gebhart/patrepeval huggingface dataset:
A silybin-phospholipids complex counteracts rat fatty liver degeneration and mitochondrial oxidative changes (2013)

Realsil administration effectively contrasts hepatocyte fat deposition, NO derivatives formation, and mitochondrial alterations, allowing the liver to maintain a better glutathione and thioredoxin antioxidant activity.
On the efficiency of local decoding procedures for error-correcting codes (2000)

We consider error-correcting codes where a bit of the message can be probabilistically recovered by looking at a limited number of bits (or blocks of bits) of a (possibly) corrupted encoding. Such codes can be derived from multivariate polynomial encodings, and have several applications in complexity theory, such as worst-case to average-case reductions, probabilistically checkable proofs, and private information retrieval. Such codes could have practical applications if they had at the same time constant information rate, the ability to correct a linear number of errors, and very efficient (ideally, constant-time) reconstruction procedures. In particular they would give fault-tolerant data storage with unlimited scalability. We show a negative result on the existence of such codes; namely, that linear encoding length is incompatible with a decoding procedure making a constant number of queries (which is necessary if one is to have constant reconstruction time). In particular, if a bit of a message of length n can be retrieved by looking at q blocks of length l, and the reconstruction procedure is robust to a fraction 5 of errors, then the encoding is made of m = f/(poly(1/q, 6, e)(n/l) q/(q-t))
Regulation of flagellar dynein by an axonemal type-1 phosphatase in <i>Chlamydomonas</i> (1996)

ABSTRACT Physiological studies have demonstrated that flagellar radial spokes regulate inner arm dynein activity in Chlamydomonas and that an axonemal cAMP-dependent kinase inhibits dynein activity in radial spoke defective axonemes. These studies also suggested that an axonemal protein phosphatase is required for activation of flagellar dynein. We tested whether inhibitors of protein phosphatases would prevent activation of dynein by the kinase inhibitor PKI in Chlamydomonas axonemes lacking radial spokes. As predicted, preincubation of spoke defective axonemes (pf14 and pf17) with ATPγS maintained the slow dynein-driven microtubule sliding characteristic of paralyzed axonemes lacking spokes, and blocked activation of dynein-driven microtubule sliding by subsequent addition of PKI. Preincubation of spoke defective axonemes with the phosphatase inhibitors okadaic acid, microcystin-LR or inhibitor-2 also potently blocked PKI-induced activation of microtubule sliding velocity: the non-inhibitory okadaic acid analog, 1-norokadaone, did not. ATPγS or the phosphatase inhibitors blocked activation of dynein in a double mutant lacking the radial spokes and the outer dynein arms (pf14pf28). We concluded that the axoneme contains a type-1 phosphatase required for activation of inner arm dynein. We postulated that the radial spokes regulate dynein through the activity of the type-1 protein phosphatase. To test this, we performed in vitro reconstitution experiments using inner arm dynein from the double mutant pf14pf28 and dynein-depleted axonemes containing wild-type radial spokes (pf28). As described previously, microtubule sliding velocity was increased from ∼2 μm/second to ∼7 μm/second when inner arm dynein from pf14pf28 axonemes was reconstituted with axonemes containing wild-type spokes. In contrast, pretreatment of inner arm dynein from pf14pf28 axonemes with ATPγS, or reconstitution in the presence of microcystin-LR, blocked increased velocity following reconstitution, despite the presence of wild-type radial spokes. We conclude that the radial spokes, through the activity of an axonemal type-1 phosphatase, activate inner arm dynein by dephosphorylation of a critical dynein component. Wild-type radial spokes also operate to inhibit the axonemal cAMP-dependent kinase, which would otherwise inhibit axonemal dynein and motility.
[Medicines interacting with mitochondria: anti-ischemic effects of trimetazidine]. (2000)

While mitochondria are key factors in energy production in cells they are also key factors in their life cycle because under certain circumstances they can provoke cellular apoptosis. Some 45 per cent of myocardial volume is taken up by mitochondria. Furthermore, mitochondria are key to many aspects of neuronal activity and can trigger neurodegenerative processes. Lipid oxidation is responsible for the production of much ATP resynthesis in the heart but this process is less oxygen efficient than glucose oxidation. During ischaemia, lipid oxidation is suddenly blocked, but markedly increased during reperfusion, causing accumulation of potentially toxic metabolites (acylcarnitines, acyl-CoA, lysophospholipids). These metabolites can change calcium handling, inducing arrhythmias. Trimetazidine, and another product in development, ranolazine, by inhibiting lipid oxidation favours glucose oxidation and inhibits the production of deleterious lipid metabolites. Thus this class of drugs can have beneficial effects on myocardial metabolism without direct haemodynamic effects.
Ovarian cancer classification based on mass spectrometry analysis of sera. (2007)

In our previous study [1], we have compared the performance of a number of widely used discrimination methods for classifying ovarian cancer using Matrix Assisted Laser Desorption Ionization (MALDI) mass spectrometry data on serum samples obtained from Reflectron mode. Our results demonstrate good performance with a random forest classifier. In this follow-up study, to improve the molecular classification power of the MALDI platform for ovarian cancer disease, we expanded the mass range of the MS data by adding data acquired in Linear mode and evaluated the resultant decrease in classification error. A general statistical framework is proposed to obtain unbiased classification error estimates and to analyze the effects of sample size and number of selected m/z features on classification errors. We also emphasize the importance of combining biological knowledge and statistical analysis to obtain both biologically and statistically sound results.Our study shows improvement in classification accuracy upon expanding the mass range of the analysis. In order to obtain the best classification accuracies possible, we found that a relatively large training sample size is needed to obviate the sample variations. For the ovarian MS dataset that is the focus of the current study, our results show that approximately 20-40 m/z features are needed to achieve the best classification accuracy from MALDI-MS analysis of sera. Supplementary information can be found at http://bioinformatics.med.yale.edu/proteomics/BioSupp2.html.
6W/25mm<sup>2</sup> inductive power transfer for non-contact wafer-level testing (2011)

Wafer-level testing allows detection of manufacturing errors and removes non functional devices early in the fabrication process. It is commonly performed by placing a probe card directly above a device under test (DUT) and establishing a mechanical contact between them by means of an array of probes. This is an invasive technique that may damage fragile low-k dielectric layers and deform pads or bumps. More importantly, it is very difficult to flip thinned wafers face up for probing if they were earlier positioned face down for back grinding. Additional difficulty in handling of thinned wafers arises if dies have to be flipped again for bumping. One solution to above problems is wireless probing. With a number of proposed techniques for establishing high-speed inductive-coupling data links and measuring DC analog signal wirelessly, the largest remaining obstacle to non-contact wafer-level testing is supplying power to the DUT. This is because wireless power transfer solutions reported earlier do not provide an output power that is sufficient for testing modern high performance devices.This paper presents an inductive power transfer system that is capable of delivering up to 6W of DC power to the on-chip load. The system is partitioned into 8 power transfer channels, each containing two cir cuits: a power transmitter implemented in the probe card, and an on-chip power receiver. This paper focuses on the design of the power receiver, as the receiver performance limits the output power of the whole system.
Targeting angiogenesis inhibits tumor infiltration and expression of the pro-invasive protein SPARC (2000)

The solid growth of high-grade glioma appears to be critically dependent on tumor angiogenesis. It remains unknown, however, whether the diffuse infiltration of glioma cells into healthy adjacent tissue is also dependent on the formation of new tumor vessels. Here, we analyze the relationship between tumor angiogenesis and tumor cell infiltration in an experimental glioma model. C6 cells were implanted into the dorsal skinfold chamber of nude mice, and tumor angiogenesis was monitored by intravital fluorescence videomicroscopy. Glioma infiltration was assessed by the extent of tumor cell invasion into the adjacent chamber tissue and by expression of SPARC, a cellular marker of glioma invasiveness. To test the hypothesis that glioma angiogenesis and glioma infiltration are codependent, we assessed tumor infiltration in both the presence and the absence of the angiogenesis inhibitor SU5416. SU5416 is a selective inhibitor of the VEGF/Flk-1 signal-transduction pathway, a critical pathway implicated in angiogenesis. Control tumors demonstrated both high angiogenic activity and tumor cell invasion accompanied by strong expression of SPARC in invading tumor cells at the tumor-host tissue border. SU5416-treated tumors demonstrated reduced vascular density and vascular surface in the tumor periphery accompanied by marked inhibition of glioma invasion and decreased SPARC expression. A direct effect of SU5416 on glioma cell motility and invasiveness was excluded by in vitro migration and invasion assays. These results suggest a crucial role for glioma-induced angiogenesis as a prerequisite for diffuse tumor invasion and a possible therapeutic role for anti-angiogenic compounds as inhibitors of both solid and diffuse infiltrative tumor growth.
Decision tree induction: how effective is the greedy heuristic? (1995)

Most existing decision tree systems use a greedy approach to induce trees --- locally optimal splits are induced at every node of the tree. Although the greedy approach is suboptimal, it is believed to produce reasonably good trees. In the current work, we attempt to verify this belief. We quantify the goodness of greedy tree induction empirically, using the popular decision tree algorithms, C4.5 and CART. We induce decision trees on thousands of synthetic data sets and compare them to the corresponding optimal trees, which in turn are found using a novel map coloring idea. We measure the effect on greedy induction of variables such as the underlying concept complexity, training set size, noise and dimensionality. Our experiments show, among other things, that the expected classification cost of a greedily induced tree is consistently very close to that of the optimal tree. Introduction Decision trees are known to be effective classifiers in a variety of domains. Most of the methods ...
Retinal Ganglion Cells Downregulate Gene Expression and Lose Their Axons within the Optic Nerve Head in a Mouse Glaucoma Model (2008)

Little is known about molecular changes occurring within retinal ganglion cells (RGCs) before their death in glaucoma. Taking advantage of the fact that gamma-synuclein (Sncg) mRNA is expressed specifically and highly in adult mouse RGCs, we show in the DBA/2J mouse model of glaucoma that there is not only a loss of cells expressing this gene, but also a downregulation of gene expression of Sncg and many other genes within large numbers of RGCs. This downregulation of gene expression within RGCs occurs together with reductions in FluoroGold (FG) retrograde transport. Surprisingly, there are also large numbers of Sncg-expressing cells without any FG labeling, and among these many that have a marker previously associated with disconnected RGCs, accumulation of phosphorylated neurofilaments in their somas. These same diseased retinas also have large numbers of RGCs that maintain the intraocular portion while losing the optic nerve portion of their axons, and these disconnected axons terminate within the optic nerve head. Our data support the view that RGC degeneration in glaucoma has two separable stages: the first involves atrophy of RGCs, whereas the second involves an insult to axons, which causes the degeneration of axon portions distal to the optic nerve head but does not cause the immediate degeneration of intraretinal portions of axons or the immediate death of RGCs.
Questions about Chemokine and Chemokine Receptor Antagonism in Renal Inflammation (2009)

Chemokines remain attractive therapeutic targets for modulating inflammatory diseases in all areas of medicine including acute and chronic kidney disease. Industry has launched huge programs for the development of chemokine antagonists, and clinical trials with chemokine and chemokine receptor antagonists are ongoing. However, chemokine biology remains an area of unexpected discoveries. Here we discuss a number of questions which need to be addressed to further explore the potential of chemokine antagonism in renal inflammation: Why does renal expression of chemokines and chemokine receptors not always correlate with their functional significance? Why does chemokine antagonism only partially reduce renal leukocyte counts? Will antagonist combinations be more effective in reducing renal inflammation? What are the functional roles of homeostatic chemokines and atypical, nonsignaling chemokine receptors in renal inflammation? And finally, what classes of chemokine antagonists are available to address these questions experimentally?
LAETRILE: A STUDY OF ITS PHYSICOCHEMICAL AND BIOCHEMICAL PROPERTIES. (1965)

A study was made of the composition and biochemical behaviour of the drug, Laetrile, distributed for clinical trial in the United States and Canada. It was established that the Canadian and the American product are different pharmaceutical formulations, displaying different physicochemical and biochemical properties. The investigation demonstrated, furthermore, that neither preparation can be considered as a palliative in cancer therapy on the basis of the biological rationale advanced by their manufacturers.
Management of imidazolinone-tolerant (IT) rice in drill- and water-seeded rice (2002)

Field studies were conducted over two years in drill- and water-seeded rice to evaluate weed control and crop response with imazethapyr programs. Barnyardgrass [Echinochloa crus-galli (L.) Beauv.] was evaluated with imazethapyr applied alone at various rates and timings. Imazethapyr controlled barnyardgrass 95 to 97% with a soil application at 87 or 70 g/ha fb 53 or 70 g/ha EPOST or LPOST. A single EPOST application of imazethapyr at 140 g/ha controlled barnyardgrass and rice yield was equal to or above those treatments receiving two applications of imazethapyr. Research was also conducted at Crowley, LA and Rayne, LA to evaluate the addition of a herbicide with broadleaf activity into imazethapyr programs applied alone early postemergence (EPOST) and in combination with imazethapyr postemergence (POST). Weeds evaluated included barnyardgrass, red rice (Oryza sativa L.), alligatorweed [Alternanthera philoxeroides (Mart.) Griseb.], and hemp sesbania [Sesbania exaltata (Raf.) Rydb. ex A.W. Hill]. Treatments consisting of imazethapyr applied at 87 g/ha alone to the soil fb a POST imazethapyr application at 53 g/ha controlled barnyardgrass above 90% late season in all studies, expect in water-seeded rice when an imazethapyr application was made at the three- to four-leaf rice stage. Red rice control with a total imazethapyr program was equivalent to, or higher, than other treatments in both drill- and water-seeded studies. Single imazethapyr applications resulted in reduced control of red rice indicating two applications of imazethapyr are required to obtain adequate control. Alligatorweed control increased with soil applications of imazethapyr. However, alligatorweed control with imazethapyr as the only herbicide in a weed control program was inconsistent and suggested only suppression. Treatments receiving a broadleaf herbicide application increased hemp sesbania control as compared with the total imazethapyr program; however, treatments with bensulfuron and triclopyr were inconsistent at controlling hemp sesbania. In drill-seeded studies, hemp sesbania was less of a problem and red rice had a greater impact on rice yield. Rice yields with total imazethapyr programs were equal to, or higher than, other treatments. However, in water-seeded studies, hemp sesbania growth was favored and yields from rice treated with broadleaf herbicides were higher than total imazethapyr programs.
Potential for Raman spectroscopy to provide cancer screening using a peripheral blood sample (2009)

Cancer poses a massive health burden with incidence rates expected to double globally over the next decade. In the United Kingdom screening programmes exists for cervical, breast, and colorectal cancer. The ability to screen individuals for solid malignant tumours using only a peripheral blood sample would revolutionise cancer services and permit early diagnosis and intervention. Raman spectroscopy interrogates native biochemistry through the interaction of light with matter, producing a high definition biochemical 'fingerprint' of the target material. This paper explores the possibility of using Raman spectroscopy to discriminate between cancer and non-cancer patients through a peripheral blood sample. Forty blood samples were obtained from patients with Head and Neck cancer and patients with respiratory illnesses to act as a positive control. Raman spectroscopy was carried out on all samples with the resulting spectra being used to build a classifier in order to distinguish between the cancer and respiratory patients' spectra; firstly using principal component analysis (PCA)/linear discriminant analysis (LDA), and secondly with a genetic evolutionary algorithm. The PCA/LDA classifier gave a 65% sensitivity and specificity for discrimination between the cancer and respiratory groups. A sensitivity score of 75% with a specificity of 75% was achieved with a 'trained' evolutionary algorithm. In conclusion this preliminary study has demonstrated the feasibility of using Raman spectroscopy in cancer screening and diagnostics of solid tumours through a peripheral blood sample. Further work needs to be carried out for this technique to be implemented in the clinical setting.
Reaction and Fired‐Property Studies of Cordierite Compositions (1954)

Ceramic bodies approaching the theoretical composition of cordierite were prepared from mixtures of talc and clay; talc, clay, and varying amounts of MgCO 3 ; talc, clay, and alumina; and prochlorite and clay. Additions of BaCO 3 and PbSiO, were made. Differential thermal analysis and X‐ray diffraction methods were used in reaction studies of each composition. Bodies had thermal expansions from 0.344 to 0.109% (25° to 900°C.). BaCO 3 and PbSiO 3 affected thermal expansion. Dielectric properties were improved by additions of BaCO 3 and were markedly improved by additions of both BaCO 3 and PbSiO l . Cordierite started to crystallize at about 1250°. Additions of PbSiO 3 lowered this temperature about 50°C. With sufficient BaCO 3 , the Ba‐C phase, as described by Wisely, crystallized in place of cordierite. The crystallization temperature for the Ba‐C phase was about 1200°C. With insufficient BaCO 3 , both cordierite and Ba‐C formed. Additions of PbSiO 3 reduced the crystallization temperature of the Ba‐C phase by 50°C. and increased the glassy phase. Several of the compositions should haw considerable practical value.
Large-scale Cloze Test Dataset Designed by Teachers (2017)

Cloze test is widely adopted in language exams to evaluate students' language proficiency. In this paper, we propose the first large-scale human-designed cloze test dataset CLOTH, in which the questions were used in middle-school and high-school language exams. With the missing blanks carefully created by teachers and candidate choices purposely designed to be confusing, CLOTH requires a deeper language understanding and a wider attention span than previous automatically generated cloze datasets. We show humans outperform dedicated designed baseline models by a significant margin, even when the model is trained on sufficiently large external data. We investigate the source of the performance gap, trace model deficiencies to some distinct properties of CLOTH, and identify the limited ability of comprehending a long-term context to be the key bottleneck.
SmartPulse, a machine learning approach for calibration‐free dynamic RF shimming: Preliminary study in a clinical environment (2019)

The proposed method paves the way toward an efficient trade-off between tailored and universal pulse design approaches for large inter-subject variability. With no need for on-line field mapping or pulse design, it can fit seamlessly into a clinical protocol.
Multi-Agent Learning in Mobilized Ad-Hoc Networks. (2004)

In large, distributed systems such as mobilized ad-hoc networks, centralized learning of routing or movement policies may be impractical. We need to employ multi-agent learning algorithms that can learn independently, without the need for extensive coordination. Using only a simple coordination signals such as a global reward value, we show that reinforcement learning methods can be used to control both packet routing decisions and node mobility.
A robotic molecular method for <i>in situ</i> detection of marine invertebrate larvae (2007)

Knowledge of the temporal and spatial abundance of invertebrate larvae is critical to understanding the dispersal capabilities and recruitment potential of marine and aquatic organisms. Traditional microscopic analyses are time-consuming and difficult given the diversity of larval species and a frequent lack of discriminating morphological characteristics. Here, we describe a sensitive rRNA targeted sandwich hybridization assay (SHA) that uses oligonucleotide probes to detect and enumerate the larvae of invasive green crabs (Carcinus maenas), native blue mussels (Mytilus), native barnacles (Balanus) and polychaetes (Osedax and Ophelia) that occur in the Monterey Bay National Marine Sanctuary, California. Laboratory-based assays demonstrate specificity, high sensitivity, and a quantitative response to cultured samples from three of the target organisms. Oligonucleotide probes were then printed in arrays on nitrocellulose membranes and deployed in our robotic Environmental Sample Processor (ESP) to detect larvae in situ and autonomously. We demonstrate that the SHA-detection method and ESP robot can be used for near real-time, in situ detection of larval species in the marine environment.