gebhart/patrepeval huggingface dataset:
Cells and Cell Lines (1990)

The establishment of successful tissue cultures requires several important pieces of equipment: a flow hood, a temperature-, humidity-, and CO2-controlled incubator, an inverted microscope, a 4°C refrigerator, a −20°C freezer, and a liquid-nitrogen freezer for long-term cell storage. It is important that the flow hood, incubator, and microscope are located such that they are separate from the facilities used for the manipulation of bacterial or yeast cultures and that this area be kept absolutely clean. This is because sterility is the most important concern for the tissue culturist attempting to propagate and manipulate tissue culture cells for long periods of time. In fact, culture contamination is perhaps the greatest cause of wasted time and materials in gene-transfer experiments. Careful execution of the techniques described in this chapter will ensure a high degree of reproducibility and sterility and eliminate the possibility of cross-contamination during culture manipulations. A few minutes a day spent ensuring sterility will save the investigator weeks or months of grief regenerating precious but contaminated cultures.KeywordsEmbryonal Stem CellLeukemia Inhibitory FactorGiemsa StainUndifferentiated Embryonal Stem CellCareful ExecutionThese keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.
Evaluation of disease activity in patients with moderately active ulcerative colitis: comparisons between a new activity index and Truelove and Witts' classification. (1995)

This study suggests that AI will be useful in evaluation of response to medical therapy and prediction of remission and colectomy in patients with moderately active ulcerative colitis.
Inhibitory Effects of Green Tea Polyphenols on the Production of a Virulence Factor of the Periodontal-Disease-Causing Anaerobic Bacterium Porphyromonas gingivalis (2004)

The effect of polyphenolic compounds isolated from green tea (Camellia sinensis) on the production of toxic end metabolites of Porphyromonas gingivalis was investigated. Green tea polyphenols completely inhibited the production of n-butyric acid and propionic acid at a concentration of 1.0-2.0 mg/mL in general anaerobic medium (GAM). (-)-Epigallocatechin gallate (EGCg), which is a major component of tea polyphenols also inhibited the production of phenylacetic acid at 0.5 mg/mL in GAM broth. In the experiment using resting cells of P. gingivalis, phenylacetic acid was produced from l-phenylalanine and phenylpyruvic acid, but this reaction was also inhibited by EGCg, (-)-epicatechin gallate, and (-)-gallocatechin gallate. However, (+)-catechin, (+)-gallocatechin, (-)-epicatechin, and (-)-epigallocatechin did not inhibit those reactions. These results indicate that the inhibitory effect on the production of toxic end metabolites of P. gingivalis can be attributed to the presence of the galloyl moiety, which is ester-linked with the 3-OH of the catechin moiety in the polyphenolic compounds. This study shows that continuous application of tea polyphenols on a daily basis can be considered as a useful and practical method for the prevention of periodontal diseases.
Stop Explaining Black Box Machine Learning Models for High Stakes Decisions and Use Interpretable Models Instead (2018)

Black box machine learning models are currently being used for high stakes decision-making throughout society, causing problems throughout healthcare, criminal justice, and in other domains. People have hoped that creating methods for explaining these black box models will alleviate some of these problems, but trying to \textit{explain} black box models, rather than creating models that are \textit{interpretable} in the first place, is likely to perpetuate bad practices and can potentially cause catastrophic harm to society. There is a way forward -- it is to design models that are inherently interpretable. This manuscript clarifies the chasm between explaining black boxes and using inherently interpretable models, outlines several key reasons why explainable black boxes should be avoided in high-stakes decisions, identifies challenges to interpretable machine learning, and provides several example applications where interpretable models could potentially replace black box models in criminal justice, healthcare, and computer vision.
THE FINE STRUCTURE OF ACOUSTIC GANGLIA IN THE RAT (1962)

Nerve cell bodies in the spiral and vestibular ganglia of the adult rat are surrounded by thin (about ten lamellae) myelin sheaths which differ in several respects from typical axonal myelin. In some instances lamellae surrounding perikarya appear as typical major dense lines, and in others as thin Schwann cell sheets in which cytoplasm persists. Discontinuities and irregularities appear in the structure of perikaryal myelin. Lamellae may terminate anywhere within the sheaths; they may bifurcate; they may reverse their direction; or they may merge with each other. The number of lamellae varies from one part of a sheath to another. In addition, the myelin of a single perikaryal sheath may receive contributions from more than one Schwann cell, which overlap and interleave with each other. The ganglion cells are of two types: those which are densely packed with the usual cytoplasmic organelles but have few neurofilaments (granular neurons), and those which exhibit large areas containing few organelles but have a high concentration of neurofilaments (filamented neurons). The latter cell type is ensheathed by myelin which is generally more compact that that surrounding the former. The formation and the physiologic significance of perikaryal myelin are discussed.
Albumin enhances superoxide production in cultured microglia (1997)

Microglial activation and disruption of blood-brain barrier (BBB) are known to occur and contribute to neuronal damages in cerebral ischemic conditions and in some neurodegenerative diseases. To investigate whether a serum factor leaked out from circulation enhances microglial activation, we examined the effect of normal rat serum on superoxide (O2-) production by cultured microglia. Microglia cultured from neonatal rat brains were studied on their O2- production induced by the addition of phorbol myristate acetate by a method of acetyl-cytochrome c reduction. The O2- production was significantly increased by the addition of 0.01% rat serum, and the maximal enhancement was observed at about 0.1% rat serum. After the serum was fractionated using a molecular sieve membrane, we observed the enhancing effect only in a greater molecular weight fraction (>50 kDa). Furthermore, three kinds of bovine serum albumin (BSA) with different purity, and human serum and plasma albumins, also enhanced O2- production to a similar extent to that by rat serum. However, other proteins tested showed no significant effect. The enhancement of O2- production by BSA was observed dose-dependently, and the effect of 50 microg/ml of purified BSA was equivalent to that of 0.1% rat serum, suggesting that albumin itself enhances O2- production by microglia. These results imply that albumin leaked out through impaired BBB may activate microglia and that the potentiation of O2- production by albumin results in the pathogenesis of neuronal damage in cerebral ischemia and some neurodegenerative diseases.
Specific, Sensitive, and Quantitative Enzyme-Linked Immunosorbent Assay for Human Immunoglobulin G Antibodies to Anthrax Toxin Protective Antigen (2002)

The bioterrorism-associated human anthrax epidemic in the fall of 2001 highlighted the need for a sensitive, reproducible, and specific laboratory test for the confirmatory diagnosis of human anthrax. The Centers for Disease Control and Prevention developed, optimized, and rapidly qualified an enzyme-linked immunosorbent assay (ELISA) for immunoglobulin G (IgG) antibodies to Bacillus anthracis protective antigen (PA) in human serum. The qualified ELISA had a minimum detection limit of 0.06 micro g/mL, a reliable lower limit of detection of 0.09 micro g/mL, and a lower limit of quantification in undiluted serum specimens of 3.0 micro g/mL anti-PA IgG. The diagnostic sensitivity of the assay was 97.8%, and the diagnostic specificity was 97.6%. A competitive inhibition anti-PA IgG ELISA was also developed to enhance diagnostic specificity to 100%. The anti-PA ELISAs proved valuable for the confirmation of cases of cutaneous and inhalational anthrax and evaluation of patients in whom the diagnosis of anthrax was being considered.
Minireview: The Glucagon-Like Peptides (2001)

The glucagon-like peptides GLP-1 and GLP-2 are produced in enteroendocrine L cells of the small and large intestine and secreted in a nutrient-dependent manner. GLP-1 regulates nutrient assimilation via inhibition of gastric emptying and food intake. GLP-1 controls blood glucose following nutrient absorption via stimulation of glucose-dependent insulin secretion, insulin biosynthesis, islet proliferation, and neogenesis and inhibition of glucagon secretion. Experiments using GLP-1 antagonists and GLP-1 receptor-/- mice indicate that the glucoregulatory actions of GLP-1 are essential for glucose homeostasis. In the central nervous system, GLP-1 regulates hypothalamic-pituitary function and GLP-1-activated circuits mediate the CNS response to aversive stimulation. GLP-2 maintains the integrity of the intestinal mucosal epithelium via effects on gastric motility and nutrient absorption, crypt cell proliferation and apoptosis, and intestinal permeability. Both GLP-1 and GLP-2 are rapidly inactivated in the circulation as a consequence of amino-terminal cleavage by the enzyme dipeptidyl peptidase IV (DP IV). The actions of these peptides on nutrient absorption and energy homeostasis and the efficacy of GLP-1 and GLP-2 in animal models of diabetes and intestinal diseases, respectively, suggest that analogs of these peptides may be clinically useful for the treatment of human disease.
[3-Methylthio-, 3-(amino-substituted)ethylthio-, 3-carboxymethylthio-, 3,3'-(dithiobis)-5-aryl-4H(R)-1,2,4-triazoles and 2-aminomethyl-N-substituted derivatives of 5-aryl-4H(R)-1,2,4-triazolin-3-thione: synthesis and biological activity]. (1981)

Following previous research which showed the antibacterial and antimycotic activity of triazolin-3-thiones (II), a series of compounds has been prepared and tested to correlate and clarify the structure-activity relationships. The compounds were of the type represented in (II) where (R = H, CH3 or C6H5) and were in detail: 3-methylthiotriazoles (III-VIII), 3-(amino-substituted)ethylthiotriazolines (IX-XXVI), 3-carboxymethylthiotriazolines (XXVII-XXX), 3,3'dithiobistriazolines (XXXI-XXXVI) and 2-amino-methyl-N-substituted triazolin-3-thiones (XLVIII-LXVI). The 2-aminooxadiazoles (XXXVII-XLII), obtained in place of the expected 1-aroyl-S-methylisothiosemicarbazides (II a) from the reaction between thiosemicarbazides (I) (R = H; CH3, C6H5) and methyl iodide, are also described.
Uncoiling c-Jun coiled coils: Inhibitory effects of truncated Fos peptides on Jun dimerization and DNA binding in vitro (1998)

c-Jun is an oncoprotein that comprises a portion of the AP-1 transcription factor and belongs to the basic-leucine zipper (bZIP) DNA binding protein family. Using peptides derived from the leucine zipper region of Fos, we have developed agents that inhibit Jun's DNA binding in the low micromolar range. Fos peptides that were effective inhibitors in the DNA binding assay were also found to inhibit cellular Jun binding to an AP-1 site in a luciferase reporter plasmid in MCF-7 cells. Size exclusion studies confirmed that peptides that inhibit the DNA binding of Jun also inhibit its dimerization. These peptides were found to have a cytotoxic effect on the MCF-7 cell line when delivered with the transfecting agent Tfx-50, possibly due to their role as transcription factor regulators.
The VN Project: Endoscopic Image Processing for Neurosurgery (1998)

We developed a navigation support system for endoscopic interventions that allows three-dimensional (3-D) information to be extracted from endoscopic video data and superimposed on to such live video sequences. The endoscope is coupled to a position measurement system and a video camera as components of a calibrated system. in this article we show that the radial distortions of the wide-angle endoscopic lens system can be successfully corrected and an overall accuracy of about 0.7 mm is achievable. Tracking on live endoscopic video sequences allows accurate 3-D depth data to be obtained from multiple camera views.
Molecular techniques: divide or share (2000)

The second half of the 20th century was the era in which fundamental questions regarding the genetic basis of biological function were addressed. The emerging discipline of molecular genetics harnessed the newly evolving technologies and the result has been the dawning of a genetic revolution which will lead to an understanding of how genes direct biology. The application of this science to the study of human genetics has resulted in an unprecedented growth in our understanding of the basic mechanism of disease and the basis of the new clinical field of molecular medicine.

The genetic basis of an exponentially increasing number of diseases is being identified and this will have a major impact for diagnosis, prognosis, and informed management of patients. Virtually all the major clinical disciplines will find molecular diagnosis to be increasingly necessary in modern clinical management. A challenge for the pathology services in this new era is to support molecular medicine to ensure that technical innovations and novel developments can be delivered as routine service in a timely, efficient, cost–effective manner, for the benefit of the maximum number of patients.

Current molecular genetic techniques have been developed, in only a few years, from basic academic research in many scientific fields. Some scientific milestones have been seminal.1,2 The 1953 paper in Nature by Watson and Crick, which correctly proposed the double stranded structure of DNA, led to an understanding of gene function in molecular terms and marks the beginning of the molecular revolution. In 1975, Nathans and Smith3 purified restriction enzymes, the ubiquitous tools of in vitro DNA manipulation. These were central to the isolation and amplification of specific DNA fragments by in vivo cloning, a technology developed from the recombinant DNA techniques of Berg in 1972.4 In 1975, the novel method of Southern …
Effect of variable power levels on the yield of total aerosol mass and formation of aldehydes in e-cigarette aerosols (2015)

The study objective was to determine the effect of variable power applied to the atomizer of refillable tank based e-cigarette (EC) devices. Five different devices were evaluated, each at four power levels. Aerosol yield results are reported for each set of 25 EC puffs, as mass/puff, and normalized for the power applied to the coil, in mass/watt. The range of aerosol produced on a per puff basis ranged from 1.5 to 28 mg, and, normalized for power applied to the coil, ranged from 0.27 to 1.1 mg/watt. Aerosol samples were also analyzed for the production of formaldehyde, acetaldehyde, and acrolein, as DNPH derivatives, at each power level. When reported on mass basis, three of the devices showed an increase in total aldehyde yield with increasing power applied to the coil, while two of the devices showed the opposite trend. The mass of formaldehyde, acetaldehyde, and acrolein produced per gram of total aerosol produced ranged from 0.01 to 7.3 mg/g, 0.006 to 5.8 mg/g, and <0.003 to 0.78 mg/g, respectively. These results were used to estimate daily exposure to formaldehyde, acetaldehyde, and acrolein from EC aerosols from specific devices, and were compared to estimated exposure from consumption of cigarettes, to occupational and workplace limits, and to previously reported results from other researchers.
A randomized, open-label phase II study of nanoliposomal irinotecan (nal-IRI)-containing regimens versus nab-paclitaxel plus gemcitabine in patients with previously untreated metastatic pancreatic adenocarcinoma (mPAC). (2016)

TPS482 Background: Two combination chemotherapy regimens have emerged as standard of care options for first-line treatment of mPAC: 5-fluorouracil (5-FU)/leucovorin (LV) + irinotecan + oxaliplatin (FOLFIRINOX), and nab-paclitaxel + gemcitabine. Nal-IRI (MM-398) is a nanoliposomal formulation of irinotecan. In a randomized phase 3 study (NAPOLI-1), of patients with mPAC who had been previously treated with gemcitabine-based therapy, nal-IRI + 5-FU/LV demonstrated its safety and significant clinical activity, increasing overall survival (OS) and progression-free survival (PFS) relative to 5-FU/LV. The goal of this current study is to determine the preliminary safety and efficacy of nal-IRI+ + 5-FU/LV with or without oxaliplatin as compared to nab-paclitaxel + gemcitabine in previously untreated patients with mPAC. Methods: This open-label, phase 2 comparative study will be conducted in two parts. Part 1 is a safety run-in of a nal-IRI+5-FU/LV + oxaliplatin regimen. The safety run-in will enroll small cohorts of patients following a traditional 3 + 3 dose escalation design to confirm the target dose of oxaliplatin (n = ~6-18). The primary objective of Part 1 is the safety and tolerability of nal-IRI + 5FU/LV + oxaliplatin. Part 2 is a randomized, efficacy study of a nal-IRI + 5-FU/LV + oxaliplatin regimen (Arm 1), the nal-IRI + 5-FU/LV combination that previously demonstrated efficacy in the NAPOLI-1 trial (Arm 2), versus a nab-paclitaxel + gemcitabine control arm (Arm 3) (n = ~156-168). The primary objective of Part 2 is to assess the efficacy of nal-IRI-containing regimens in first-line mPAC patients compared to nab-paclitaxel + gemcitabine using the progression-free survival (PFS) rate at 24 weeks as the primary endpoint. Secondary of part 1 is a PK study and Part 2 secondary endpoints will include OS, PFS, objective response rate (per RECIST, v1.1), decrease in CA19-9 levels and quality of life assessments. Clinical trial information: NCT02551991.
Kiwifruit promotes laxation in the elderly (2002)

Numerous anecdotal reports have suggested that kiwifruit (Actinidia deliciosa) has laxative effects. This could be an acceptable dietary supplement, especially for elderly people who often present with constipation. We wished to obtain objective evidence as to whether or not kiwifruit eaten regularly could promote laxation in elderly people. Thirty-eight healthy adults of age > 60 years consumed their normal diet, with or without one kiwifruit per 30 kg bodyweight for three weeks, followed by a 3-week crossover period. Daily records were taken on frequency of defecation and characteristics of the stools. Kiwifruit significantly enhanced all tested measures of laxation in these adults. The regular use of kiwifruit appeared to lead to a bulkier and softer stool, as well as more frequent stool production. Kiwifruit as a natural remedy appears palatable to most of the population and provides improved laxation for elderly individuals who are otherwise healthy. It is likely that a number of factors in the whole fruit are involved, but the nature of the stools suggest fibre is important. This study provides evidence of the potential for improvement in bowel function, health and well-being through changes in diet.
IBM POWER6 microarchitecture (2007)

This paper describes the implementation of the IBM POWER6™ microprocessor, a two-way simultaneous multithreaded (SMT) dual-core chip whose key features include binary compatibility with IBM POWER5™ microprocessor-based systems; increased functional capabilities, such as decimal floating-point and vector multimedia extensions; significant reliability, availability, and serviceability enhancements; and robust scalability with up to 64 physical processors. Based on a new industry-leading high-frequency core architecture with enhanced SMT and driven by a high-throughput symmetric multiprocessing (SMP) cache and memory subsystem, the POWER6 chip achieves a significant performance boost compared with its predecessor, the POWER5 chip. Key extensions to the coherence protocol enable POWER6 microprocessor-based systems to achieve better SMP scalability while enabling reductions in system packaging complexity and cost.
Asymmetric addition of a nitrogen nucleophile to an enoate in the presence of a chiral phase‐transfer catalyst: A novel approach toward enantiomerically enriched protected β‐amino acids (2012)

Abstract A proof of concept for the asymmetric organocatalytic aza‐Michael addition reaction of nitrogen nucleophiles with simple and readily available alkyl enoates as acceptor molecules in the presence of a chiral phase‐transfer catalyst has been demonstrated. The desired enantiomerically enriched β‐amino acid derivatives were obtained in up to 86% yield and with enantioselectivities of up to 37% ee. © 2012 Wiley Periodicals, Inc. Heteroatom Chem 23:202–209, 2012; View this article online at wileyonlinelibrary.com . DOI 10.1002/hc.21004
Bioorganometallic Chemistry - Transition Metal Complexes withα-Amino Acids and Peptides (1998)

A new, interdisciplinary research area has emerged known as bioorganometallic chemistry. It focuses on the introduction of organometallic fragments into biomolecules (see, for example, structure on the right). "Classical" α-amino acid and peptide ligands have proven particularly versatile, and provide access to compounds that display interesting stereochemistry. α-Amino acids and peptides can be synthesized, labeled, stabilized, or activated by organometallic fragments.
Unequal signal and coding joint formation in human V(D)J recombination. (1993)

Substrates for studying V(D)J recombination in human cells and two human pre-B-cell lines that have active V(D)J recombination activity are described. Using these substrates, we have been able to analyze the relative efficiency of signal joint and coding joint formation. Coding joint formation was five- to sixfold less efficient than signal joint formation in both cell lines. This imbalance between the two halves of the reaction was demonstrated on deletional substrates, where each joint is assayed individually. In both cell lines, the inversional reaction (which requires formation of both a signal and a coding joint) was more than 20-fold less efficient than signal joint formation alone. The signal and coding sequences are identical in all of these substrates. Hence, the basis for these differential reaction ratios appears to be that coding joint and signal joint formation are both inefficient and their combined effects are such that inversions (two-joint reactions) reflect the product of these inefficiencies. Physiologically, these results have two implications. First, they show how signal and coding joint formation efficiencies can affect the ratio of deletional to inversional products at endogenous loci. Second, the fact that not all signal and coding joints go to completion implies that the recombinase is generating numerous broken ends. Such unresolved ends may participate in pathologic chromosomal rearrangements even when the other half of the same reaction may have proceeded to resolution.