QCD resummation in hadron production

We present calculations of next-to-leading order and resummed QCD corrections for semi-inclusive deep-inelastic scattering and single-inclusive e+e− annihilation. The resummation is performed to next-to-leading logarithmic accuracy. Knowing these QCD corrections is important in order to extract parton distribution functions and fragmentation functions from present and future data for these reactions. We present phenomenological results relevant for the COMPASS, HERMES, and BELLE experiments

Prospects for a Statistical Theory of LC/TOFMS Data

The critical importance of employing sound statistical arguments when seeking to draw inferences from inexact measurements is well-established throughout the sciences. Yet fundamental statistical methods such as hypothesis testing can currently be applied to only a small subset of the data analytical problems encountered in LC/MS experiments. The means of inference that are more generally employed are based on a variety of heuristic techniques and a largely qualitative understanding of their behavior. In this article, we attempt to move towards a more formalized approach to the analysis of LC/TOFMS data by establishing some of the core concepts required for a detailed mathematical description of the data. Using arguments that are based on the fundamental workings of the instrument, we derive and validate a probability distribution that approximates that of the empirically obtained data and on the basis of which formal statistical tests can be constructed. Unlike many existing statistical models for MS data, the one presented here aims for rigor rather than generality. Consequently, the model is closely tailored to a particular type of TOF mass spectrometer although the general approach carries over to other instrument designs. Looking ahead, we argue that further improvements in our ability to characterize the data mathematically could enable us to address a wide range of data analytical problems in a statistically rigorous manner

The effects of social determinants of health on acquired immune deficiency syndrome in a low-income population of Brazil: a retrospective cohort study of 28.3 million individuals.

BACKGROUND: Social determinants of health (SDH) include factors such as income, education, and race, that could significantly affect the human immunodeficiency virus and acquired immunodeficiency syndrome (HIV/AIDS). Studies on the effects of SDH on HIV/AIDS are limited, and do not yet provide a systematic understanding of how the various SDH act on important indicators of HIV/AIDS progression. We aimed to evaluate the effects of SDH on AIDS morbidity and mortality. METHODS: A retrospective cohort of 28.3 million individuals was evaluated over a 9-year period (from 2007 to 2015). Multivariable Poisson regression, with a hierarchical approach, was used to estimate the effects of SDH-at the individual and familial level-on AIDS incidence, mortality, and case-fatality rates. FINDINGS: A total of 28,318,532 individuals, representing the low-income Brazilian population, were assessed, who had a mean age of 36.18 (SD: 16.96) years, 52.69% (14,920,049) were female, 57.52% (15,360,569) were pardos, 34.13% (9,113,222) were white/Asian, 7.77% (2,075,977) were black, and 0.58% (154,146) were indigenous. Specific socioeconomic, household, and geographic factors were significantly associated with AIDS-related outcomes. Less wealth was strongly associated with a higher AIDS incidence (rate ratios-RR: 1.55; 95% confidence interval-CI: 1.43-1.68) and mortality (RR: 1.99; 95% CI: 1.70-2.34). Lower educational attainment was also greatly associated with higher AIDS incidence (RR: 1.46; 95% CI: 1.26-1.68), mortality (RR: 2.76; 95% CI: 1.99-3.82) and case-fatality rates (RR: 2.30; 95% CI: 1.31-4.01). Being black was associated with a higher AIDS incidence (RR: 1.53; 95% CI: 1.45-1.61), mortality (RR: 1.69; 95% CI: 1.57-1.83) and case-fatality rates (RR: 1.16; 95% CI: 1.03-1.32). Overall, also considering the other SDH, individuals experiencing greater levels of socioeconomic deprivation were, by far, more likely to acquire AIDS, and to die from it. INTERPRETATION: In the population studied, SDH related to poverty and social vulnerability are strongly associated with a higher burden of HIV/AIDS, most notably less wealth, illiteracy, and being black. In the absence of relevant social protection policies, the current worldwide increase in poverty and inequalities-due to the consequences of the COVID-19 pandemic, and the effects of war in the Ukraine-could reverse progress made in the fight against HIV/AIDS in low- and middle-income countries (LMIC). FUNDING: National Institute of Allergy and Infectious Diseases (NAIDS), National Institutes of Health (NIH), US Grant Number: 1R01AI152938

Peak intensity prediction in MALDI-TOF mass spectrometry: A machine learning study to support quantitative proteomics

Timm W, Scherbart A, Boecker S, Kohlbacher O, Nattkemper TW. Peak intensity prediction in MALDI-TOF mass spectrometry: A machine learning study to support quantitative proteomics. BMC Bioinformatics. 2008;9(1):443.Background: Mass spectrometry is a key technique in proteomics and can be used to analyze complex samples quickly. One key problem with the mass spectrometric analysis of peptides and proteins, however, is the fact that absolute quantification is severely hampered by the unclear relationship between the observed peak intensity and the peptide concentration in the sample. While there are numerous approaches to circumvent this problem experimentally (e. g. labeling techniques), reliable prediction of the peak intensities from peptide sequences could provide a peptide-specific correction factor. Thus, it would be a valuable tool towards label-free absolute quantification. Results: In this work we present machine learning techniques for peak intensity prediction for MALDI mass spectra. Features encoding the peptides' physico-chemical properties as well as string-based features were extracted. A feature subset was obtained from multiple forward feature selections on the extracted features. Based on these features, two advanced machine learning methods (support vector regression and local linear maps) are shown to yield good results for this problem (Pearson correlation of 0.68 in a ten-fold cross validation). Conclusion: The techniques presented here are a useful first step going beyond the binary prediction of proteotypic peptides towards a more quantitative prediction of peak intensities. These predictions in turn will turn out to be beneficial for mass spectrometry-based quantitative proteomics

A multi-disciplinary commentary on preclinical research to investigate vascular contributions to dementia

Although dementia research has been dominated by Alzheimer's disease (AD), most dementia in older people is now recognised to be due to mixed pathologies, usually combining vascular and AD brain pathology. Vascular cognitive impairment (VCI), which encompasses vascular dementia (VaD) is the second most common type of dementia. Models of VCI have been delayed by limited understanding of the underlying aetiology and pathogenesis. This review by a multidisciplinary, diverse (in terms of sex, geography and career stage), cross-institute team provides a perspective on limitations to current VCI models and recommendations for improving translation and reproducibility. We discuss reproducibility, clinical features of VCI and corresponding assessments in models, human pathology, bioinformatics approaches, and data sharing. We offer recommendations for future research, particularly focusing on small vessel disease as a main underpinning disorder

A Multi-disciplinary Commentary on Preclinical Research to investigate Vascular Contributions to Dementia

Although dementia research has been dominated by Alzheimer's disease (AD), most dementia in older people is now recognised to be due to mixed pathologies, usually combining vascular and AD brain pathology. Vascular cognitive impairment (VCI), which encompasses vascular dementia (VaD) is the second most common type of dementia. Models of VCI have been delayed by limited understanding of the underlying aetiology and pathogenesis. This review by a multidisciplinary, diverse (in terms of sex, geography and career stage), cross-institute team provides a perspective on limitations to current VCI models and recommendations for improving translation and reproducibility. We discuss reproducibility, clinical features of VCI and corresponding assessments in models, human pathology, bioinformatics approaches, and data sharing. We offer recommendations for future research, particularly focusing on small vessel disease as a main underpinning disorder.</p

LC-MSsim – a simulation software for liquid chromatography mass spectrometry data

<p>Abstract</p> <p>Background</p> <p>Mass Spectrometry coupled to Liquid Chromatography (LC-MS) is commonly used to analyze the protein content of biological samples in large scale studies. The data resulting from an LC-MS experiment is huge, highly complex and noisy. Accordingly, it has sparked new developments in Bioinformatics, especially in the fields of algorithm development, statistics and software engineering. In a quantitative label-free mass spectrometry experiment, crucial steps are the detection of peptide features in the mass spectra and the alignment of samples by correcting for shifts in retention time. At the moment, it is difficult to compare the plethora of algorithms for these tasks. So far, curated benchmark data exists only for peptide identification algorithms but no data that represents a ground truth for the evaluation of feature detection, alignment and filtering algorithms.</p> <p>Results</p> <p>We present <it>LC-MSsim</it>, a simulation software for LC-ESI-MS experiments. It simulates ESI spectra on the MS level. It reads a list of proteins from a FASTA file and digests the protein mixture using a user-defined enzyme. The software creates an LC-MS data set using a predictor for the retention time of the peptides and a model for peak shapes and elution profiles of the mass spectral peaks. Our software also offers the possibility to add contaminants, to change the background noise level and includes a model for the detectability of peptides in mass spectra. After the simulation, <it>LC-MSsim </it>writes the simulated data to mzData, a public XML format. The software also stores the positions (monoisotopic m/z and retention time) and ion counts of the simulated ions in separate files.</p> <p>Conclusion</p> <p><it>LC-MSsim </it>generates simulated LC-MS data sets and incorporates models for peak shapes and contaminations. Algorithm developers can match the results of feature detection and alignment algorithms against the simulated ion lists and meaningful error rates can be computed. We anticipate that <it>LC-MSsim </it>will be useful to the wider community to perform benchmark studies and comparisons between computational tools.</p

Enhancement of Cell Membrane Invaginations, Vesiculation and Uptake of Macromolecules by Protonation of the Cell Surface

The different pathways of endocytosis share an initial step involving local inward curvature of the cell’s lipid bilayer. It has been shown that to generate membrane curvature, proteins or lipids enforce transversal asymmetry of the plasma membrane. Thus it emerges as a general phenomenon that transversal membrane asymmetry is the common required element for the formation of membrane curvature. The present study demonstrates that elevating proton concentration at the cell surface stimulates the formation of membrane invaginations and vesiculation accompanied by efficient uptake of macromolecules (Dextran-FITC, 70 kD), relative to the constitutive one. The insensitivity of proton induced uptake to inhibiting treatments and agents of the known endocytic pathways suggests the entry of macromolecules to proceeds via a yet undefined route. This is in line with the fact that neither ATP depletion, nor the lowering of temperature, abolishes the uptake process. In addition, fusion mechanism such as associated with low pH uptake of toxins and viral proteins can be disregarded by employing the polysaccharide dextran as the uptake molecule. The proton induced uptake increases linearly in the extracellular pH range of 6.5 to 4.5, and possesses a steep increase at the range of 4> pH>3, reaching a plateau at pH≤3. The kinetics of the uptake implies that the induced vesicles release their content to the cytosol and undergo rapid recycling to the plasma membrane. We suggest that protonation of the cell’s surface induces local charge asymmetries across the cell membrane bilayer, inducing inward curvature of the cell membrane and consequent vesiculation and uptake