gebhart/patrepeval huggingface dataset:
A technique for isolating differences between files (1978)

A simple algorithm is described for isolating the differences between two files. One application is the comparing of two versions of a source program or other file in order to display all differences. The algorithm isolates differences in a way that corresponds closely to our intuitive notion of difference, is easy to implement, and is computationally efficient, with time linear in the file length. For most applications the algorithm isolates differences similar to those isolated by the longest common subsequence. Another application of this algorithm merges files containing independently generated changes into a single file. The algorithm can also be used to generate efficient encodings of a file in the form of the differences between itself and a given “datum” file, permitting reconstruction of the original file from the diference and datum files.
Immune Cell–Poor Melanomas Benefit from PD-1 Blockade after Targeted Type I IFN Activation (2014)

Using a genetically engineered mouse melanoma model, we demonstrate that targeted activation of the type I IFN system with immunostimulatory RNA in combination with blockade of immune-inhibitory receptors is a rational strategy to expose immune cell-poor tumors to cellular immune surveillance.
Syntheses of the two epimeric 5′-methylcytidines, their 5′-phosphates and [5-3H]-5′-pyrophosphates, and the two 5′-methyldeoxycytidines. A novel cystosine anhydro-nucleoside with two oxygen bridges between the base and the sugar (1982)

In a series of experiments the starting materials were methyl 2,3-O-isopropylidene-β-D-alto- and -α-L-talofuranosides. These were converted in two steps into the corresponding 2,3,5-tri-O-benzoyl esters, (5) and (11), which were coupled with N-acetylbis(trimethylsilyl)cytosine in the presence of tin(IV) chloride, to the protected nucleosides (19) and (20). Alkaline methanolysis gave the free cytidine homologues, 1-(6-deoxy-β-D-alto- and -α-L-talo-furanosyl)cytosine (23) and (28), which were converted into the crystalline 5′-phosphates (24) and (29), and hence to the dilithium salts of the 5′-pyrophosphates, (25) and (30), by standard procedures. These were labelled at C-5 by bromination, followed by catalytic reduction in tritium gas. The same methyl furanoside starting materials were converted into the 3,5-dibenzoates, (3) and (9), by deacetalation followed by monobenzoylation by the stannylene procedure. Substitution of iodine via the 2-trifluoromethanesulphonates gave iodides which were reduced by tributylstannane to methyl 3,5-di-O-benzoyl-2,6-dideoxy-β-D-ribo- and -α-L-lyxo-hexofuranosides (7) and (13). Coupling of these in the same way as above, followed by alkaline methanolysis, gave the two deoxycytidine homologues, 1-(2,6-dideoxy-β-D-ribo- and -α-L-lyxo-hexofuranosyl)cytosine, (16) and (17), together with their anomers (14) and (15). In another approach to these nucleosides, 4-N-acetyl-2′,3′-O-isopropylidenecytidine was oxidized to the aldehyde (33) which was condensed with dimethylsuiphoxonium methylide to a mixture of epoxides (34) and (35). Hydrogen bromide opening, followed by tributylstannane reduction, converted these epoxides into 4-N-acetyl-1-(2,3-O-isopropylidene-6-deoxy-β-D-allo- and -α-L-talo-furanosyl)cytosine (36) and (37). Treatment of the same mixture dissolved in tetrahydrofuran (THF) by boron trifluorideether gave 4-acetamido-1-(2,5′; 2,6′-dianhydro-2′,3′-O-isopropylidene-α-L-talofuranosyl)-2H-pyrimidine (39), the first reported anhydro-nucleoside with two oxygen bridges between the base and the sugar, available in 18% overall yield from protected cytidine.
A New Inhibitor of Mitochondrial Fatty Acid Oxidation (1996)

The mitochondrial enoyl-CoA hydratase/3-hydroxyacyl-CoA dehydrogenase/3-ketoacyl-CoA thiolase trifunctional protein (trifunctional protein) plays a major role in mitochondrial fatty acid oxidation. The enzyme complex consists of four molecules of alpha-subunit containing both hydratase and dehydrogenase domains and four molecules of beta-subunit containing the thiolase domain. The primary structure of a gastrin-binding protein (GBP) was highly homologous to that of the alpha-subunit of the trifunctional protein. Here, we report that gastrin inhibits the hydratase, dehydrogenase, and thiolase activities of the trifunctional protein. The gastrin/cholecystokinin receptor antagonist benzotript, which inhibited binding of gastrin to the GBP, also inhibited all three activities of the trifunctional protein. In addition, benzotript inhibits the activities of multifunctional enzymes having similar structures, such as the peroxisomal enoyl-CoA hydratase/3-hydroxyacyl-CoA dehydrogenase bifunctional protein and the Pseudomonas fragi fatty acid oxidation enzyme complex. This reagent, however, hardly inhibited various monofunctional enzymes involved in fatty acid oxidation.
Neurotoxicity of Intra-arterial Papaverine Preserved with Chlorobutanol Used for the Treatment of Cerebral Vasospasm After Aneurysmal Subarachnoid Hemorrhage (2004)

Intra-arterial delivery of papaverine preserved with chlorobutanol into vasospastic anterior cerebral arteries may result in marked neurological deterioration with selective gray matter changes on MRI imaging. This effect is consistent with a permanent toxic effect to human brain. It is unclear whether this toxicity is caused by papaverine or chlorobutanol, and its use in the treatment of cerebral vasospasm should be reserved for cases without alternatives.
Simplified Method of Preparing Colloidal Chitin Used For Screening of Chitinase- Producing Microorganisms (2012)

A simplified and efficient method of preparing colloidal chitin from inexpensive crab shell flakes was developed. It modifies some steps of existing techniques to provide significant saving in effort and materials for colloidal chitin preparation. In colloidal chitin preparation, unless the initial chitin flakes are ground to a fine powder, it becomes difficult to later separate the chitin chunks from the precipitated colloidal chitin. The modified technique reported here involves the use of simple everyday lab materials to extract colloidal chitin from crab shell flakes, without the need of powdering the chitin flakes to a uniformly fine size. Utility of the colloidal chitin obtained was shown by using it in plate assays to screen for extracellular chitinase producers, and labeling it with Remazol Brilliant Blue (RBB) for chitinase assays.
Bend theory of river meanders. Part 1. Linear development (1981)

Instability of the alternate-bar type in straight channels has long been identified as the cause of fluvial meandering. The condition of inerodible sidewalls, however, does not allow a meandering channel to develop. Herein a stability analysis of a sinuous channel with erodible banks allows for delineation of a ‘bend’ instability that does not occur in straight channels, and differs from the alternate-bar instability. In the case of alluvial meanders, the two mechanisms are shown to operate at similar characteristic wavelengths. This provides a rationale for the continuous evolution of alternate bars into true bends such that each bend contains one alternate bar. The same bend instability applies to incised meanders. A mechanism for incised alternate bars which differs from that for the alluvial case appears to operate at different characteristic wavelengths than that of bend instability. Analysis of data suggests that meandering in supraglacial meltwater streams is primarily due to the alternate bar mechanism, whereas the meandering of rills incised in cohesive material and of caves is likely due to the bend mechanism. The meander wavelength of incised reaches of meandering streams is often longer than that of adjacent alluvial reaches. An explanation is offered in terms of bend instability.
Pharmacological detection of AMPA receptor heterogeneity by use of two allosteric potentiators in rat hippocampal cultures (1998)

1. In order to examine whether a recently developed allosteric potentiator for AMPA receptors, 4-[2-(phenylsulphonylamino)ethylthio]-2,6-difluoro-phenoxyaceta mide (PEPA), can be utilized as an indicator of AMPA receptor heterogeneity, the action of PEPA upon the increase of intracellular free calcium ion concentration ([Ca2+]i) elicited by AMPA was investigated in rat hippocampal cultures, and the action was compared with that of cyclothiazide, a well characterized allosteric modulator of AMPA receptors. 2. PEPA dose-dependently potentiated AMPA-induced increase of [Ca2+]i. In 90% (72 out of 80) of the cells in which cyclothiazide acts, PEPA potentiated the increased [Ca2+]i induced by AMPA with pronounced cell-to-cell variation in rat hippocampal cultures. 3. The ratio of the potentiation by PEPA to the potentiation by cyclothiazide (P/C ratio) also varied with cells between 0 and 2.15. It was found that the cultured hippocampal cells consisted of multiple populations with different P/C ratios. Among them two populations exhibited characteristic P/C ratios; low (0 to 0.15; 27 out of 80 cells, 34%) and high (> or = 2.00; 1 out of 80 cells, 1%) P/C ratios. The P/C ratios of the other populations were between 0.25 and 1.20, and these cells constituted 65% (52 out of 80 cells) of the cells tested. 4. Reverse transcriptase-polymerase chain reaction analysis suggested that GluR2-flip, GluR1-flip, GluR2-flop, and GluR1-flop were abundantly expressed (in this rank order) in the cultures used. 5. In Xenopus oocytes expressing GluR1, GluR3, or these subunits plus GluR2, the potentiation of AMPA response by PEPA and by cyclothiazide varied with subunit and splice-variant combinations, and the P/C ratio was between 0.19 and 2.20. Oocytes with low P/C ratios (0.19 to 0.50) and low sensitivity to PEPA potentiation (1.9 fold to 6.41 fold) were those expressing flip variants predominantly, and oocytes with high P/C ratios (1.8 to 2.2) were those expressing flop variants predominantly. Oocytes with intermediate P/C ratios (0.51 to 1.20) were those expressing various combinations of flip and flop variants, and it was impossible to specify the relative abundance of flip and flop variants in these cells. Therefore, the P/C ratio can be used to infer subunit/splice variant expression only when the ratio is low or high. 6. These results suggest that the potentiation by PEPA alone reveals cell-to-cell heterogeneity of AMPA receptors, but a comparison of the actions of PEPA and cyclothiazide further facilitates the detection of the heterogeneity.
Necrosis of skin induced by coumarin in a patient deficient in protein S. (1989)

weeks plasma total thyroxine and thyroid stimulating hormone concentrations were normal. He had no diarrhoea or allergic symptoms and was more active and lively. Iodine supplements were stopped. After eight weeks his response to thyrotrophin releasing hormone was normal. He had gained 1 5 kg in weight and 2 0 cm in height.
Perivascular Mast Cells Promote Atherogenesis and Induce Plaque Destabilization in Apolipoprotein E–Deficient Mice (2007)

This is the first study to demonstrate that mast cells play a crucial role in plaque progression and destabilization in vivo. We propose that mast cell stabilization could be a new therapeutic approach to the prevention of acute coronary syndromes.
Complete amino acid sequence of protein B (1988)

The complete amino acid sequence of protein B (= CAMP factor) of Streptococcus agalactiae has been determined. The sequence data were obtained mainly by manual sequencing of peptides derived from digestion with lysyl-peptidase, clostripain and Staphylococcus aureus protease and by solid phase sequencing of cyanogen bromide fragments. The protein contains 226 amino acids and has an Mr of 25,263. The sequence was compared with sequences of other Fc-binding proteins and partial sequence homology was found between protein B and the Fc-binding region of protein A.
Complement activation by photooxidation products of A2E, a lipofuscin constituent of the retinal pigment epithelium (2006)

Recent studies have implicated local inflammation and activation of complement amongst the processes involved in the pathogenesis of age-related macular degeneration (AMD). Several lines of investigation also indicate that bis-retinoid pigments, such as A2E, that accumulate as lipofuscin in retinal pigment epithelial (RPE) cells, contribute to the disease process. In an investigation of a potential trigger for complement activation in AMD, we explored the notion that the complex mixture of products resulting from photooxidation of A2E might include a range of fragments that could be recognized by the complement system as "foreign" and that could serve to activate the complement system, leading to low-grade inflammation. To this end, we established an in vitro assay by using human serum as a source of complement, and we measured products of C3 activation by enzyme immunoassay. Accordingly, we found that the C3 split products inactivated C3b (iC3b) and C3a were elevated in serum, overlying ARPE-19 cells that had accumulated A2E and were irradiated to induce A2E photooxidation. Precoating of microtiter plates with two species of oxidized A2E, peroxy-A2E, and furano-A2E, followed by incubation with serum, also activated complement. We suggest that products of the photooxidation of bis-retinoid lipofuscin pigments in RPE cells could serve as a trigger for the complement system, a trigger than would predispose the macula to disease and that, over time, could contribute to chronic inflammation. These findings link four factors that have been posited as being associated with AMD: inflammation, oxidative damage, drusen, and RPE lipofuscin.
Factors Affecting the Sensitivity of Limulus Lysate (1974)

Limulus lysate clots when mixed with picogram quantities of endotoxins. The sensitivity of the lysate was improved 100-fold by the removal of an inhibitor and addition of divalent cations. The methods developed in this investigation eliminated much of the seasonable variability of the lysate, improved the heat stability after lyophilization, and made it possible to use the lysate with saline solutions.
Modeling and base-calling for Dna Sequencing-By-Synthesis (2006)

The process of DNA sequencing-by-synthesis and its non-idealities are modeled as a noisy switched linear system parameterized by the unknown DNA sequence. The base-calling problem is then formulated as a parameter detection problem. As this system can have long memory, performing exact maximum-likelihood decoding is computationally prohibitive. An approximate ML method applied to experimental Pyrosequencing data demonstrates reliable read lengths exceeding 200 bases, which is significantly longer than that achieved by current methods
Mobile vehicle crash detection system (2018)

Vehicle collision detection (VCD) system is an Android Apps. VCD system requires the assistance of on-board sensors: (1) GPS, and (2) Accelerometer, and (3) Linear Acceleration. GPS is used to calculate the car speed, while the accelerometer is used to calculate the acceleration force. Our idea is to combine both sensors decision to evaluate an accident condition, i.e. the severity of potential accidents. Connectivity is required, as the database is located at the backend using backendless API, for data creation/updates. User can be service provider or driver, (1) providers will receive accidents sent by driver and (2) driver has to provide information surrounding the trip. The typical flow of the application (for driver) is: Step 1: Driver activate application and key-in relevant information, Step 2: When potential accident is detected, the system will automatically check for the closest Service Provider(s), and Step 3: Relevant information and notification to them. The application begins by prompting the number of passengers from the user (integer value). Then, the user activates the detection; the application will monitor speed and acceleration force of the vehicle. When a potential dangerous event data occurs, it will prompt the user to confirm whether an accident has occurred. User can cancel if no accident has happened, whereas if there is no responds from user for 20 seconds, the application will search for the nearest providers within 10km radius. If no providers are found within 10km radius, a message will be sent to 911. If a Provider is found within 10km radius, details of the accidents including number of passenger, current victim and location will be stored in a database and assigned to the provider. Lastly, a notification will be delivered to the assigned provider.
The Epidemiology of Adult Obstructive Sleep Apnea (2008)

Obstructive sleep apnea is a chronic condition characterized by frequent episodes of upper airway collapse during sleep. Its effect on nocturnal sleep quality and ensuing daytime fatigue and sleepiness are widely acknowledged. Increasingly, obstructive sleep apnea is also being recognized as an independent risk factor for several clinical consequences, including systemic hypertension, cardiovascular disease, stroke, and abnormal glucose metabolism. Estimates of disease prevalence are in the range of 3% to 7%, with certain subgroups of the population bearing higher risk. Factors that increase vulnerability for the disorder include age, male sex, obesity, family history, menopause, craniofacial abnormalities, and certain health behaviors such as cigarette smoking and alcohol use. Despite the numerous advancements in our understanding of the pathogenesis and clinical consequences of the disorder, a majority of those affected remain undiagnosed. Simple queries of the patient or bed-partner for the symptoms and signs of the disorder, namely, loud snoring, observed apneas, and daytime sleepiness, would help identify those in need of further diagnostic evaluation. The primary objective of this article is to review some of the epidemiologic aspects of obstructive sleep apnea in adults.
The response of mouse ocular tissues to continuous near-UV light exposure. (1975)

Continuous exposure of mice to near-ultraviolet (UV) light (black light) over a period of 19 weeks induces adverse alterations in lens protein chemistry, in lens epithelial cell differentiation, and in retinal photoreceptor structure at more than a doubled rate as for 12 hours a day of intermittent exposure. No histologic changes were found in the cornea. The results may indicate the presence of repair mechanisms in these ocular tissues for damage induced by radiant energy.
Clinical Predictors of Renal Allograft Histopathology: A Comparative Study of Single-Lesion Histology Versus a Composite, Quantitative Scoring System (2007)

Our study reveals a missing link between specific clinical risk factors and early histopathological findings that are known to presage accelerated failure of clinically healthy grafts. Given the complex relationship between clinical risk factors, early histopathological changes, and graft outcome, we conclude that composite, quantitative histological indices are best suited to for evaluation of the histological status of the transplant.
Mars rover pair cooperatively transporting a long payload (2003)

The objective of the Robot Work Crew (RWC) project is to investigate key challenges in multi-robot coordination when performing tightly coupled coordination tasks such as transporting and handling of long objects on challenging planetary terrain. In this paper, we focus on tightly coupled coordination of two Mars rovers transporting a long payload. We have developed practical decentralized compliancy control and coordinated comply control algorithms that effectively address compliant control for compliantly coupled multiple mobile robots. Experiments at the Jet Propulsion Lab in Pasadena, CA of two Mars rovers carry an extended payload over uneven, natural terrain are used to validate and illustrate the approach.
Cancer in inflammatory bowel disease (2008)

Patients with long-standing inflammatory bowel disease (IBD) have an increased risk of developing colorectal cancer (CRC). Many of the molecular alterations responsible for sporadic colorectal cancer, namely chromosomal instability, microsatellite instability, and hypermethylation, also play a role in colitis-associated colon carcinogenesis. Colon cancer risk in inflammatory bowel disease increases with longer duration of colitis, greater anatomic extent of colitis, the presence of primary sclerosing cholangitis, family history of CRC and degree of inflammation of the bowel. Chemoprevention includes aminosalicylates, ursodeoxycholic acid, and possibly folic acid and statins. To reduce CRC mortality in IBD, colonoscopic surveillance with random biopsies remains the major way to detect early mucosal dysplasia. When dysplasia is confirmed, proctocolectomy is considered for these patients. Patients with small intestinal Crohn's disease are at increased risk of small bowel adenocarcinoma. Ulcerative colitis patients with total proctocolectomy and ileal pouch anal-anastomosis have a rather low risk of dysplasia in the ileal pouch, but the anal transition zone should be monitored periodically. Other extra intestinal cancers, such as hepatobiliary and hematopoietic cancer, have shown variable incidence rates. New endoscopic and molecular screening approaches may further refine our current surveillance guidelines and our understanding of the natural history of dysplasia.
Nano-flares for mRNA Regulation and Detection (2009)

We build off the previously described concept of a nanoflare to develop an oligonucleotide gold nanoparticle conjugate that is capable of both detecting and regulating intracellular levels of mRNA. We characterize the binding rate and specificity of these materials using survivin, a gene associated with the diagnosis and treatment of cancer, as a target. The nanoconjugate enters cells and binds mRNA, thereby decreasing the relative abundance of mRNA in a dose- and sequence-dependent manner, resulting in a fluorescent response. This represents the first demonstration of a single material capable of both mRNA regulation and detection. Further, we investigate the intracellular biochemistry of the nanoconjugate, elucidating its mechanism of gene regulation. This work is important to the study of biologically active nanomaterials such as the nanoflare and is a first step toward the development of an mRNA responsive "theranostic".
Substrate Specificity of the Glycosyl Donor for Oligosaccharyl Transferase (2001)

Oligosaccharyl transferase (OT) catalyzes the co-translational transfer of a dolichol-linked tetradecasaccharide (Dol-PP-GlcNAc(2)Man(9)Glc(3), 1a) to an asparagine side chain of a nascent polypeptide inside the lumen of the endoplasmic reticulum (ER). The glycosyl acceptor requires an Asn-Xaa-Thr/Ser sequon, where Xaa can be any natural amino acid except proline, for N-linked glycosylation to occur. To address the substrate specificity of the glycosyl donor, three unnatural dolichol-linked disaccharide analogues (Dol-PP-GlcNTFA-GlcNAc 1c, Dol-PP-2DFGlc-GlcNAc 1d, and Dol-PP-GlcNAc-Glc 1e) were synthesized and evaluated as substrates or inhibitors for OT from yeast. The synthetic analogue Dol-PP-GlcNAc-Glc 1e, with substitution in the distal sugar, was found to be a substrate (K(m)(app)() = 26 microM) for OT. On the other hand, the analogues Dol-PP-GlcNTFA-GlcNAc 1c (K(i) = 154 microM) and Dol-PP-2DFGlc-GlcNAc 1d (K(i) = 252 microM), with variations in the proximal sugar, were inhibitors for OT. The dolichol-linked monosaccharide Dol-PP-GlcNAc 3 was found to be the minimum unit for glycosylation to occur.