gebhart/patrepeval huggingface dataset:
SILVER helps assign peptides to tandem mass spectra using intensity-based scoring (2004)

Tandem mass spectrometry is commonly used to identify peptides (and thereby proteins) that are present in complex mixtures. Peptide identification from tandem mass spectra is partially automated, but still requires human curation to resolve "borderline" peptide-spectrum matches (PSMs). SILVER is web-based software that assists manual curation of tandem mass spectra, using a recently developed intensity-based machine-learning approach to scoring PSMs, Elias et al. In this method, a large training set of peptide, fragment, and peak-intensity properties for both matched and mismatched PSMs was used to develop a score measuring consistency between each predicted fragment ion of a candidate peptide and its corresponding observed spectral peak intensity. The SILVER interface provides a visual representation of match quality between each candidate fragment ion and the observed spectrum, thereby expediting manual curation of tandem mass spectra. SILVER is available online at http://llama.med.harvard.edu/Software.html.
Mycotoxin contamination of sorghum and its contribution to human dietary exposure in four sub-Saharan countries (2018)

This research aimed at evaluating the safety, and the type, level and prevalence of mycotoxins in grain sorghum of four sub-Saharan African (SSA) countries (Burkina Faso, Ethiopia, Mali and Sudan). A multi-analyte LC-MS/MS method for quantification of 23 mycotoxins (nivalenol, deoxynivalenol, fusarenon X, neosolaniol, 3-acetyl deoxynivalenol, 15-acetyl deoxynivalenol, diacetoxyscirpenol, roquefortine C, HT-2 toxin, alternariol, T-2 toxin, FB1, FB2, FB3, zearalenone, aflatoxin G<sub>1</sub>, aflatoxin G<sub>2</sub>, aflatoxin B<sub>1</sub>, aflatoxin B<sub>2</sub>, sterigmatocystin, OTA, altenuene, alternariol monomethylether) was applied to different sorghum matrices. Of the 1533 analysed samples, 33% were contaminated with at least one of the following mycotoxins: aflatoxins, fumonisins, sterigmatocystin, Alternaria toxins, OTA and zearalenone. Country of origin, colour, source and collection period of sorghum samples significantly influenced the type, level and prevalence of mycotoxins. Sterigmatocystin (15%), fumonisins (17%) and aflatoxins (13%) were the most prevalent. FB1 (274 ± 585 µg/kg) had the highest mean concentration followed by FB2 (214 ± 308 µg/kg) while diacetoxyscirpenol (8.12 ± 19.2 µg/kg) and HT-2 (11.9 ± 0.00 µg/kg) had the lowest concentrations. Neosolaniol, fusarenon-X, 3-acetyl deoxynivalenol, 15-acetyl deoxynivalenol, T-2 toxin, nivalenol and roquefortine C were not detected in any of the samples. Sudan had the lowest prevalence and mean concentration of all mycotoxins. Pink sorghum had the highest concentrations of fumonisins and aflatoxins. Mycotoxins from Aspergillus spp. and Alternaria spp. are the mycotoxins of concern in SSA grain sorghum with regard to prevalence, concentration and possible health risk from exposure. Based on the performed risk characterisation, daily consumption of sorghum containing aflatoxins, alternariol, alternariol monomethyl ether, sterigmatocystin and OTA could result in exceeding the established health-based guidance values for these toxins.
The effect of growth phase and medium on the use of the firefly adenosine triphosphate (ATP) assay for the quantitation of bacteria (1975)

Luciferase assay for adenosine triphosphate (ATP) was used as a rapid method to determine the number of bacteria in a urine sample after nonbacterial components were removed. Accurate cellular ATP values, determined when bacteria were grown in an environment similar to that in which they were found, were necessary for the calculation of bacterial titer in urine. Cellular ATP values vary depending on the extraction method, the cell growth phase, and cell growth conditions. ATP per cell values of stationary E. coli grown in urine were two times greater than ATP per cell values of cells grown in trypticase soy broth. Glucose and urea were examined as possible components responsible for the cellular ATP variation.
Phase I and Pharmacokinetic Study of MS-275, a Histone Deacetylase Inhibitor, in Patients With Advanced and Refractory Solid Tumors or Lymphoma (2005)

The MS-275 oral formulation on the daily schedule was intolerable at a dose and schedule explored. The q14-day schedule is reasonably well tolerated. Histone deacetylase inhibition was observed in peripheral-blood mononuclear-cells. Based on PK data from the q14-day schedule, a more frequent dosing schedule, weekly x 4, repeated every 6 weeks is presently being evaluated.
A peptide library expressed in yeast reveals new major epitopes from human immunodeficiency virus type 1 (1991)

In order to characterize novel human immunodeficiency virus type 1 (HIV-1) continuous epitopes, we designed a simple method, based on recombinant DNA, providing a complete set of peptides derived from HIV-1. A library (4 × 104 clones) was first constructed in a new expression/secretion vector, using as inserts small fragments of HIV-1 DNA (50–150 bp) generated by random DNAse I cleavage. This peptide library, expressed in the yeast Saccharomyces cerevisiae, was screened with sera of HIV-1 infected individuals and human and murine anti-HIV-1 monoclonal antibodies. Plasmids from immunoreactive colonies were recovered and the sequences of the HIV-1 derived inserts were determined. By using human sera, we have detected classical HIV-1 epitopes and identified two novel major epitopes, which may be used to improve diagnostic tests, localized in the p24 core protein and in the endonuclease. In addition, four minor epitopes were also defined by screening the library with monoclonal antibodies: in the protease, in the p17 core protein, in gp120 and near the C-terminal of gp41. This method is general and can be used for any protein from which a cloned cDNA is available.
ChemInform Abstract: The Most Stable and Fully Characterized Functionalized Heptacene. (2009)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Realizing the potential of marine biotechnology: CHALLENGES & OPPORTUNITIES (2009)

A paid open access option is available for this journal. Author's final version or publisher's version/PDF Authors may deposit in funding agency designated repository after 12 months
Supplementary Table 2 from Mapping of Chromosome 1p Deletions in Myeloma Identifies <i>FAM46C</i> at 1p12 and <i>CDKN2C</i> at 1p32.3 as Being Genes in Regions Associated with Adverse Survival (2023)

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Bilinexin, a Snake C-type Lectin from Agkistrodon bilineatus Venom Agglutinates Platelets via GPIb and α2β1 (2001)

Summary A new snake protein, named bilinexin, has been purified from Agkistrodon bilineatus venom by ion-exchange chromatography and gel filtration chromatography. Under non-reducing conditions it has a mass of 110 kDa protein on SDS-PAGE. On reduction, it can be separated into five subunits with masses in the range 13-25 kDa. The N-terminal sequences of these subunits are very similar to those of convulxin or the alboaggregins, identifying bilinexin as a new member of the snake C-type lectin family, unusual in having multiple subunits. Bilinexin agglutinates fixed platelets, washed platelets and platelet rich plasma (PRP) without obvious activation (shape change) as confirmed by light microscope examination. Both inhibitory and binding studies indicate that antibodies against α2β1 inhibit not only platelet agglutination induced by bilinexin, but also bilinexin binding to platelets. VM16d, a monoclonal anti-GPIbα antibody, completely inhibits platelet agglutination induced by bilinexin, and polyclonal antibodies against GPIbα prevent its binding to platelets. However, neither convulxin, polyclonal anti-GPVI antibodies, nor GPIIb/IIIa inhibitors affect its binding to and agglutination of platelets. Bilinexin neither activates GPIIb/IIIa integrin on platelets nor induces tyrosine phosphorylation of platelet proteins, nor increases intracellular Ca2+ in platelets. Like alboaggregin B, bilinexin agglutinates platelets, which makes it a good tool to investigate the differences in mechanism between snake C-type lectins causing platelet agglutination and those that induce full activation.
Contrast enhancement in X-ray phase contrast tomography (2014)

We demonstrate phase contrast enhancement of X-ray computed tomography derived from propagation based imaging. In this method, the absorption and phase components are assumed to be correlated, allowing for phase retrieval from a single image. Experimental results are shown for liquid samples. Signal-to-noise ratio is greatly enhanced relative to pure attenuation based imaging.
Two New Mixed-Valence Iron Phosphates Templated by Piperazine:  (C4H12N2)[Fe4(OH)2(HPO4)5] and (C4H11N2)0.5[Fe3(HPO4)2(PO4)(H2O)] (1998)

Two piperazine-templated iron phosphates, (C4H12N2)[Fe4(OH)2(HPO4)5] (1) and (C4H11N2)0.5[Fe3(HPO4)2(PO4)(H2O)] (2), have been synthesized under solvothermal conditions and characterized by single-crystal X-ray diffraction, Mössbauer spectroscopy, and thermogravimetric analysis. Compound 1 crystallizes in the monoclinic space group C2/m (no. 12) with a = 25.706(3), b = 6.4492(6), c = 6.3790(6) Å, β = 102.601(2)°, V = 1032.0(3) Å3 and Z = 2. The 3-D framework structure consists of layers of iron phosphate which are pillared through HPO4 groups to generate intersecting 8-ring channels with piperazinium dications at the intersections of these channels. Each layer contains infinite chains of edge-sharing FeIIO6 octahedra which are connected to each other via corner-sharing FeIIIO6 octahedra and HPO4 groups. Compound 2 crystallizes in the monoclinic space group C2/c (no. 15) with a = 30.8924(4), b = 6.3733(1), c = 12.5552(2) Å, β = 101.946(1)°, V = 2418.41(7) Å3, and Z = 8. The compound has a layered structure with piperazinium monocations in the interlayer space. Each layer consists of a dimer of edge-sharing octahedra with the composition FeIIFeIIIO10 which shares edges with four FeIIO5 trigonal bipyramids to form a hexamer as the building unit. Each such hexamer is connected to others by corner sharing and through phosphate groups. Both compounds are mixed-valence as indicated from bond valence calculations, Mössbauer measurements, and electric field gradient calculations.
IC‐P‐008: Alterations of brain glucose metabolism in aged APP/PS1 mice: An original voxel‐based statistical analysis using BrainRAT and SPM (2009)

Glucose brain metabolism is a widely used clinical biomarker in Alzheimer's disease (AD), usually examined on 2D post mortem autoradiographic data in AD animal models. We propose an innovative method to analyze these data in 3D without a priori anatomical information, to derive brain metabolic activity maps using voxel-based approach in APP/PS1 mice. Results will be discussed relative to previous findings in this field. Uptake of [14C]-2-deoxyglucose was measured in adult awake APP/PS1 (64 ± 1 weeks, n = 4) and PS1 (65 ± 2 weeks, n = 3) transgenic mice. Glucose uptake was evaluated by autoradiography on the right hemisphere while the left hemisphere was processed for Congo red staining. Data acquisition was performed with a digital camera (blockface photographs) and a high resolution flatbed scanner (autoradiography, histology). Blockface, autoradiographic and histological post mortem volumes were 3D-reconstructed using BrainRAT in-house software (freely available, http://brainvisa.info) while statistical analysis was achieved using SPM5. We successfully combined BrainRAT (computerized procedures for acquisition and 3D reconstruction of anatomic and functional volumes) and SPM5 (voxel-wise statistical analysis) methodologies to data sets mapping brain metabolic activity in a transgenic mouse model of AD. We were able to extract accurate parametric mapping of both hypo- and hypermetabolic regions in the APP/PS1 animals relative to PS1 controls. Decreased glucose uptake was observed within cortex (cingulate -36%, retrosplenial -26%, somatosensory -23%), striatum (-22%), thalamus (-29%) and hippocampus (-25%). Increased glucose uptake was also detected within other cortical areas (piriform +22%, perirhinal +19%), amygdala (+23%), dorsal endopiriform (+34%) and accumbens (+20%) nuclei, dentate gyrus (+25%) and dorsal hippocampus (+26%). We have demonstrated the ability to robustly and automatically reconstruct post mortem functional volumes. We also provided accurate cerebral glucose uptake mapping in a murine AD model, in 3D, without a priori hypotheses. We offer an efficient and standardized method to compare local changes in mice cerebral glucose utilization across ages, lines or drugs. Furthermore, our work demonstrates the possibility of using functional brain imaging and dedicated software to help bridge the gap, in translational studies, between features of neurodegenerative diseases in human beings and animal models.Acknowledgements: Sanofi-Aventis for sharing the mouse strains.
Matrix approach to the kinetics of open systems (1968)

A matrix treatment of the kinetic behaviour of monomolecular open systems is developed. The coupled differential rate equations are transformed to the normal form. The resulting uncoupled differential equations are thereby rendered in a form convenient for computation and the study of system dynamics. The treatment offers an essentially time-free method for the experimental study of open system kinetics and presents powerful tools for the study of the morphology of open systems.
Subspace based meg source detection (2004)

The effect of mapping data into a subspace prior to performing detection of dipolar sources in white noise is assessed in this paper. The subspace transformations are designed to accurately represent sources in a specified region of interest. The transformation attenuates sources outside the region, reducing the sensitivity of the detector to external interference. A statistical analysis of detector performance and illustrative examples are provided.
Digital holographic measurements of shape and three-dimensional sound-induced displacements of tympanic membrane (2013)

Acoustically-induced vibrations of the Tympanic Membrane (TM) play a primary role in the hearing process, in that these motions are the initial mechanical response of the ear to airborne sound. Characterization of the shape and 3D displacement patterns of the TM is a crucial step to a better understanding of the complicated mechanics of sound reception by the ear. In this paper, shape and sound-induced 3D displacements of the TM in cadaveric chinchillas are measured by a lensless Dual-Wavelength Digital Holography system (DWDHS). The DWDHS consists of Laser Delivery (LD), Optical Head (OH), and Computing Platform (CP) subsystems. Shape measurements are performed in double-exposure mode and with the use of two wavelengths of a tunable laser while nanometer-scale displacements are measured along a single sensitivity direction and with a constant wavelength. In order to extract the three principal components of displacement in full-field-of-view, and taking into consideration the anatomical dimensions of the TM, we combine principles of thin-shell theory together with both, displacement measurements along the single sensitivity vector and TM surface shape. To computationally test this approach, Finite Element Methods (FEM) are applied to the study of artificial geometries.
Abstract P180: Genetic screen identifies PDPK1 as a synergistic target to enhancing the efficacy of MEK1/2 inhibitors in NRAS mutant melanoma (2021)

Abstract Melanomas frequently harbor activating NRAS mutations; however, there has been little advance in targeted therapy options for NRAS mutant melanoma patients. MEK inhibitors (MEKi) showed modest efficacy in clinic, which is insufficient to be approved by FDA. In this study, we performed a genome-wide CRISPR/Cas9-based screening, identified PDPK1 (Phosphoinositide-dependent kinase-1) as a therapeutic target to enhancing the efficacy of MEKi, and validated it in various NRAS mutant melanoma cell lines via pharmacological and genetic approaches. Combined inhibition of PDPK1 and MEK (PDPK1i+MEKi) profoundly inhibited NRAS mutant tumor growth in a xenograft model. Notably, the combinatorial treatment induced pyroptosis, and increased ratio of intratumoral CD8+ T cells, delayed tumor growth and prolonged survival in an immune competent allograft model whereas it showed a significantly weaker potency in an isogenic immune deficient model. These data suggest PDPK1i + MEKi is an efficient strategy against NRAS mutant melanoma in an immune-response-dependent manner. Significance: NRAS is still an 'undruggable' target in melanoma. Our discovery rationalizes the clinical development of PDPK1i plus MEKi in NRAS mutant melanoma patients and suggests further synergy of targeted therapy and immunotherapy. Citation Format: Weijia Cai, Mai Nguyen, nicole wilski, timothy purwin, Manoela TiagodosSantos, Andrew Aplin. Genetic screen identifies PDPK1 as a synergistic target to enhancing the efficacy of MEK1/2 inhibitors in NRAS mutant melanoma [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2021 Oct 7-10. Philadelphia (PA): AACR; Mol Cancer Ther 2021;20(12 Suppl):Abstract nr P180.
Gastroesophageal reflux and pulmonary aspiration: incidence, functional abnormality, and results of surgical therapy. (1979)

The incidence of aspiration, the causative esophageal pathophysiology, and the results of surgical therapy were evaluated in 100 patients with abnormal gastroesophageal reflux documented by 24-hour esophageal pH monitoring. Based on historical evidence, 48 patients were suspected to be aspirators. Eight patients had documented episodes of aspiration (drop on esophagela pH, followed by acid taste in mouth and onset of cough or wheezing spell) during the monitoring period. Nine patients were considered to be potential aspirators because they presented oral acid regurgitation without development of pulmonary symptoms. In five patients a primary respiratory disorder (PRD) induced gastroesophageal reflux. The remaining 78 patients had abnormal reflux without aspiartion or regurgitation. Aspirators had a 75% incidence of esophageal motor abnormality on manometry, and the clearance of refluxed acid was significantly delayed in the supine position. A history of heartburn and endoscopic evidence of esophagitis were present in only half of the patients who were documented aspirators. Potential aspirators were spared from aspiration by rapid esophageal clearance of refluxed acid unaffected by changes in body position. Patients with a PRD had higher distal esophageal segment (DES) pressure and normal esophageal motility with minimal esophagitis. Nonaspirators significantly improved their clearance while in the supine position, emphasizing the protective effect of esophageal peristalsis against aspiration. An antireflux procedure in five aspirators raised the DES pressure significantly and returned the reflux status to normal by 24-hour pH-monitoring standards. The incidence of aspiration appears to be less than that suspected by history and is due to a motor disorder that interferes with the ability of the esophagus to clear reflex acid. Abnormal pulmonary symptoms can induce or result from gastroesophageal reflux and, when the latter occurs, an antireflex procedure stops both reflux and aspiration.
Glass-Based Photonic Crystals: From Fabrication to Applications (2014)

We report on the fabrication and on the assessment of the properties of two glass-based photonic crystals (PhCs) obtained using alternative approaches such as rf-sputtering and sol-gel techniques. (i) By means of rf-sputtering a one-dimensional dielectric photonic crystal constituted by an Er 3+ -doped SiO 2 active layer inserted between two Bragg reflectors consisting of 10 pairs of SiO 2 ∕TiO 2 layers has been realized. Near infrared transmittance spectra evidenced the presence of a stop band from 1500 to 2000 nm with a cavity resonance centered at 1749 nm. Intensity enhancement and narrowing of the emission band of Er 3+ ions, due to the cavity effect have been observed and a cavity quality factor of 890 has been achieved. (ii) Through chemical route a 3D colloidal crystal based on polystyrene (PS) nanoparticles (NPs) embedded in elastomeric matrix has been realized. In the specific has been shown that the structure can produce a variation of its color applying different organic solvents that can be also easily observed by the naked eye. Optical measurements have evidenced a red shift of the diffraction peak as a function of the solvents applied. This feature has been exploited in order to create a sensitive material showing high sensitivity and reversibility of the signal change.
An examination of the relative contribution of saturation and selective attention to memory deficits in patients with recent-onset schizophrenia and their unaffected parents. (2010)

Cognitive dysfunctions in patients suffering from schizophrenia (SZ) are also found in their unaffected parents though to a lesser degree. According to several researchers, short-term memory (STM) deficits are a potential marker of vulnerability to SZ. However, the cognitive processes underlying the observed STM deficits remain underspecified in SZ (Lee & Park, 2005). In the present study, our goal was to pinpoint those processes at play in the manifestation of STM deficits by using the paradigm of the sandwich effect (e.g., Hitch, 1975) to manipulate information load (5 vs. 7 to-be-remembered items) and distraction (control vs. sandwich) in the verbal domain. Our study comprises four groups: patients with SZ (n = 25), their unaffected parents (n = 25), and their respective healthy controls. The pattern of results indicates a generalized dysfunction of STM in patients with SZ characterized by saturation and an increased susceptibility to distraction. The impact of saturation and distraction was also observed in unaffected parents of patients with SZ to a lesser degree. The methodological strategy adopted here allowed us to show that the dysfunction of STM is genuine, can be aggravated by deficits in selective attention, and is a good candidate for further research on genetic epidemiology.
Antibodies to kidney endothelial cells contribute to a “leaky” glomerular barrier in patients with chronic kidney diseases (2011)

Anti-endothelial cell antibodies (AECA) have been reported to cause endothelial dysfunction, but their clinical importance for tissue-specific endothelial cells is not clear. We hypothesized that AECA reactive with human kidney endothelial cells (HKEC) may cause renal endothelial dysfunction in patients with chronic kidney diseases. We report that a higher fraction (56%) of end-stage renal disease (ESRD) patients than healthy controls (5%) have AECA reactive against kidney endothelial cells (P <0.001). The presence of antibodies was associated with female gender (P < 0.001), systolic hypertension (P < 0.01), and elevated TNF-α (P < 0.05). These antibodies markedly decrease expression of both adherens and tight junction proteins VE-cadherin, claudin-1, and zonula occludens-1 and provoked a rapid increase in cytosolic free Ca(2+) and rearrangement of actin filaments in HKEC compared with controls. This was followed by an enhancement in protein flux and phosphorylation of VE-cadherin, events associated with augmented endothelial cell permeability. Additionally, kidney biopsies from ESRD patients with AECA but not controls demonstrated a marked decrease in adherens and tight junctions in glomerular endothelium, confirming our in vitro data. In summary, our data demonstrate a causal link between AECA and their capacity to induce alterations in glomerular vascular permeability.