gebhart/patrepeval huggingface dataset:
Blockade of renin–angiotensin system in antifibrotic therapy (2007)

Recent studies have shown that the renin-angiotensin system (RAS) plays a pivotal role in liver fibrosis. An intrahepatic RAS is expressed in chronically damaged livers, and angiotensin-II (AT-II) reportedly stimulates contraction and proliferation of the activated hepatic stellate cells (Ac-HSC), and increases the transforming growth factor-beta (TGF-beta) expression through angiotensin type-I receptors (AT1-R). Some studies have demonstrated that the clinically used angiotensin-converting enzyme (ACE) inhibitor (ACE-I), and AT1-R blockers (ARB) significantly attenuated experimental liver fibrosis along with suppression of the Ac-HSC and hepatic TGF-beta expression. Angiotensin-II also stimulates the tissue inhibitor of metalloproteinases-1 (TIMP-1) in a dose- and time-dependent manner via protein kinase-C as an intracellular signaling cascade in the Ac-HSC, and these effects are completely suppressed by ARB. Combination treatment with low-dose interferon (IFN) and ACE-I exerts a stronger inhibitory effect than either single agent on its own. In humans it has been reported that ARB markedly improved the liver fibrosis score and TGF-beta expression in patients with chronic hepatitis C and non-alcoholic steatohepatitis. Serum fibrosis markers also significantly improved by treatment with low-dose IFN and ACE-I in patients with chronic hepatitis C, refractory to IFN monotherapy. Collectively, these data suggest that the interaction between AT-II and AT1-R plays a pivotal role in liver fibrosis development. Because both ACE-I and ARB are widely used in clinical practice without serious side-effects, these drugs in combination with IFN may provide a new strategy for antifibrosis therapy.
Failure to Induce Hypersensitivity Reactions to Opaque Contrast Media Analogs in Guinea Pigs (1975)

In a further exploration of idiosyncratic reactions to injections of contrast media, a systematic study of immediate or delayed hypersensitivity in guinea pigs injected with contrast media analogs was performed. No evidence of immediate or delayed hypersensitivity could be ascertained to either contrast media analogs alone, or analogs bound to protein carriers. This does not represent conclusive evidence against the notion of antibody formation as a factor in the production of some adverse reactions, but makes such a pathogenesis less likely.
Notch Signaling Induces Osteogenic Differentiation and Mineralization of Vascular Smooth Muscle Cells (2009)

These results imply a new mechanism for osteogenic differentiation of vascular SMCs in which Notch/RBP-Jk signaling directly induces Msx2 gene expression and suggest its crucial role in mediating vascular calcification.
Follicular Neoplasms of the Thyroid: What to Recommend (2005)

Follicular neoplasms of the thyroid are usually diagnosed following fine-needle aspiration (FNA) biopsy of a dominant thyroid nodule. An FNA diagnosis of a follicular neoplasm represents a heterogeneous group of lesions including benign follicular hyperplasia, follicular adenomas, follicular carcinomas, and the follicular variant of papillary carcinoma. Hürthle cell neoplasms are also often included in this group. Because the criteria for malignancy in both follicular and Hürthle cell neoplasms requires vascular or capsular invasion seen on permanent histology, the majority of these patients undergo surgical resection. Intraoperative frozen section analysis of follicular neoplasms rarely renders informative information. Approximately 20% of these lesions prove to be malignant and for lesions greater than 1.0 cm in size, the majority of surgeons and endocrinologists recommend a total thyroidectomy. Postoperative treatment generally includes therapeutic doses of 131I for follicular carcinomas.
Analysis of chronic lymphotic leukemia transcriptomic profile: differences between molecular subgroups (2009)

B cell chronic lymphocytic leukemia (CLL) is a lymphoproliferative disorder with a variable clinical course. Patients with unmutated IgV(H) gene show a shorter progression-free and overall survival than patients with immunoglobulin heavy chain variable regions (IgV(H)) gene mutated. In addition, BCL6 mutations identify a subgroup of patients with high risk of progression. Gene expression was analysed in 36 early-stage patients using high-density microarrays. Around 150 genes differentially expressed were found according to IgV(H) mutations, whereas no difference was found according to BCL6 mutations. Functional profiling methods allowed us to distinguish KEGG and gene ontology terms showing coordinated gene expression changes across subgroups of CLL. We validated a set of differentially expressed genes according to IgV(H) status, scoring them as putative prognostic markers in CLL. Among them, CRY1, LPL, CD82 and DUSP22 are the ones with at least equal or superior performance to ZAP70 which is actually the most used surrogate marker of IgV(H) status.
BUBBLE FORCES AND DETACHMENT MODELS (2001)

The forces acting on growing and sliding vapor bubbles associated with heterogeneous boiling are identified. Closed form expressions have been suggested which approximate the magnitude of these forces. Beginning with Newton's second law, a rational basis is proposed for predicting vapor bubble detachment diameters and sliding trajectories in heterogeneous boiling. Model closure is achieved without introducing arbitrary constants. The predicted detachment diameters and sliding trajectories are compared with extensive data for pool and flow boiling in both horizontal and vertical orientations. Good agreement is observed for all cases considered.
FRASH: A framework to test algorithms of similarity hashing (2013)

Automated input identification is a very challenging, but also important task. Within computer forensics this reduces the amount of data an investigator has to look at by hand. Besides identifying exact duplicates, which is mostly solved using cryptographic hash functions, it is necessary to cope with similar inputs (e.g., different versions of a file), embedded objects (e.g., a JPG within a Word document), and fragments (e.g., network packets), too. Over the recent years a couple of different similarity hashing algorithms were published. However, due to the absence of a definition and a test framework, it is hardly possible to evaluate and compare these approaches to establish them in the community. The paper at hand aims at providing an assessment methodology and a sample implementation called FRASH: a framework to test algorithms of similarity hashing. First, we describe common use cases of a similarity hashing algorithm to motivate our two test classes efficiency and sensitivity & robustness. Next, our open and freely available framework is briefly described. Finally, we apply FRASH to the well-known similarity hashing approaches ssdeep and sdhash to show their strengths and weaknesses.
Studies on the Synthesis of Compounds Related to Adenosine 3',5'-Cyclic Phosphate. IX. Synthesis and Cytotoxic Effect of Adenosine 3',5'-Cyclic Alkylphosphoramidates. (1991)

A series of adenosine 3',5'-cyclic monophosphoramidates (3, cAMP amidates), including long-chain alkyl amidates, were synthesized from adenosine 3',5'-cyclic monophosphate (1, cAMP) by means of a one-pot reaction. This reaction proceeded by the treatment of cAMP tributylammonium salt (2) with phosphorus pentachloride (PCl5) and alkylamine in N,N-dimethylformamide (DMF). Compounds 3 synthesized were investigated to determine their cytotoxic activities on the growth of mouse mastocytoma P-815 cells, mouse mammary tumor FM3A cells, and human mammary tumor ZR-75 cells in culture. It was found that compounds 3h-m showed significant cytotoxic activities against these cell lines, and that cAMP decylamidate (3j) was the most cytotoxic compound (the concentration required for 50% inhibition of cell growth, ID50 = 6.0, 15.0, 2.2 microM, respectively); the antitumor effect on P-815 cells by a total packed cell volume method showed 81.8% inhibition. The cytotoxic activity of 3 increased with the increase in alkyl chain length up to 10 carbon atoms and decreased in compounds having longer alkyl chain.
Applicability of several seismic wave parameters in earthquake prediction (2012)

This paper introduces several important seismic parameters that is carried by seismic wave and discusses the applicability of those parameters in earthquake prediction. Methods are presented and examples are demonstrated to show how to correctly apply the seismic wave method to achieve accurate earthquake prediction data. Current limitations that prevent those parameters from being further applied for earthquake prediction are also discussed.
Solid-Supported Benzotriazoles:  Synthetic Auxiliaries and Traceless Linkers for the Combinatorial Synthesis of Amine Libraries (1999)

This paper describes the successful transfer of benzotriazole-based chemistry on solid support. The strategy followed to anchor this peculiar heterocycle on solid phase and the full analytical characterization of the various supported benzotriazoles are herein described. The chemistry assessment process on solid phase, the preparation of discrete libraries by parallel synthesis, the semiautomated purification procedures, and the complete analytical characterization of the library components are also presented and discussed.
Topological Rules for Membrane Protein Assembly in Eukaryotic Cells (1997)

Insertion into the endoplasmic reticulum membrane of model proteins with one, two, and four transmembrane segments and different distributions of positively charged residues in the N-terminal tail and the polar loops has been studied both in vitro and in vivo. Membrane insertion of these same constructs has previously been analyzed in Escherichia coli, thus making possible a detailed comparison between the topological rules for membrane protein assembly in prokaryotic and eukaryotic cells. In general, we find that positively charged residues have similar effects on the membrane topology in both systems when they are placed in the N-terminal tail but that the effects of charged residues in internal loops clearly differ. Our results rule out a sequential start-stop transfer model where successive hydrophobic segments insert with alternating orientations starting from the most N-terminal one as the only mechanism for membrane protein insertion in eukaryotic cells.
Anatomical variations in human carotid bodies. (1988)

The variations in anatomical structure and position of both carotid bodies were noted in 100 consecutive subjects who came to necropsy. Considerable variations in form were found. Although most carotid bodies (83% on the right and 86% on the left) were of the classic ovoid type, an appreciable minority was bilobed (9% on the right and 7% on the left) or double (7% on the right and 6% on the left); 1% were leaf shaped. All these anatomical variants have to be distinguished from the pathologically enlarged carotid body that may have a smooth or finely nodular surface. Anatomical variants (such as the bilobed) may themselves enlarge as a consequence of carotid body hyperplasia.
Improving the effectiveness of software prefetching with adaptive executions (2002)

The effectiveness of software prefetching for tolerating latency depends mainly on the ability of programmers and/or compilers to: 1) predict in advance the magnitude of the run-time remote memory latency, and 2) insert prefetches at a distance that minimizes stall time without causing cache pollution. Scalable heterogeneous multiprocessors, such as network of computers (NOWs), present special challenges to static software prefetching because on these systems the network topology and node configuration are not completely determined at compile time. Furthermore, dynamic software prefetching cannot do much better because individual nodes on heterogeneous large NOWs would tend to experience different remote memory delays over time. A fixed prefetch distance, even when computed at run-time, cannot perform well for the whole duration of a software pipeline. Here we present an adaptive scheme for software prefetching that makes it possible for nodes to dynamically change, not only the amount of prefetching, but the prefetch distance as well. Doing this makes it possible to tailor the execution of software pipeline to the prevailing conditions affecting each node. We show how simple performance data collected by hardware monitors can allow programs to observe, evaluate and change their prefetching policies. Our results show that on the benchmarks we simulated adaptive prefetching was capable of improving performance over static and dynamic prefetching by 10% to 60%. More important, future increases in the heterogeneity and size of NOWs will increase the advantages of adaptive prefetching over static and dynamic schemes.
Do Deep Nets Really Need to be Deep? (2013)

Currently, deep neural networks are the state of the art on problems such as speech recognition and computer vision. In this extended abstract, we show that shallow feed-forward networks can learn the complex functions previously learned by deep nets and achieve accuracies previously only achievable with deep models. Moreover, in some cases the shallow neural nets can learn these deep functions using a total number of parameters similar to the original deep model. We evaluate our method on the TIMIT phoneme recognition task and are able to train shallow fully-connected nets that perform similarly to complex, well-engineered, deep convolutional architectures. Our success in training shallow neural nets to mimic deeper models suggests that there probably exist better algorithms for training shallow feed-forward nets than those currently available.
Design and Optimization of Hybrid Ex Situ / In Situ Steam Generation Recovery Processes for Heavy Oil and Bitumen (2008)

Abstract Given the enormous capital costs, operating expenses, flue gas emissions, water consumption and handling conducted in thermal in situ bitumen recovery processes, improving overall efficiency by lowering energy requirements and environmental impact of these production techniques is a priority. Steam Assisted Gravity Drainage (SAGD) is a common thermal technique used in Athabasca reservoirs. Although SAGD is effective at producing bitumen, its energy efficiency can be poor due to enormous heat losses on the surface and in the wellbore. Given current attention to carbon dioxide emissions and water handling, there is a need to design and implement Reduced Emissions to Atmosphere Recovery (REAR) processes for heavy oil and bitumen extraction. One alternative is to generate steam in situ by in situ combustion (ISC) by injecting air or oxygen into the formation thus reducing or even avoiding transfer heat losses. In ISC, an energy generating oxidation zone propagates within the formation and generates heat which enables in situ steam generation from formation and injected water within the reservoir. In this research, design and optimization of hybrid in situ steam generation recovery processes are examined by using advanced three-dimensional reactive thermal reservoir simulation. Hybrid techniques combine the advantages of both ex situ steam and in situ steam generation processes in that it raises overall energy efficiency, lowers natural gas consumption as fuel, reduces overall gas emissions as well as water usage to generate steam, all on a per unit oil basis. The research here identifies steam-air based hybrid processes that use roughly 70% of the energy of conventional SAGD to recover the same amount of oil with substantial reduction of flue gas emissions and water use as viable REAR processes worthy of scaled physical model and potentially field testing. Introduction Two requirements of in situ heavy oil recovery processes must be met for successful performance: first, make the heavy oil or bitumen mobile, and second, move the mobilized oil to a production well. Since virgin viscosities of Athabasca bitumen generally exceed several million cP, especially near the base of the oil leg (Larter et al., 2006; Gates et al., 2008), the key to success is first measured by the process' ability to mobilize the heavy oil or bitumen. There are four main methods to accomplish this: heat, solvent dilution, solvent deasphalting, and in situ upgrading. An efficient source of heat is in situ combustion (ISC) which also provides combustion gases that could potentially aid movement of mobilized bitumen in the reservoir.
A Randomized, Open-Label, Multicenter Trial of Topical Tacrolimus for the Treatment of Pruritis in Patients with Atopic Dermatitis (2012)

Use of topical tacrolimus is effective in controlling pruritis of AD compared to emollient.
Vitamin E Prevents Increase in Oxidative Damage to Lipids and DNA in Liver of ODS Rats Given Total Body X-ray Irradiation (2002)

We examined the effects of dietary vitamin E (VE) on oxidative damage to DNA and lipids in the liver a few days after total body irradiation (TBI). ODS rats, which lack vitamin C synthesis, were fed either a low VE diet (4.3 mg VE/kg) or a basal VE diet (75.6 mg VE/kg) for 5 weeks while vitamin C was supplied in the drinking water. The VE level in the liver of the low VE group was lower and the levels of lipid peroxides were higher compared to those of the basal VE group: the relative levels in the two groups were 1:30 for VE, 18:1 for 4-hydroxynonenal (HNE), and 10:1 for hexanal (HA). The level of 8-hydroxydeoxyguanosine (8OHdG), a marker of oxidative DNA damage, did not differ between the low VE and the basal VE groups. When the rats received TBI at the dose of 3 Gy and were killed on day 6, the levels of HNE, HA and 8OHdG increased by 2.2-, 2-, and 1.5-times, respectively, in the low VE group, but TBI did not cause such increases in the basal VE group. Changes in antioxidative enzymes (glutathione peroxidase, catalase, and Cu/Zn-SOD) in the liver could not explain the different responses of the two diet groups to TBI-induced oxidative damage. The concentrations of vitamin C and glutathione in the liver did not differ between the two groups. These results suggest that dietary VE can prevent the oxidative damage to DNA and lipids in the liver which appear a few days after TBI at dose of 3 Gy.
Gradient LASSO for feature selection (2004)

LASSO (Least Absolute Shrinkage and Selection Operator) is a useful tool to achieve the shrinkage and variable selection simultaneously. Since LASSO uses the L1 penalty, the optimization should rely on the quadratic program (QP) or general non-linear program which is known to be computational intensive. In this paper, we propose a gradient descent algorithm for LASSO. Even though the final result is slightly less accurate, the proposed algorithm is computationally simpler than QP or non-linear program, and so can be applied to large size problems. We provide the convergence rate of the algorithm, and illustrate it with simulated models as well as real data sets.
Dual Role of Prostratin in Inhibition of Infection and Reactivation of Human Immunodeficiency Virus from Latency in Primary Blood Lymphocytes and Lymphoid Tissue (2004)

To design strategies to purge latent reservoirs of human immunodeficiency virus type 1 (HIV-1), we investigated mechanisms by which a non-tumor-promoting phorbol ester, prostratin, inhibits infection of CD4(+) T lymphocytes and at the same time reactivates virus from latency. CD4(+) T lymphocytes from primary blood mononuclear cells (PBMC) and in blocks of human lymphoid tissue were stimulated with prostratin and infected with HIV-1 to investigate the effects of prostratin on cellular susceptibility to the virus. The capacity of prostratin to reactivate HIV from latency was tested in CD4(+) T cells harboring preintegrated and integrated latent provirus. Prostratin stimulated CD4(+) T cells in an aberrant way. It induced expression of the activation markers CD25 and CD69 but inhibited cell cycling. HIV-1 uptake was reduced in prostratin-stimulated CD4(+) T PBMC and tissues in a manner consistent with a downregulation of CD4 and CXCR4 receptors in these systems. At the postentry level, prostratin inhibited completion of reverse transcription of the viral genome in lymphoid tissue. However, prostratin facilitated integration of the reverse-transcribed HIV-1 genome in nondividing CD4(+) T cells and facilitated expression of already integrated HIV-1, including latent forms. Thus, while stimulation with prostratin restricts susceptibility of primary resting CD4(+) T cells to HIV infection at the virus cell-entry level and at the reverse transcription level, it efficiently reactivates HIV-1 from pre- and postintegration latency in resting CD4(+) T cells.
Does Wearing a Noseclip during Inhalation Improve Lung Deposition? (2004)

Using nebulization, only a small proportion of the dose reaches the lungs, while the remainder is swallowed, exhaled into the atmosphere, or remains in the nebulizer. It was the purpose of this study to investigate whether wearing a noseclip during inhalation can improve lung deposition. Relative lung deposition was compared by inhalation of the marker substance, sodium cromoglycate (SCG), and measurement of urinary excretion of SCG. The SCG absorption half-life allows one to differentiate indirectly between a more or less peripheral deposition. Ten CF patients (9-18 years old) inhaled, under routine conditions, a solution containing 20 mg of SCG in a randomized crossover design through a mouthpiece, without and with a noseclip being worn. Following inhalation without and with a noseclip, no statistically significant difference was seen in the amount of SCG excreted in urine (0.9 +/- 0.4 mg vs. 1.0 +/- 0.5 mg; p = 0.402) and absorption half-life (93 +/- 25 min vs. 113 +/- 36 min; p = 0.083). In conclusion, wearing a noseclip during inhalation under conditions relevant to practice does not increase the amount deposited into the lungs of CF patients and, also, there has been no indication of a more peripheral lung deposition.
Exact and efficient analytical calculation of the accessible surface areas and their gradients for macromolecules (1998)

A new method for exact analytical calculation of the accessible surface areas and their gradients with respect to atomic coordinates is described. The new surface routine, GETAREA, finds solvent-exposed vertices of intersecting atoms, and thereby avoids calculating buried vertices which are not needed to determine the accessible surface area by the Gauss–Bonnet theorem. The surface routine was implemented in FANTOM, a program for energy minimization and Monte Carlo simulation, and tested for accuracy and efficiency in extensive energy minimizations of Met-enkephalin, the α-amylase inhibitor tendamistat, and avian pancreatic polypeptide (APP). The CPU time for the exact calculation of the accessible surface areas and their gradients has been reduced by factors of 2.2 (Met-enkephalin) and 3.2 (tendamistat) compared with our previous approach. The efficiency of our exact method is similar to the recently described approximate methods MSEED and SASAD. The performance of several atomic solvation parameter sets was tested in searches for low energy conformations of APP among conformations near the native X-ray crystal structure and highly distorted structures. The protein solvation parameters from Ooi et al. [Proc. Natl. Acad. Sci. USA, 84, 3086 (1987)] and from Wesson and Eisenberg [Prot. Sci., 1, 227 (1992)] showed a good correlation between solvation energies of the conformations and their root-mean-square deviations from the X-ray crystal structure of APP. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 319–333, 1998