI was determined by trapezoidal integration of the first few points with subsequent points fit by a decreasing monoexponential. The AUC was then divided by counts in the total body, and resulting residence times were entered into the MIRDOSE3 program. Results The animals tolerated the procedure well. The ligand was eliminated via the hepatobiliary and renal systems. In the adult male and female reference the gallbladder received the highest estimated radiation dose and was the critical organ (3.9E–02 mGy/MBq and 4.3E–02 mGy/MBq respectively). Conclusion In the United States, the absorbed dose to the gallbladder would limit [C-11]-6-OH-BTA-1 administered with the approval of a Radioactive Drug Research Committee (RDRC) to a single injection of 1295 MBq (35 mCi) in the adult male, and 1314 MBq (35 mCi) in the adult female.