gebhart/patrepeval huggingface dataset:
Selecting and amplifying one fragment from a DNA fragment mixture by polymerase chain reaction with a pair of selective primers (1996)

A new method for selecting and amplifying a single DNA fragment from a mixture is proposed. This method is applicable for the rapid classification of DNA fragments from a mixture and for preparation of sequencing templates. DNAs of several to tens of kilobases (kb) are digested with a four-base recognition restriction enzyme to produce smaller fragments. The complementary strand extension reactions are then carried out to produce fluorophore-labeled DNA fragments from the digestion products. These fragments can be rapidly classified according to their terminal-base sequences and their sizes are analyzed by capillary-array gel electrophoresis (CAGE). Electropherograms are used to characterize the fragments and to select polymerase chain reaction (PCR) primers. Any fragment in a digestion mixture can be amplified by PCR with a pair of primers selected from a primer pool by referring to the electropherograms of the fragments. This method was successfully used to compare the electropherograms of two different DNA strands and to sequence a several-kb DNA fragment without subcloning. Combined with CAGE, this method could be used to dramatically simplify DNA fragment analysis.
Speech Acts (1969)

Written in an outstandingly clear and lively style, this 1969 book provokes its readers to rethink issues they may have regarded as long since settled.
A Mechanistic Approach to Understanding the Factors Affecting Drug Absorption: A Review of Fundamentals (2002)

This article provides an overview of the patient-specific and drug-specific variables that can affect drug absorption following oral product administration. The oral absorption of any chemical entity reflects a complex spectrum of events. Factors influencing product bioavailability include drug solubility, permeability, and the rate of in vivo dissolution. In this regard, the Biopharmaceutics Classification System has proven to be an important tool for predicting compounds likely to be associated with bioavailability problems. It also helps in identifying those factors that may alter the rate and extent of drug absorption. Product bioavailability can also be markedly influenced by patient attributes such as the integrity of the gastrointestinal tract, physiological status, site of drug absorption, membrane transporters, presystemic drug metabolism (intrinsic variables), and extrinsic variables such as the effect of food or concomitant medication. Through an awareness of a drug's physicochemical properties and the physiological processes affecting drug absorption, the skilled pharmaceutical scientist can develop formulations that will maximize product availability. By appreciating the potential impact of patient physiological status, phenotype, age, gender, and lifestyle, dosing regimens can be tailored to better meet the needs of the individual patient.
The Diagnosis and Management of Attention-Deficit/Hyperactivity Disorder in Pediatric Patients (2001)

Attention-deficit/hyperactivity disorder (ADHD), characterized by developmentally inappropriate inattentiveness, impulsivity, and hyperactivity, is the most common and thoroughly researched neuropsychiatric disorder affecting children and adolescents. The diagnosis of ADHD requires a comprehensive clinical assessment including a detailed patient history, clinical interview and observation, and a thorough physical examination. A variety of other disorders can masquerade as ADHD or coexist with the disorder. The clinician must recognize environmental influences that may affect the severity of symptoms exhibited in the child or adolescent with ADHD. Clinically, treatment with a stimulant can be expected to result in an immediate, often dramatic, improvement in the core symptoms of ADHD. Studies published over the past 20 years indicate that the symptoms of ADHD, which were originally thought to diminish as a child matured, may persist into adolescence and adulthood. This article is a review of the most recent recommendations and clinical data regarding the diagnosis and management of ADHD in children and adolescents to assist with appropriate and prudent clinical decision making.
T cell receptor-mediated signaling is defective in T cells obtained from patients with primary intracranial tumors (1997)

It has been well established that patients with malignant glioblastomas exhibit T cell anergy. In this report, we further investigate the nature of this T cell anergy. The results demonstrate that tumor size but not location correlates with decreased mitogen or anti-CD3 mAb responsiveness of T cells obtained from patients. Stimulation of the TCR/CD3 complex on these patients' T cells revealed defects in early transmembrane signaling. Both PHA and anti-CD3 mAb activated PBL and T cells obtained from patients exhibited a marked decrease in the tyrosine phosphorylation of a number of proteins. In particular, decreased phosphorylation of pp100 and phospholipase Cgamma1 (PLCgamma1) was observed. In addition, PLCgamma1 and p56(lck) protein levels were dramatically reduced in T cells obtained from patients harboring a glioma. In contrast, the protein levels of p59(fyn) were normal or only slightly reduced in T cells obtained from patients with gliomas. Quantitation of free intracellular calcium concentrations ([Ca2+]i) after mitogen (PHA) stimulation or ionomycin treatment of T cells obtained from patients revealed that they mobilize less calcium than do T cells obtained from normal subjects. Stimulation of T cells obtained from patients with PMA and ionomycin, which should bypass the requirement for PLCgamma1 activation as well as directly activate the p21(ras) signaling pathway, did not restore the proliferative capacity of these T cells to normal levels. These results indicate that the anergy observed in T cells obtained from these patients is a consequence of one or more defects in the early transmembrane signaling events associated with TCR/CD3 stimulation.
Results of intraoperative 5-fluorouracil in patients undergoing trabeculectomy--pilot trial. (1996)

To study the effect of 5-Fluorouracil (5-FU) in glaucoma filtration surgery, 13 eyes of 12 patients with glaucoma were subjected to trabeculectomy with intraoperative one minute exposure of 50 mg/ml 5-FU. The average age of patients was 36.42 +/- 18.78 years. Two of the patients had developed hypotony in the fellow eye following the use of Mitomycin C with trabeculectomy. The mean follow-up period was 9.54 +/- 5.17 weeks. Two patients developed a shallow anterior chamber with choroidals postoperatively which responded to conservative treatment. One patient developed an encysted bleb one month after surgery. Single one minute intraoperative exposure to 5-FU is a convenient and inexpensive method which appears to have no significant side effects. It may be a useful adjunctive treatment to optimise the results of glaucoma filtration surgery particularly in young and myopic patients. The long term effects, however, are not known.
Microwave-Assisted Syntheses of Regioisomerically Pure Bromorhodamine Derivatives (2003)

[structure: see text] Regioisomerically pure bromo-substituted rhodamine derivatives (bromorosamines) were prepared via microwave-accelerated condensation reactions followed by oxidation with chloranil. Reaction optimization was conveniently performed by monitoring UV absorptions attributed to the product.
Progressive Supranuclear Palsy (1964)

Introduction In this report we are describing a progressive brain disease featured by supranuclear ophthalmoplegia affecting chiefly vertical gaze, pseudobulbar palsy, dysarthria, dystonic rigidity of the neck and upper trunk, and other less constant cerebellar and pyramidal symptoms. Dementia has usually remained mild. This disease would appear to be predominantly a nerve cell degeneration centered chiefly in the brain stem. The fully developed clinical picture presented by this disease seems to follow a fairly definitive pattern and does not conform to the classical system degenerations such as motor neurone disease, paralysis agitans, cerebellar degeneration, Creuzfeldt-Jakob disease, or the presenile dementias. Yet it would seem unlikely that the disease shown by our cases is a new one, and similar earlier cases may well have been accepted as arteriosclerotic parkinsonism when that diagnosis was used in a very broad sense such as in Critchley's monograph of 1929. 1 There are some resemblances to
Combined Therapeutic Efficacy of the Thymidylate Synthase Inhibitor ZD1694 (TOMUDEX) and the Immunotoxin B43(Anti-CD19)-PAP in a SCID Mouse Model of Human B-Lineage Acute Lymphoblastic Leukemia (1998)

The quinazoline antifolate N-(5-[N-(3,4-dihydro-2-methyl-4-oxoquinazolin-6-ylmethyl)-N- methylamino]-2-thenoyl)-L-glutamic acid (ZD1694; Tomudex) is a potent inhibitor of thymidylate synthase and causes cell death through disruption of DNA synthesis and repair by blocking the obligatory thymidine nucleotide synthesis. B43(anti-CD19)-PAP immunotoxin is a potent inhibitor of protein synthesis in CD19+ B-lineage acute lymphoblastic leukemia (ALL) cells and causes apoptosis. In this model, 100% of SCID mice challenged with 1 x 10(6) human NALM-6 B-lineage ALL cells develop overt and invariably fatal leukemia. All of the 22 control SCID mice treated with phosphate-buffered saline died of disseminated human leukemia between 31 and 61 days with a median survival of 41.2 days. Treatment with ZD 1694 resulted in improved leukemia-free survival with a median survival of 69.2 days (P < 0.001, log-rank test). B43-PAP treatment was more effective than ZD1694 (P=0.026) and resulted in 51.0% long-term leukemia-free survival with a median survival of 187.5 days (P < 0.0001. log-rank test). The combination of ZD1694 and B43-PAP was more effective than either agent alone and resulted in 100% long-term leukemia-free survival. To our knowledge, this preclinical study is the first to demonstrate the feasibility and therapeutic advantage of combining an anti-leukemia immunotoxin with a thymidylate synthase inhibitor.
Water and Electrolyte Content of Normal and Hypertensive Arteries in Dogs (1964)

This study was designed to establish values for the water and electrolyte content along the arterial tree in the dog under normal conditions and to determine how the normal electrolyte pattern was altered in renal hypertension. Determinations of vessel wall water, potassium, sodium, and chloride contents have shown that the water and electrolyte contents from the various sites along the arterial tree differ significantly from each other. Total water and potassium contents decrease progressively from the ascending aorta to the femoral and carotid sites, while the sodium and chloride contents showed the opposite trend. These differences were significant statistically. These trends may not persist along the entire vascular tree to very small arteries, as indicated by analysis of mesenteric arterial samples. Studies of vessel wall inulin space supported the view that these differences result from the relative distribution of cellular and noncellular material; thus the proximal aorta contains a relatively greater proportion of cellular (smooth muscle) material than more distal sites such as the femoral and carotid arteries. A review of the literature further supports these findings. In experimentally induced renal hypertension the same trends persist along the aorta, but the total water and sodium contents are significantly elevated at all sites.
Differential responses to psychotherapy versus pharmacotherapy in patients with chronic forms of major depression and childhood trauma (2003)

Major depressive disorder is associated with considerable morbidity, disability, and risk for suicide. Treatments for depression most commonly include antidepressants, psychotherapy, or the combination. Little is known about predictors of treatment response for depression. In this study, 681 patients with chronic forms of major depression were treated with an antidepressant (nefazodone), Cognitive Behavioral Analysis System of Psychotherapy (CBASP), or the combination. Overall, the effects of the antidepressant alone and psychotherapy alone were equal and significantly less effective than combination treatment. Among those with a history of early childhood trauma (loss of parents at an early age, physical or sexual abuse, or neglect), psychotherapy alone was superior to antidepressant monotherapy. Moreover, the combination of psychotherapy and pharmacotherapy was only marginally superior to psychotherapy alone among the childhood abuse cohort. Our results suggest that psychotherapy may be an essential element in the treatment of patients with chronic forms of major depression and a history of childhood trauma.
Inhibition of gastric H+,K+-ATPase and acid secretion by SCH 28080, a substituted pyridyl(1,2a)imidazole. (1987)

A hydrophobic amine, SCH 28080, 2-methyl-8-(phenylmethoxy)imidazo(1,2a)pyridine-3-acetonitrile, previously shown to inhibit gastric acid secretion in vivo and in vitro, was also shown to inhibit basal and stimulated aminopyrine accumulation in isolated gastric glands when histamine, high K+ concentrations, or dibutyryl cAMP were used as secretagogues. Stimulated, but not basal, oxygen consumption was also inhibited. Neutralization of the acid space of the parietal cell by high concentrations of the weak base, imidazole, reduced the potency of the drug, suggesting that SCH 28080 was active when protonated. Studies on the isolated H+,K+-ATPase showed that the compound inhibited the enzyme competitively with K+, whether ATP or p-nitrophenyl phosphate were used as substrates. In contrast, the inhibition was mixed with respect to p-nitrophenyl phosphate and uncompetitive with respect to ATP. The drug reduced the steady state level of the phosphoenzyme but not the observed rate constant for phosphoenzyme formation in the absence of K+ nor the quantity of phosphoenzyme reacting with K+. The drug quenched the fluorescence of fluorescein isothiocyanate-modified enzyme and also inhibited the ATP-independent K+ exchange reaction of the H+,K+-ATPase. Its action on gastric acid secretion can be explained by inhibition of the H+,K+-ATPase by reversible complexation of the enzyme. This class of compound, therefore, acts as a reversible inhibitor of gastric acid secretion.
Genus-Specific Detection of Salmonellae using the Polymerase Chain Reaction (PCR) (1993)

Oligonucleotide primers for the polymerase chain reaction (PCR) that enable genus-specific detection of members of the genus Salmonella were developed. The primers amplify a 496-bp genetic sequence of members of the genus Salmonella. Amplification of DNA extracted from all other genera of the family Enterobacteriaceae and various other gram-positive aerobic and anaerobic bacteria yielded negative results. Applications of the PCR using these genus-specific primers are discussed.
Hexanal Accumulation and DETBA Value in Homogenate of Soybean Seeds Lacking Two or Three Lipoxygenase Isoenzymes (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTHexanal Accumulation and DETBA Value in Homogenate of Soybean Seeds Lacking Two or Three Lipoxygenase IsoenzymesYoichi Nishiba, Shu Furuta, Makita Hajika, Kazunori Igita, and Ikuo SudaCite this: J. Agric. Food Chem. 1995, 43, 3, 738–741Publication Date (Print):March 1, 1995Publication History Published online1 May 2002Published inissue 1 March 1995https://pubs.acs.org/doi/10.1021/jf00051a033https://doi.org/10.1021/jf00051a033research-articleACS PublicationsRequest reuse permissionsArticle Views162Altmetric-Citations25LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Measurement and analysis of a streaming-media workload (2001)

The increasing availability of continuous-media data is provoking a significant change in Internet workloads. For example, video from news, sports, and entertainment sites, and audio from Internet broadcast radio, telephony, and peer-to-peer networks, are becoming commonplace. Compared with traditional Web workloads, multimedia objects can require significantly more storage and transmission bandwidth. As a result, performance optimizations such as streaming-media proxy caches and multicast delivery are attractive for minimizing the impact of streaming-media workloads on the Internet. However, because few studies of streaming-media workloads exist, the extent to which such mechanisms will improve performance is unclear.

This paper (1) presents and analyzes a client-based streaming-media workload generated by a large organization, (2) compares media workload characteristics to traditional Web-object workloads, and (3) explores the effectiveness of performance optimizations on streaming-media workloads. To perform the study, we collected traces of streaming-media sessions initiated by clients from a large university to servers in the Internet. In the week-long trace used for this paper, we monitored and analyzed RTSP sessions from 4,786 clients accessing 23,738 distinct streaming-media objects from 866 servers. Our analysis of this trace provides a detailed characterization of streaming-media for this workload.
A mutant of DNA polymerase I (Klenow fragment) with reduced fidelity (1991)

The kinetic parameters governing incorporation of correct and incorrect bases into synthetic DNA duplexes have been investigated for Escherichia coli DNA polymerase I [Klenow fragment (KF)] and for two mutants, Tyr766Ser and Tyr766Phe. Tyr766 is located at the C-terminus of helix O in the DNA-binding cleft of KF. The catalytic efficiency for correct incorporation of dNTP is reduced 5-fold for Tyr766Ser. The catalytic efficiencies of all 12 possible misincorporations have been determined for both KF and Tyr766Ser by using single-turnover kinetic conditions and a form of the enzyme that is devoid of the 3'-5' exonuclease activity because of other single amino acid replacements. Tyr766Ser displays an increased efficiency of misincorporation (a reduction in fidelity) for several of the 12 mismatches. The largest increase in efficiency of misincorporation for Tyr766Ser occurs for the misincorporation of TMP opposite template guanosine, a 44-fold increase. In contrast, the efficiencies of misincorporation of dAMP opposite template A, G, or C are little affected by the mutation. A determination of the kinetic parameters associated with a complete kinetic scheme has been made for Tyr766Ser. The rate of addition of the next correct nucleotide onto a preexisting mismatch is decreased for Tyr766Ser. The fidelity of Tyr766Phe was not substantially different from that of KF for the misincorporations examined, indicating that it is the loss of the phenolic ring of the side chain of Tyr766 that leads to the significant decrease in fidelity. The results indicate that KF actively participates in the reduction of misincorporations during the polymerization event and that Tyr766 plays an important role in maintaining the high fidelity of replication by KF.
Elastin Stabilization for Treatment of Abdominal Aortic Aneurysms (2007)

Periadventitial administration of PGG hinders the development of AAA in a clinically relevant animal model. Stabilization of aortic elastin in aneurysm-prone arterial segments offers great potential toward the development of safe and effective therapies for AAAs.
Glucocorticoid-Induced Tumour Necrosis Factor Receptor-Related Protein: A Key Marker of Functional Regulatory T Cells (2015)

Glucocorticoid-induced tumour necrosis factor receptor-related protein (GITR, TNFRSF18, and CD357) is expressed at high levels in activated T cells and regulatory T cells (Tregs). In this review, we present data from mouse and human studies suggesting that GITR is a crucial player in the differentiation of thymic Tregs (tTregs), and expansion of both tTregs and peripheral Tregs (pTregs). The role of GITR in Treg expansion is confirmed by the association of GITR expression with markers of memory T cells. In this context, it is not surprising that GITR appears to be a marker of active Tregs, as suggested by the association of GITR expression with other markers of Treg activation or cytokines with suppressive activity (e.g., IL-10 and TGF-β), the presence of GITR(+) cells in tissues where Tregs are active (e.g., solid tumours), or functional studies on Tregs. Furthermore, some Treg subsets including Tr1 cells express either low or no classical Treg markers (e.g., FoxP3 and CD25) and do express GITR. Therefore, when evaluating changes in the number of Tregs in human diseases, GITR expression must be evaluated. Moreover, GITR should be considered as a marker for isolating Tregs.
SPECTROSCOPIC DIAGNOSIS OF COLONIC DYSPLASIA (1991)

We have developed a method for defining diagnostic algorithms for pathologic conditions based on fluorescence spectroscopy. We apply this method to human colon tissue and show that fluorescence can be used to diagnose the presence or absence of colonic adenoma. This method uses fluorescence excitation-emission matrices (EEM) to identify optimal excitation regions for obtaining fluorescence emission spectra which can be used to differentiate normal and pathologic tissues. In the case of normal and adenomatous colon tissue, these were found to be: 330, 370, and 430 nm +/- 10 nm. At these excitation wavelengths, emission wavelengths for use in diagnostic algorithms are identified from average difference and ratio of the spectra from normal and pathologic tissues. In colon tissue, at 370 nm excitation, 404, 480, and 680 nm were found to be useful emission wavelengths for diagnosing the presence of adenoma in vitro. The basis of colon tissue autofluorescence was investigated using EEM of pure molecules and relevant excitation-emission maxima in the literature.
Annotating and searching web tables using entities, types and relationships (2010)

Tables are a universal idiom to present relational data. Billions of tables on Web pages express entity references, attributes and relationships. This representation of relational world knowledge is usually considerably better than completely unstructured, free-format text. At the same time, unlike manually-created knowledge bases, relational information mined from "organic" Web tables need not be constrained by availability of precious editorial time. Unfortunately, in the absence of any formal, uniform schema imposed on Web tables, Web search cannot take advantage of these high-quality sources of relational information. In this paper we propose new machine learning techniques to annotate table cells with entities that they likely mention, table columns with types from which entities are drawn for cells in the column, and relations that pairs of table columns seek to express. We propose a new graphical model for making all these labeling decisions for each table simultaneously, rather than make separate local decisions for entities, types and relations. Experiments using the YAGO catalog, DB-Pedia, tables from Wikipedia, and over 25 million HTML tables from a 500 million page Web crawl uniformly show the superiority of our approach. We also evaluate the impact of better annotations on a prototype relational Web search tool. We demonstrate clear benefits of our annotations beyond indexing tables in a purely textual manner.