gebhart/patrepeval huggingface dataset:
Discovery of Candidate DNA Methylation Cancer Driver Genes (2021)

Epigenetic alterations, such as promoter hypermethylation, may drive cancer through tumor suppressor gene inactivation. However, we have limited ability to differentiate driver DNA methylation (DNAme) changes from passenger events. We developed DNAme driver inference-MethSig-accounting for the varying stochastic hypermethylation rate across the genome and between samples. We applied MethSig to bisulfite sequencing data of chronic lymphocytic leukemia (CLL), multiple myeloma, ductal carcinoma <i>in situ</i>, glioblastoma, and to methylation array data across 18 tumor types in TCGA. MethSig resulted in well-calibrated quantile-quantile plots and reproducible inference of likely DNAme drivers with increased sensitivity/specificity compared with benchmarked methods. CRISPR/Cas9 knockout of selected candidate CLL DNAme drivers provided a fitness advantage with and without therapeutic intervention. Notably, DNAme driver risk score was closely associated with adverse outcome in independent CLL cohorts. Collectively, MethSig represents a novel inference framework for DNAme driver discovery to chart the role of aberrant DNAme in cancer. SIGNIFICANCE: MethSig provides a novel statistical framework for the analysis of DNA methylation changes in cancer, to specifically identify candidate DNA methylation driver genes of cancer progression and relapse, empowering the discovery of epigenetic mechanisms that enhance cancer cell fitness.<i>This article is highlighted in the In This Issue feature, p. 2113</i>.
Bioinformatic identification of FGF, p38-MAPK, and calcium signalling pathways associated with carcinoma in situin the urinary bladder (2008)

We conclude that it is possible to use pathway analysis for molecular classification of bladder tumors.
Structural Characterisation of the E. coli Heat Stable Enterotoxin STh (2009)

E. coli heat stable enterotoxin STa is an agonist of the membrane guanylate cyclase C whose endogenous ligands are the peptide hormones guanylin and uroguanylin. Whereas these peptides contain only two disulfide bonds, STa is stabilized by one additional disulfide bridge. We chemically synthesized the enterotoxin STh that originates from the E. coli strain found in humans, and we determined its structure and its dynamics by nuclear magnetic resonance spectroscopy and molecular dynamics calculations. Chemical synthesis clearly proved successful and resulted in the formation of the native disulfide bonds. The endogenous ligands guanylin and uroguanylin show the same general structural features and dynamics properties as the enterotoxin.
Effect of transparent wood on the polarization degree of light (2019)

We report on the study of polarization properties of light propagating through transparent wood (TW), which is an anisotropically scattering medium, and consider two cases: completely polarized and totally unpolarized light. It was demonstrated that scattered light distribution is affected by the polarization state of incident light. Scattering is the most efficient for light polarized parallel to cellulose fibers. Furthermore, unpolarized light becomes partially polarized (with a polarization degree of 50%) after propagating through the TW. In the case of totally polarized incident light, however, the degree of polarization of transmitted light is decreased, in an extreme case to a few percent, and reveals an unusual angular dependence on the material orientation. The internal hierarchical complex structure of the material, in particular cellulose fibrils organized in lamellae, is believed to be responsible for the change of the light polarization degree. It was demonstrated that the depolarization properties are determined by the angle between the polarization of light and the wood fibers, emphasizing the impact of their internal structure, unique for different wood species.
Loop Diuretics Can Cause Clinical Natriuretic Failure: A Prescription for Volume Expansion (2009)

Ultrafiltration enhances volume removal and weight reduction vs diuretics. However, their differential impact on total body sodium, potassium, and magnesium has not been described. Fifteen patients with congestion despite diuretic therapy had urine electrolytes measured after a diuretic dose. Ultrafiltration was initiated and ultrafiltrate electrolytes were measured. The urine sodium after diuretics (60+/-47 mmol/L) was less than in the ultrafiltrate (134+/-8.0 mmol/L) (P=.000025). The urine potassium level after diuretics (41+/-23 mmol/L) was greater than in the ultrafiltrate (3.7+/-0.6 mmol/L) (P=.000017). The urine magnesium level after diuretics (5.2+/-3.1 mg/dL) was greater than in the ultrafiltrate (2.9+/-0.7 mg/dL) (P=.017). In acute decompensated heart failure patients with congestion despite diuretic therapy, diuretics are poor natriuretics and cause significant potassium and magnesium loss. Ultrafiltration extracts more sodium while sparing potassium and magnesium. The sustained clinical benefits of ultrafiltration compared with diuretics may be partly related to their disparate effects on total body sodium, potassium, and magnesium, in addition to their differential efficacy of volume removal.
Phosphodiesterase 3 inhibitors suppress oocyte maturation and consequent pregnancy without affecting ovulation and cyclicity in rodents. (1998)

During each reproductive cycle, a preovulatory surge of gonadotropins induces meiotic maturation of the oocyte in the preovulatory follicle followed by ovulation. Although gonadotropins stimulate cAMP production in somatic cells of the follicle, a decrease in intra-oocyte cAMP levels is required for resumption of meiosis in oocytes. Based on the observed compartmentalization of the cAMP-degrading enzyme, phosphodiesterase, in follicular somatic and germ cells, inhibitors of phosphodiesterase 3 were used to block meiosis in ovulating oocytes in rodents. By this strategy, we demonstrated that fertilization and pregnancy could be prevented without disturbing follicle rupture and normal estrous cyclicity. In contrast to conventional contraceptive pills that disrupt ovarian steroidogenesis and reproductive cycles, the present strategy achieves effective contraception by selective blockage of oocyte maturation and development without alterations in ovulation and reproductive cyclicity.
Type III machines of pathogenic yersiniae secrete virulence factors into the extracellular milieu (1999)

In the discussion of this paper, which was published in Molecular Microbiology31: 1619–1629, we stated the following ‘Hence, one likely explanation for the discrepancy between our results and the previous work is that these studies used yopB mutations with a polar effect on yopD, which is required for type III targeting.’ This statement referred to the following publications: Rosqvist et al. (1994) EMBO J13: 964–972; Sory and Cornelis (1994) Mol Microbiol14: 583–594; Boland et al. (1996) EMBO J15: 5191–5201; Hakansson et al. (1996) EMBO J15: 5812–5823; Hakansson et al. (1996) Mol Microbiol20: 593–603; Frithz-Lindsten et al. (1998) Mol Microbiol29: 1155–1166. Dr. Hans Wolf-Watz has now kindly pointed out to us that this statement is incorrect as the yopB mutant strain described by Hakansson et al. (1996) (EMBO J15: 5812–5823) was complemented in trans by a plasmid encoding lcrGVHyopB. As this plasmid complemented the yopB mutant strain and did not contain the yopD gene, the reason for the observed discrepancy (the type III targeting of effector Yops in yopB mutant strains) can not be due to a polar effect of the yopB mutation on yopD.
Estimating Android applications' CPU energy usage via bytecode profiling (2012)

Optimizing the energy efficiency of mobile applications can greatly increase user satisfaction. However, developers lack easily applied tools for estimating the energy consumption of their applications. This paper proposes a new approach, eCalc, that is lightweight in terms of its developer requirements and provides code-level estimates of energy consumption. The approach achieves this using estimation techniques based on program analysis of the mobile application. In evaluation, eCalc is able to estimate energy consumption within 9.5% of the ground truth for a set of mobile applications. Additionally, eCalc provides useful and meaningful feedback to the developer that helps to characterize energy consumption of the application.
NICE-SLAM: Neural Implicit Scalable Encoding for SLAM (2021)

Neural implicit representations have recently shown encouraging results in various domains, including promising progress in simultaneous localization and mapping (SLAM). Nevertheless, existing methods produce over-smoothed scene reconstructions and have difficulty scaling up to large scenes. These limitations are mainly due to their simple fully-connected network architecture that does not incorporate local information in the observations. In this paper, we present NICE-SLAM, a dense SLAM system that incorporates multi-level local information by introducing a hierarchical scene representation. Optimizing this representation with pre-trained geometric priors enables detailed reconstruction on large indoor scenes. Compared to recent neural implicit SLAM systems, our approach is more scalable, efficient, and robust. Experiments on five challenging datasets demonstrate competitive results of NICE-SLAM in both mapping and tracking quality. Project page: https://pengsongyou.github.io/nice-slam
InGaN/GaN Laser Diodes and their Applications (2018)

Gallium nitride (GaN) laser diodes are becoming popular sources not only for lighting but for applications ranging from communications to quantum. This paper presents the use of a commercial, off-the-shelf laser diode, with an emission wavelength of 450 nm, for visible light communication, both in free space and for underwater scenarios. Data rates up to 15 Gbit/s have been achieved by making use of orthogonal frequency division multiplexing (OFDM). In addition, distributed feedback (DFB) lasers have been realised emitting at a single wavelength which lend themselves towards applications where high spectral purity is crucial such as atomic clocks or filtered free space transmission systems. These devices have the grating structure etched into the sidewall of the ridge and work is ongoing to measure the linewidth of these lasers with the intended application of cooling Sr+ ions.
Development of an Evidence-Based Antimicrobial Stewardship Smartphone App in a Tertiary Academic Pediatric and Women’s Health Centre in Canada (2017)

Smart phone use by medical professionals is ubiquitous. In a recent survey, > 90% of health care providers were interested in locally developed antimicrobial stewardship (AMS) and infectious diseases applications (“apps”). We describe the process by which our antimicrobial stewardship program (ASP) developed an app to provide guidance regarding empiric antimicrobial choice, and education about antimicrobials and pathogens, integrating local laboratory data. We also describe early app uptake. The IWK Health Centre is a 271-bed tertiary care Pediatric and Women’s health centre serving the Maritime Provinces in eastern Canada. Using the Spectrum Mobile Health platform, our ASP developed an app in consultation with pediatric and women’s health clinical divisions. Through collaboration with the microbiology laboratory, the app was integrated with our laboratory information system (LIS) allowing real-time access to local antibiogram results. The iPhone- and Android- compatible app was introduced to health care providers through presentations, hospital intranet, email, and word of mouth. Following the official launch, uptake was monitored both in number of app downloads and number of hits. Adherence to empiric treatment guidelines included in the app will be assessed utilizing our existing ASP prospective audit and feedback service. From December 2015 to March 2017, the ASP created content for the IWK AMS App. Three sections were developed. (1) Syndromes: evidence-based empiric treatment guidelines for common syndromes. (2) Antimicrobials: spectrum of activity, dosing regimens, drug monitoring, common usage, adverse effects, drug interactions and pharmacology. (3) Pathogens: information on precautions, local susceptibilities through linkage with our recently developed virtual antibiogram, associated syndromes, and epidemiology. In May 2017, the app was launched. Within the first 24 hours, it was downloaded 157 times and accessed 1,193 times. We describe the process and early uptake of a locally developed AMS app to complement our ASP, which includes a virtual antibiogram through interfacing with our LIS. This is the first AMS app available in a Pediatric and Women’s Health Care Centre in Canada. Further analysis of the app’s impact on antimicrobial usage is planned. K. A. Top, Pfizer: Investigator, Research support. GSK: Investigator, Research grant. J. M. Langley, GSK: Investigator, Research grant. Canadian Institutes of Health Research: Investigator, Research grant.S. A. Halperin, GSK: Scientific Advisor, Consulting fee. GSK: Grant Investigator, Research grant
R3PAuCN Complexes: [{Ph2(cyclohexyl)P}AuCN] and [{(m-Tolyl)3P}AuCN] (1998)

Linear complexes of cyanogold with cyclohexyldiphenylphosphine {cyano(cycohexyldiphenylphosphine)gold(I), [Au(CN)(C18H21P)]} and tri(m-tolyl)phosphine {cyano[tri(m-tolyl)phosphine]gold(I), [Au(CN)(C21H21P)]} were synthesized and their crystal structures were compared with those of similar complexes. Irrespective of the differences in the anions (CN− versus Cl−), or in the steric and electronic requirements of the various phosphines, the Au—C and Au—P distances are similar in all the compared AuCN complexes. The CN− ligand in each of the two complexes reported here is tilted with respect to the P—Au—C axis, with the Au—C—N angle deviating by about 7.0 (1)° from linearity.
On event-driven knowledge graph completion in digital factories (2017)

Smart factories are equipped with machines that can sense their manufacturing environments, interact with each other, and control production processes. Smooth operation of such factories requires that the machines and engineering personnel that conduct their monitoring and diagnostics share a detailed common industrial knowledge about the factory, e.g., in the form of knowledge graphs. Creation and maintenance of such knowledge is expensive and requires automation. In this work we show how machine learning that is specifically tailored towards industrial applications can help in knowledge graph completion. In particular, we show how knowledge completion can benefit from event logs that are common in smart factories. We evaluate this on the knowledge graph from a real world-inspired smart factory with encouraging results.
ZnCl<sub>2</sub>-Promoted Intramolecular Hetero-Diels–Alder Reaction of <i>o</i>-Alkynylphenylcarbodiimides for Synthesis of Dihydrodibenzo[<i>b</i>,<i>g</i>][1,8]naphthyridines (2016)

The ZnCl2-promoted intramolecular hetero-Diels-Alder reaction of N-(ortho-propargylphenyl)-N'-arylcarbodiimides, in which the aryl-N=C moiety functioned as a 2-azabuta-1,3-diene, 4π component, has been achieved. By this method, very rare 5,12-dihydrodibenzo[b,g][1,8]naphthyridines and fully aromatized dibenzo[b,g][1,8]naphthyridines were successfully synthesized.
Familial expression of anti- Saccharomyces cerevisiae mannan antibodies in affected and unaffected relatives of patients with Crohn's disease (2000)

BACKGROUND Crohn's disease is a familial disorder, and antiglycan antibodies to the cell wall mannan of Saccharomyces cerevisiae (ASCA) are highly correlated with Crohn's disease. AIMS To determine whether there is a familial pattern for expression of serum levels of anti-mannan Ig, and whether this trait is expressed in clinically unaffected Crohn's disease family members. METHODS 349 patients with Crohn's disease, 87 Crohn's disease affected relatives, 333 inflammatory bowel disease (IBD) free relatives, 58 spouses, and 190 healthy control patients were studied. Serum IgG and IgA binding activity to S cerevisiae cell wall mannan was quantitated by ELISA. RESULTS A high percentage of patients with Crohn's disease (51.9%) and affected family members (56.3%) were seropositive for anti-mannan Ig, compared with the normal control population (3.7%). Seropositive and seronegative phenotypes of Crohn's disease probands were correlated among all affected relatives, and this association was stronger in affected first degree relatives. Statistical intraclass correlations of quantitative anti-mannan Ig levels revealed significantly less variation within, rather than between families. A significant familial aggregation was observed for affected relatives; this was even stronger for unaffected relatives. While a significant familial aggregation was observed among unaffected siblings pairs, there was no significant correlation among marital pairs. CONCLUSION Results show that anti-mannan Ig in family members affected and unaffected with Crohn's disease is a familial trait for both affected and unaffected relatives. The lack of concordance in marital pairs indicates that familiality is due in part to a genetic factor or childhood environmental exposure.
Evaluation of a synthetic tripeptide as antigen for detection of IgM and IgG antibodies to Trypanosoma cruzi in serum samples from patients with Chagas disease or viral diseases (1999)

An enzyme-linked immunosorbent assay (ELISA) has been developed to detect IgG and IgM antibodies in human sera against a synthetic tripeptide derived from a hybrid peptide containing 3 specific epitopes from Trypanosoma cruzi. This assay was compared in Brazil with one using conventional antigen, the alkaline crude extract. Serum samples were divided into positive (40 samples) or negative (107 samples) for Chagas disease. Positive samples included 9 serum samples from patients with acute Chagas disease, while negative samples included 57 samples from patients suffering from viral diseases. The total percentages of IgG positive samples from patients with chronic Chagas disease for alkaline extract and synthetic tripeptide were 93.5% and 100%, respectively. All samples from patients with acute Chagas disease were confirmed positive for IgM antibodies by using both the tripeptide and the alkaline extract. However, the results for anti-T. cruzi IgM in the group of chronic Chagas disease patients demonstrated that 41.9% were positive for IgM with the alkaline extract, while the synthetic peptide showed a significantly lower number of positive samples (12.9%). The serum samples from healthy people showed similar results for both antigens. However, 40% of the serum samples from patients presenting with viral diseases were IgM positive for Chagas disease when assayed with conventional antigen; with the synthetic tripeptide as antigen, 100% of this group of samples were found to be negative. Thus, as the results of ELISA with synthetic tripeptide showed higher rates of sensitivity and specificity than ELISA with conventional antigen, the former should be included as a laboratory tool in the serodiagnosis of Chagas disease.
Friction free bilateral robot based on twin drive control system considering two resonant frequencies (2005)

This paper proposes a new friction free bilateral system based on twin drive control system considering it's resonant frequency. The twin drive system consists of two motors that are coupled by the differential gear. The output torque becomes a differential torque of both motors. The nonlinear friction torque of the twin drive system is easily compensated. However, this system has the resonant frequencies and the anti-resonant frequencies which are caused by the torsional vibration. This paper proposes a new three-inertial-model of twin drive system, and identifies the resonant frequencies and it's friction torque. This paper proposes a new vibration suppression controller for the three-inertial model without high order control system. Therefore, the operationality of bilateral teleoperation is improved by the proposed system.
Aerobic training increases skin perfusion by a nitric oxide mechanism in type 2 diabetes (2010)

Abstract: It is well known that a number of locally released vasodilatory and ­vasoconstrictive ­compounds can affect skin perfusion. This study investigated the effects of aerobic training on the contribution of nitric oxide (NO), prostaglandins (PG), and endothelial-derived ­hyperpolarizing factor (EDHF) in stimulated dorsal foot skin perfusion in individuals with type 2 diabetes (T2DM). Ten previously sedentary, older individuals with T2DM (57.0 ± 3.1 years) and nine sedentary controls (53.5 ± 3.2 years) were tested before and after undertaking six months of moderate a­erobic training three times weekly in a supervised setting. All subjects underwent measurement of ­baseline (32°C) and heat-stimulated (40°C and 44°C) dorsal foot skin perfusion starting one hour after ­ingestion of a single, oral 325 mg dose of aspirin, a known inhibitor of PG synthesis. Before aspirin ­ingestion, a subcutaneous microdialysis probe was inserted into each foot dorsum to administer either saline (PG pathway only blocked by aspirin in the left foot) or L-NAME (N(G)-nitro-l-arginine methyl ester; thereby inhibiting both PG and NO pathways in the right foot). Normative data collected previously on subjects undergoing saline administration via ­microdialysis without aspirin ingestion served as a control group. Significantly lower responsiveness of maximal perfusion was found with the EDHF pathway alone unblocked compared with NO and EDHF unblocked after training. Maximal suppression attributable directly to NO, PG, and EDHF was not significantly different when examined by subject group and training status. However, ­contributions of NO, PG, and EDHF to maximal perfusion were significantly increased, decreased, and unchanged by aerobic training, respectively, with diabetic and control subjects combined due to nonsignificant differences between groups. Improvements in maximally stimulated dorsal foot skin perfusion resulting from six months of aerobic training appear to have primarily an NO basis, with lesser contributions from PG following training, regardless of diabetes status. Keywords: skin perfusion, aerobic training, type 2 diabetes, nitric oxide, prostaglandins, endothelial-derived hyperpolarizing factor, microdialysis
Ulcer Recurrence After Gastric Surgery: Is Helicobacter pylori the Culprit? (1998)

H. pylori infection cannot account for ulcer recurrence after peptic ulcer surgery.
Pattern of relapse after breast conserving therapy, a study of 1519 early breast cancer patients treated in the Central Region of Denmark 2000–2009 (2016)

Acceptable recurrence rates and DFS were observed. Patients with large tumors, lymph node involvement, and vascular invasion had an increased risk of DM.