gebhart/patrepeval huggingface dataset:
Optimizing metaproteomics database construction: lessons from a study of the vaginal microbiome (2023)

Metaproteomics, a method for untargeted, high-throughput identification of proteins in complex samples, provides functional information about microbial communities and can tie functions to specific taxa. Metaproteomics often generates less data than other omics techniques, but analytical workflows can be improved to increase usable data in metaproteomic outputs. Identification of peptides in the metaproteomic analysis is performed by comparing mass spectra of sample peptides to a reference database of protein sequences. Although these protein databases are an integral part of the metaproteomic analysis, few studies have explored how database composition impacts peptide identification. Here, we used cervicovaginal lavage (CVL) samples from a study of bacterial vaginosis (BV) to compare the performance of databases built using six different strategies. We evaluated broad versus sample-matched databases, as well as databases populated with proteins translated from metagenomic sequencing of the same samples versus sequences from public repositories. Smaller sample-matched databases performed significantly better, driven by the statistical constraints on large databases. Additionally, large databases attributed up to 34% of significant bacterial hits to taxa absent from the sample, as determined orthogonally by 16S rRNA gene sequencing. We also tested a set of hybrid databases which included bacterial proteins from NCBI RefSeq and translated bacterial genes from the samples. These hybrid databases had the best overall performance, identifying 1,068 unique human and 1,418 unique bacterial proteins, ~30% more than a database populated with proteins from typical vaginal bacteria and fungi. Our findings can help guide the optimal identification of proteins while maintaining statistical power for reaching biological conclusions. IMPORTANCE Metaproteomic analysis can provide valuable insights into the functions of microbial and cellular communities by identifying a broad, untargeted set of proteins. The databases used in the analysis of metaproteomic data influence results by defining what proteins can be identified. Moreover, the size of the database impacts the number of identifications after accounting for false discovery rates (FDRs). Few studies have tested the performance of different strategies for building a protein database to identify proteins from metaproteomic data and those that have largely focused on highly diverse microbial communities. We tested a range of databases on CVL samples and found that a hybrid sample-matched approach, using publicly available proteins from organisms present in the samples, as well as proteins translated from metagenomic sequencing of the samples, had the best performance. However, our results also suggest that public sequence databases will continue to improve as more bacterial genomes are published.
Induction of quinone reductase by tamoxifen or DPN protects against mammary tumorigenesis (2012)

We have previously shown that estrogen receptor β (ERβ)-mediated up-regulation of quinone reductase (QR) is involved in the protection against estrogen-induced mammary tumorigenesis. Our present study provides evidence that the ERβ agonist, 2,3-bis-(4-hydroxy-phenyl)-propionitrile (DPN), and the selective estrogen receptor modulator tamoxifen (Tam), inhibit estrogen-induced DNA damage and mammary tumorigenesis in the aromatase transgenic (Arom) mouse model. We also show that either DPN or Tam treatment increases QR levels and results in a decrease in ductal hyperplasia, proliferation, oxidative DNA damage (ODD), and an increase in apoptosis. To corroborate the role of QR, we provide additional evidence in triple transgenic MMTV/QR/Arom mice, wherein the QR expression is induced in the mammary glands via doxycycline, causing a decrease in ductal hyperplasia and ODD. Overall, we provide evidence that up-regulation of QR through induction by Tam or DPN can inhibit estrogen-induced ODD and mammary cell tumorigenesis, representing a novel mechanism of prevention against breast cancer. Thus, our data have important clinical implications in the management of breast cancer; our findings bring forth potentially new therapeutic strategies involving ERβ agonists.
Assessment of laser‐Induced release of drugs from liposomes: An in vitro study (1990)

We evaluated the characteristics of laser-induced release of an antimetabolite (cytosine arabinoside) from temperature-sensitive liposomes. Previous work had shown that a laser would induce breakdown of liposomes when a dye was encapsulated within the liposomes. The present investigation was performed to determine if release could be induced from liposomes that did not contain dye. In vitro, dynamic studies of the release of the drug from liposomes diluted in blood (flowing in a capillary tube at 40 microns/min) were conducted using an argon dye laser operating either in the blue-green mode (488/514 nm) or in the dye mode (577 nm). A radio-labeled marker was used to monitor the drug release. The results showed that the drug could indeed be released from liposomes that did not contain dye, at energy levels that are not likely to be harmful to the tissue. At identical power levels, the release of the drug was greater at 577 nm than at 488/514 nm, probably owing to the greater light absorbance of hemoglobin at the longer wavelength. The results indicate the potential for the site-specific release of a variety of molecules in the ocular vasculature.
Figure S2 from Theranostic Targeting of CUB Domain–Containing Protein 1 (CDCP1) in Multiple Subtypes of Bladder Cancer (2023)

&lt;p&gt;CDCP1 mRNA expression by clinical stage in the Seiler dataset. p=0.12 by Kruskal-Wallis test.&lt;/p&gt;
Widely tunable 10GHz synchronized fiber laser in the 1550nm-1750nm wavelength range via dispersion flattened DDF (2009)

In this work we experimentally demonstrate the possibility to build up the L-band tunable GHz repetition rate fiber laser via a dispersion flattened dispersion decreasing fiber. High quality fully synchronized with clock source 0.9 ps pulses are generated.
Mixed‐Model QSAR at the Glucocorticoid Receptor: Predicting the Binding Mode and Affinity of Psychotropic Drugs (2008)

Abstract The glucocorticoid receptor (GR) is a member of the nuclear receptor superfamily that affects immune response, development, and metabolism in target tissues. Glucocorticoids are widely used to treat diverse pathophysiological conditions, but their clinical applicability is limited by side effects. A prediction of the binding affinity toward the GR would be beneficial for identifying glucocorticoid‐mediated adverse effects triggered by drugs or chemicals. By identifying the binding mode to the GR using flexible docking (software Yeti) and quantifying the binding affinity through multidimensional QSAR (software Quasar), we validated a model family based on 110 compounds, representing four different chemical classes. The correlation with the experimental data (cross‐validated r 2 =0.702; predictive r 2 =0.719) suggests that our approach is suited for predicting the binding affinity of related compounds toward the GR. After challenging the model by a series of scramble tests, a consensus approach (software Raptor), and a prediction set, it was incorporated into our VirtualToxLab and used to simulate and quantify the interaction of 24 psychotropic drugs with the GR.
Exponential diffusion profile for impurity trapping at an unsaturable trap (1990)

It is shown that the exponential depth profiles observed in some cases in the diffusion of hydrogen into semiconductors, e.g., silicon and gallium arsenide, may be explained by including a term in the diffusion equation that describes the multiple trapping of hydrogen at an impurity. It is shown that the effective dimensionality of the random walk in the present case is infinite.
Abstract 15433: Very Late Recurrence After Successful Ablation of Premature Ventricular Contractions in Patients Without Structural Heart Disease (2022)

Background: Earlier studies have shown the superiority of catheter ablation over pharmacological therapy in eliminating premature ventricular contractions (PVC) in patients without structural heart disease. We investigated very late recurrences after successful PVC ablation in this cohort. Methods: Consecutive patients undergoing clinically indicated radiofrequency ablation for symptomatic idiopathic PVCs, documented by standard ECG, were included in the analysis and prospectively followed up. Those with history of structural heart disease were excluded. For all patients, 12-lead ECGs were reviewed to assess PVC morphology. During the index procedure, all PVC morphologies were targeted for ablation. Standardized RF power settings (40-50 W) were used during the procedure. Ablation was performed using 4-mm irrigated tip catheter guided by 3-D mapping system and intra-cardiac echocardiography. Patients were followed up with remote monitoring as well as ICD interrogations and office visits every 6 months for 4 years. Long-term success was defined as absence of previously targeted PVCs or any new PVC morphology on 12-lead ECG or device interrogation during all follow-up visits. Results: In total, 638 patients were included (mean age 59.2±5.6 years, 69.75% male, LVEF 54±12%). At the index ablation, PVCs were detected to be localized in the right ventricular outflow tract in 268 (42%), left ventricular outflow tract in 299 (46.8%) and multiple sites of origin in 71 (11.2%) patients. Non-inducibility was achieved in all patients at the end of the index procedure. At 4 years, 585 (91.7%) patients remained arrhythmia-free. Remaining 53 patients (8.1%) experiencing recurrence underwent repeat procedure. Median time to recurrence was 29±6.2 months. At the redo, new PVC morphologies were detected and ablated in 46/53 (86.8%) patients. One year after the repeat ablation, 50/53 (94.3%) were arrhythmia-free. Conclusion: In this prospective single-center series, very late recurrence following index PVC ablation in patients with no structural heart disease was mostly associated with new PVC morphologies that were amenable to be successfully ablated at the repeat procedure.
Seismic Reservoir Characterisation Using Vp-Vs Ratio in Tight Gas Sandstones (2006)

Behavior of Vp/Vs depends on a variety of reservoir conditions such as lithology, pressure or fluids. However, common practice in Vp/Vs interpretation focuses on the effect of only one parameter at the time. Although it is common, for instance, to associate presence of sands to lower values of Vp/Vs, other parameters such as pressure or fluids may produce changes in Vp/Vs that diminish the lithology effect we are looking for. &lt;br&gt;&lt;br&gt;In this paper we quantify the effect of different reservoir parameters on Vp/Vs to help the interpretation of Vp/Vs maps derived from seismic data. We find that in tight gas sandstones reservoirs, low Vp/Vs anomalies can be useful in prospect identification since they are related to good quality rocks (sandstones with low clay content), presence of gas, and overpressure conditions. These three conditions act in the same directions and all produce a decrease in Vp/Vs. In tight gas sandstones, gas saturation lowers Vp/Vs and the effect is larger if the reservoir is overpressured. Water saturation, however, increases Vp/Vs and this effect is enhanced with decreasing differential pressure. Tight gas sandstones typically have a Vp/Vs lower than that in shales.&lt;br&gt;
Predicting Functional Outcome and Response to Therapy of Anti-NMDAR Encephalitis, Already at Diagnosis: The NEOS2 Model. (P5-5.009) (2023)

Develop and validate a model to predict functional outcome and response to first-line therapy at the time of diagnosis of anti-NMDAR encephalitis (anti-NMDARE).
Impact of monitoring plasma 1,1-dichlorodiphenildichloroethane (o,p?DDD) levels on the treatment of patients with adrenocortical carcinoma (2001)

The results confirm the prognostic impact of the plasma o,p'DDD level in patients with metastatic ACC and its interest in avoiding toxicity.
Supplementary Table 1, Figures 1-8 from ArgBP2-Dependent Signaling Regulates Pancreatic Cell Migration, Adhesion, and Tumorigenicity (2023)

Supplementary Table 1, Figures 1-8 from ArgBP2-Dependent Signaling Regulates Pancreatic Cell Migration, Adhesion, and Tumorigenicity
A feasibility study of enhanced prompt gamma imaging for range verification in proton therapy using deep learning (2023)

<i>Background and objective</i>. Range uncertainty is a major concern affecting the delivery precision in proton therapy. The Compton camera (CC)-based prompt-gamma (PG) imaging is a promising technique to provide 3D<i>in vivo</i>range verification. However, the conventional back-projected PG images suffer from severe distortions due to the limited view of the CC, significantly limiting its clinical utility. Deep learning has demonstrated effectiveness in enhancing medical images from limited-view measurements. But different from other medical images with abundant anatomical structures, the PGs emitted along the path of a proton pencil beam take up an extremely low portion of the 3D image space, presenting both the attention and the imbalance challenge for deep learning. To solve these issues, we proposed a two-tier deep learning-based method with a novel weighted axis-projection loss to generate precise 3D PG images to achieve accurate proton range verification.<i>Materials and methods</i>: the proposed method consists of two models: first, a localization model is trained to define a region-of-interest (ROI) in the distorted back-projected PG image that contains the proton pencil beam; second, an enhancement model is trained to restore the true PG emissions with additional attention on the ROI. In this study, we simulated 54 proton pencil beams (energy range: 75-125 MeV, dose level: 1 × 10<sup>9</sup>protons/beam and 3 × 10<sup>8</sup>protons/beam) delivered at clinical dose rates (20 kMU min<sup>-1</sup>and 180 kMU min<sup>-1</sup>) in a tissue-equivalent phantom using Monte-Carlo (MC). PG detection with a CC was simulated using the MC-Plus-Detector-Effects model. Images were reconstructed using the kernel-weighted-back-projection algorithm, and were then enhanced by the proposed method.<i>Results</i>. The method effectively restored the 3D shape of the PG images with the proton pencil beam range clearly visible in all testing cases. Range errors were within 2 pixels (4 mm) in all directions in most cases at a higher dose level. The proposed method is fully automatic, and the enhancement takes only ∼0.26 s.<i>Significance</i>. Overall, this preliminary study demonstrated the feasibility of the proposed method to generate accurate 3D PG images using a deep learning framework, providing a powerful tool for high-precision<i>in vivo</i>range verification of proton therapy.
Bilateral Ethmoidal Dural Arteriovenous Fistulae: A Previously Unreported Entity: Case Report (2005)

OBJECTIVE AND IMPORTANCE: Ethmoidal dural arteriovenous fistulas (AVFs) are rare intracranial lesions associated with a high risk of intracranial hemorrhage. Reported hemorrhage rates have ranged from 62 to 91%, and an aggressive clinical course is more likely than a benign clinical course. We describe the first case of a patient with bilateral ethmoidal dural AVFs. CLINICAL PRESENTATION: A 50-year-old man presented with posterior fossa subarachnoid hemorrhage and cerebellar intraparenchymal hemorrhage. Angiography revealed a tentorial AVF and a complex anterior ethmoidal dural AVF. INTERVENTION: The tentorial AVF was treated with preoperative embolization and surgical obliteration. On follow-up angiography, the ethmoidal dural AVF was not considered amenable to embolization. A right modified orbitozygomatic approach was performed and the right-sided fistula was interrupted. Intraoperative angiography revealed obliteration of the right-sided fistula, but a persistent fistula on the left. Further surgical exploration revealed this contralateral anterior ethmoidal dural AVF, which was clip ligated. No residual fistula was noted on intraoperative angiography. CONCLUSION: Anterior ethmoidal dural AVFs may occur bilaterally. Given their complex angiographic appearance, their presence bilaterally may not be readily apparent on preoperative angiography. Intraoperative angiography is crucial to identify a contralateral fistula and to verify that ligation has been curative.
A fully integrated multiband frequency synthesizer for WLAN and WiMAX applications (2010)

This paper presents a fractional N frequency synthesizer which covers WLAN and WiMAX frequencies on a single chip. The synthesizer is fully integrated in 0.35μm BiCMOS AMS technology except crystal oscillator. The synthesizer operates at four frequency bands (3.101-3.352GHz, 3.379-3.727GHz, 3.7-4.2GHz, 4.5-5.321GHz) to provide the specifications of 802.16 and 802.11 a/b/g/y. A single on-chip LC - Gm based VCO is implemented as the core of this synthesizer. Different frequency bands are selected via capacitance switching and fine tuning is done using varactor for each of these bands. A bandgap reference circuit is implemented inside of this charge pump block to generate temperature and power supply independent reference currents. Simulated settling time is around 10μsec. Total power consumption is measured to be 118.6mW without pad driving output buffers from a 3.3V supply. The phase noise of the oscillator is lower than -116.4dbc/Hz for all bands. The circuit occupies 2.784 mm2 on Si substrate, including DC, Digital and RF pads.
Efficient approximation algorithms for floorplan area minimization (1996)

Approximation has been shown to be an effective method for reducing the time and space costs of solving various floorplan area minimization problems. In this paper, we present several approximation techniques for solving floorplan area minimization problems. These new techniques enable us to reduce both the time and space complexities of the previously best known approximation algorithms by more than a factor of n and n/sup 2/ for rectangular and L-shaped sub-floorplans, respectively (where n is the number of given implementations). The efficiency in the time and space complexities is critical to the applicability of such approximation techniques in floorplan area minimization algorithms. We also give a technique for enhancing the quality of approximation results.
Immunohistochemical application of monoclonal antibodies against myelin basic protein and neurofilament triple protein subunits: advantages over antisera and technical limitations. (1983)

Four monoclonal antibodies against guinea pig myelin basic protein (MBP), and four against subunits of bovine neurofilament triplet proteins (NF) were produced and their activity determined by enzyme-linked immunosorbant assay. The specificity and cross-reactivity of these eight monoclonal antibodies and one heterologous antiserum against each of the two central nervous system (CNS) antigens were examined in a histological study using the immunoperoxidase, antibody sandwich technique in rat and human brain tissue. Tissue sections were prepared from paraffin-embedded or fresh brain tissue that had been fixed with one of five different fixatives. The resulting immunoperoxidase labeling was then graded for intensity and examined for artifacts. One monoclonal antibody against MBP and one against NF resulted in labeling that was superior to that given by each of the antisera against their respective antigens. Of the five fixatives tested, a mercuric chloride-formalin solution gave the best preservation of these two antigens in rat and human brain tissue. The mercuric chloride-formalin solution was found to be superior to the other fixatives when immersion fixation was used, and was especially optimal when brains were perfused fixed. Three artifacts were encountered among the various antibody-fixative combinations that produced erroneous, but seemingly specific staining of Purkinje cells, neurons and axons, or astrocytes.
ChemInform Abstract: SYNTHESIS OF 10‐, 11‐, 19‐ AND 20‐MONO‐13C‐RETINAL (1983)

Abstract Die Titelverbindungen (Va), (Vb), (X) und (XIV) werden ausgehend von β‐Jonon (Munter Verwendung der markierten Verbindungen (II), (III) oder (VIII), wie im Formelsehema aufgeführt, synthetisiert.
WormBase: new content and better access (2006)

WormBase (http://wormbase.org), a model organism database for Caenorhabditis elegans and other related nematodes, continues to evolve and expand. Over the past year WormBase has added new data on C.elegans, including data on classical genetics, cell biology and functional genomics; expanded the annotation of closely related nematodes with a new genome browser for Caenorhabditis remanei; and deployed new hardware for stronger performance. Several existing datasets including phenotype descriptions and RNAi experiments have seen a large increase in new content. New datasets such as the C.remanei draft assembly and annotations, the Vancouver Fosmid library and TEC-RED 5' end sites are now available as well. Access to and searching WormBase has become more dependable and flexible via multiple mirror sites and indexing through Google.
Supplementary Methods, Table S1, Figures S1-7 from Development and Clinical Validation of an &lt;i&gt;In Situ&lt;/i&gt; Biopsy-Based Multimarker Assay for Risk Stratification in Prostate Cancer (2023)

&lt;p&gt;Supplementary Methods, Table S1, Figures S1-7. Methods for quantitative multiplex proteomics imaging (QMPI) Clinical studies: Statistical plan Table S1. Clinical Validation Study. Comparison of Predictive Value of the 8-Biomarker Assay for Favorable Pathology with D'Amico Risk Categories. Figure S1. Outline of all four quantitative multiplex immunofluorescence triplex assay formats Figure S2. Clinical validation study, full cohort (N=276): performance for "GS 6" pathology (surgical Gleason =3+3 and localized {less than or equal to}T3a). A) Sensitivity (P[risk score&gt; threshold| "non-GS 6" pathology]) of the assay, as a function of medical decision level. Figure S3. Clinical validation study, full cohort (N=274): performance for prediction of favorable pathology (surgical Gleason {less than or equal to}3+4 and organ-confined {less than or equal to}T2). Figure S4. Clinical validation study, Subset of validation cohort that contained sufficient annotation for National Comprehensive Cancer Network (NCCN) and D'Amico categorization (N=256) Figure S5. Clinical validation study: performance for prediction of favorable pathology. Figure S6. Net Reclassification Index analysis illustrates how biomarker assay categories of favorable (risk score {less than or equal to}0·33) and non-favorable (risk score &gt;0·8) may supplement NCCN Figure S7. Decision Curve Analysis provides another method for characterizing performance of different risk systems and at different cut points.&lt;/p&gt;
MONTAGE: a new tool for high-throughput detection of mosaic copy number variation (2021)

Our novel algorithm presents an efficient tool with fast computational runtime and high levels of accuracy of mosaic CNV detection. A curated mosaic CNV callset of 3716 events in 2269 samples is presented with comparability to previous reports and disease phenotype associations. The new algorithm can be freely accessed via: https://github.com/CAG-CNV/MONTAGE .