Miracle-dz/UniFAR-FTUs huggingface dataset:
Peptide Sequencing with Deep Learning

In shotgun proteomics, de novo peptide sequencing from tandem mass spectrometry data is the key technology for finding new peptide or protein sequences. It has successful applications in assembling monoclonal antibody sequences and great potentials for identifying neoantigens for personalized cancer vaccines. In this thesis, I propose a novel deep neural network-based de novo peptide sequencing model: PointNovo. The proposed PointNovo model not only outperforms the previous state-of-the-art model by a significant margin but also solves the long-standing accuracy–speed/memory trade-off problem that exists in previous de novo peptide sequencing tools. Further, our experiment results show that even though PointNovo is not trained to distinguish between true and false peptide spectrum matching, its resulting log probability score can be used as a scoring function to perform database searching. On several different datasets, we show that PointNovo, when used as a database search engine, can achieve an identification rate that is at least comparable to existing popular database search softwares. We also extend and adapt an existing model to process Data Independent Acquisition (DIA) data and propose the first de novo peptide sequencing algorithm for DIA tandem mass spectra. Finally, we develop a workflow that can identify tumor-specific antigens directly and purely from mass spectrometry data of tumor tissues and test it on a published dataset of tumor samples from melanoma patients. Our workflow applies de novo peptide sequencing to detect mutated endogenous peptides, in contrast to the prevalent indirect approach of combining exome sequencing, somatic mutation calling, and epitope prediction in existing methods. More importantly, we develop machine learning models that are tailored to each patient based on their own MS data. Such a personalized approach enables accurate identification of neoantigens for the development of personalized cancer vaccines. We applied the workflow to datasets of five melanoma patients and expanded their immunopeptidomes by 5% to 15%. Subsequently, we discovered 17 neoantigens of both HLA–I and HLA–II, including those with validated T cell responses and those novel neoantigens that had not been reported in previous studies. Chapter 3 of this thesis is based on the author’s published paper “Deep learning enables de novo peptide sequencing from data-independent-acquisition mass spectrometry,” Nature methods 16.1 (2019): 63–66. Chapter 4 and Chapter 5 are based on the author’s preprint paper “DeepNovoV2” (conditionally accepted by Nature Machine Intelligence) https://arxiv.org/abs/1904.08514
The crystal structures of WTe2 and high‐temperature MoTe2

The structures of WTe2 and a high-temperature monoclinic polymorph of MoTe2 have been solved by Patterson methods. Single crystals were grown by vapor transport methods. Cell dimensions, as measured on precession photographs, are for WTe2, a=6.282/~, b= 3.496/~, c= 14"073 A. Similarly for MoTe2, a=6.33 A, b=3.469/~, c=13.86/~, B=93°55. Intensities were measured for both crystals from zeroand first-level Weissenberg photographs. WTe2 and MoTe2 are given the space groups Pnm21 and P21/m, respectively. Minimum function maps prepared by a superposition method gave approximate trial structures for both compounds which were refined by least-squares methods to R values of 12.5 % and 13-9 % for WTe2 and MoTe2 respectively. Both compounds are layer structures with double sheets of tellurium atoms bound together by interleaving metal atoms. An off-center positioning of metal atoms in the tellurium octahedra buckles the tellurium sheets and allows metal atoms in adjacent octahedra to approach each other. Each metal atom, therefore, has eight neighbors, six tellurium atoms and two metal atoms, and a significant amount of metal-metal bonding is introduced.
Most-Probable-Number-Based Minimum Duration of Killing Assay for Determining the Spectrum of Rifampicin Susceptibility in Clinical Mycobacterium tuberculosis Isolates

Accurate antibiotic susceptibility testing is essential for successful tuberculosis treatment. Recent studies have highlighted the limitations of MIC-based phenotypic susceptibility methods in detecting other aspects of antibiotic susceptibilities in bacteria. Duration and peak of antibiotic exposure, at or above the MIC required for killing the bacterial population, has emerged as another important factor for determining antibiotic susceptibility. This is broadly defined as antibiotic tolerance. ABSTRACT Accurate antibiotic susceptibility testing is essential for successful tuberculosis treatment. Recent studies have highlighted the limitations of MIC-based phenotypic susceptibility methods in detecting other aspects of antibiotic susceptibilities in bacteria. Duration and peak of antibiotic exposure, at or above the MIC required for killing the bacterial population, has emerged as another important factor for determining antibiotic susceptibility. This is broadly defined as antibiotic tolerance. Antibiotic tolerance can further facilitate the emergence of antibiotic resistance. Currently, there are limited methods to quantify antibiotic tolerance among clinical M. tuberculosis isolates. In this study, we develop a most-probable-number (MPN)-based minimum duration of killing (MDK) assay to quantify the spectrum of M. tuberculosis rifampicin susceptibility within subpopulations based on the duration of rifampicin exposure required for killing the bacterial population. MDK90–99 and MDK99.99 were defined as the minimum duration of antibiotic exposure at or above the MIC required for killing 90 to 99% and 99.99% of the initial (pretreatment) bacterial population, respectively. Results from the rifampicin MDK assay applied to 28 laboratory and clinical M. tuberculosis isolates showed that there is variation in rifampicin susceptibility among isolates. The rifampicin MDK99/99.99 time for isolates varied from less than 2 to 10 days. MDK was correlated with larger subpopulations of M. tuberculosis from clinical isolates that were rifampicin tolerant. Our study demonstrates the utility of MDK assays to measure the variation in antibiotic tolerance among clinical M. tuberculosis isolates and further expands clinically important aspects of antibiotic susceptibility testing.
Optimization of the Effect of Pineapple By-Products Enhanced in Bromelain by Hydrostatic Pressure on the Texture and Overall Quality of Silverside Beef Cut

Dehydrated pineapple by-products enriched in bromelain using a hydrostatic pressure treatment (225 MPa, 8.5 min) were added in marinades to improve beef properties. The steaks from the silverside cut (2 ± 0.5 cm thickness and weight 270 ± 50 g), characterized as harder and cheaper, were immersed in marinades that were added to dehydrated and pressurized pineapple by-products that corresponded to a bromelain concentration of 0–20 mg tyrosine, 100 g−1 meat, and 0–24 h time, according to the central composite factorial design matrix. Samples were characterized in terms of marination yield, pH, color, and histology. Subsequently, samples were cooked in a water-bath (80 °C, 15 min), stabilized (4 °C, 24 h), and measured for cooking loss, pH, color, hardness, and histology. Marinades (12–24 h) and bromelain concentration (10–20 mg tyrosine.100 g−1 meat) reduced pH and hardness, increased marination yield, and resulted in a lighter color. Although refrigeration was not an optimal temperature for bromelain activity, meat hardness decreased (41%). Thus, the use of pineapple by-products in brine allowed for the valorization of lower commercial value steak cuts.
What Model of Nutrition Can Be Recommended to People Ending Their Professional Sports Career? An Analysis of the Mediterranean Diet and the CRON Diet in the Context of Former Athletes

Athletes who retire from their sporting career face an increase in body weight, leading to overweight or obesity. Simultaneously, a significant number of these athletes meet the criteria of metabolic syndrome. The available literature does not offer clearly defined standards of nutrition for the discussed group of people. In this situation, it seems advisable to develop different standards of dietary behavior typical of athletes finishing their sports careers. For this purpose, the study analyzed two types of diets: the Mediterranean diet and the Calorie Restriction with Optimal Nutrition (CRON) diet based on significant calorie restrictions. Both diets seem to meet the requirements of this group of people.
A genome‐wide study of the relationship between chromosomal abnormalities and gene expression in colorectal tumors

The role of somatic copy number alterations (SCNAs) that occur in colorectal tumors is poorly understood. SCNAs are correlated with corresponding gene expression changes that may contribute to neoplastic progression. Thus, we examined SCNAs and the expression of messenger RNAs (mRNAs) located at corresponding loci in colorectal neoplasia, a progression model of human neoplasm. We used 42 colorectal neoplastic samples, including adenomas, intramucosal cancers (IMC) and invasive colorectal cancers (CRC) that were microsatellite stable (MSS) using a genome‐wide SNP array and gene expression array (first cohort). In addition, validation analyses were examined (37 colorectal neoplasias). None of the mRNAs with a corresponding SCNA was found in the adenomas. However, three mRNAs, including ARFGEF2 at 20q13.13, N4BP2L2 at 13q13.1 and OLFM4 at 13q14.3 with a copy number (CN) gain at the corresponding locus were upregulated in IMCs of the first cohort. Moreover, upregulated expression of ARFGEF2 and OLFM4 was upregulated in the validation analysis. Finally, 28 mRNAs with gains of corresponding loci were pooled in invasive CRC of the first cohort. The mRNAs, including ACSS2 (20q11.22), DDX27 (20q13.13), MAPRE1 (20q11.21), OSBPL2 (20q11.22) and PHF20 (20q11.22‐q11.23) with CN gains of the corresponding loci were identified in 28 mRNAs. Four of these mRNAs (DDX27, MAPRE1, OSBPL2 and PHF20) were upregulated in the invasive CRC in the validation analysis. We conclude that specific 13q and 22q CN gains with gene expression changes in the corresponding loci may play an important role in IMC cells' progression into invasive CRC.
Mechanochemical properties of human myosin-1C are modulated by isoform-specific differences in the N-terminal extension

Myosin-1C is a single-headed, short-tailed member of the myosin class I subfamily that supports a variety of actin-based functions in the cytosol and nucleus. In vertebrates, alternative splicing of the MYO1C gene leads to the production of three isoforms, myosin-1C0, myosin-1C16, and myosin-1C35, that carry N-terminal extensions of different lengths. However, it is not clear how these extensions affect the chemomechanical coupling of human myosin-1C isoforms. Here, we report on the motor activity of the different myosin-1C isoforms measuring the unloaded velocities of constructs lacking the C-terminal lipid-binding domain on nitrocellulose-coated glass surfaces and full-length constructs on reconstituted, supported lipid bilayers. The higher yields of purified proteins obtained with constructs lacking the lipid-binding domain allowed a detailed characterization of the individual kinetic steps of human myosin-1C isoforms in their productive interaction with nucleotides and filamentous actin. Isoform-specific differences include 18-fold changes in the maximum power output per myosin-1C motor and 4-fold changes in the velocity and the resistive force at which maximum power output occurs. Our results support a model in which the isoform-specific N-terminal extensions affect chemomechanical coupling by combined steric and allosteric effects, thereby reducing both the length of the working stroke and the rate of ADP release in the absence of external loads by a factor of 2 for myosin-1C35. As the large change in maximum power output shows, the functional differences between the isoforms are further amplified by the presence of external loads.
ncVarDB: a manually curated database for pathogenic non-coding variants and benign controls

Abstract Variants within the non-coding genome are frequently associated with phenotypes in genome-wide association studies. These non-coding regions may be involved in the regulation of gene expression, encode functional non-coding RNAs, or influence splicing and other cellular functions. We have curated a list of characterized non-coding human genome variants based on the published evidence that indicates phenotypic consequences of the variation. In order to minimize annotation errors, two curators have independently verified the supporting evidence for pathogenicity of each non-coding variant in the published literature. The database consists of 721 non-coding variants linked to the published literature describing the evidence of functional consequences. We have also sampled 7228 covariate-matched benign controls, that have a population frequency of over 5%, from the single nucleotide polymorphism database (dbSNP151) database. These were sampled controlling for potential confounding factors such as linkage with pathogenic variants, annotation type (untranslated region, intron, intergenic, etc.) and variant type (substitution or indel). The dataset presented here represents a curated repository, with a potential use for the training or evaluation of algorithms used in the prediction of non-coding variant functionality. Database URL: https://github.com/Gardner-BinfLab/ncVarDB.
Use of dual-flow bioreactor to develop a simplified model of nervous-cardiovascular systems crosstalk: A preliminary assessment

Chronic conditions requiring long-term rehabilitation therapies, such as hypertension, stroke, or cancer, involve complex interactions between various systems/organs of the body and mutual influences, thus implicating a multiorgan approach. The dual-flow IVTech LiveBox2 bioreactor is a recently developed inter-connected dynamic cell culture model able to mimic organ crosstalk, since cells belonging to different organs can be connected and grown under flow conditions in a more physiological environment. This study aims to setup for the first time a 2-way connected culture of human neuroblastoma cells, SH-SY5Y, and Human Coronary Artery Smooth Muscle Cells, HCASMC through a dual-flow IVTech LiveBox2 bioreactor, in order to represent a simplified model of nervous-cardiovascular systems crosstalk, possibly relevant for the above-mentioned diseases. The system was tested by treating the cells with 10nM angiotensin II (AngII) inducing PKCβII/HuR/VEGF pathway activation, since AngII and PKCβII/HuR/VEGF pathway are relevant in cardiovascular and neuroscience research. Three different conditions were applied: 1- HCASMC and SH-SY5Y separately seeded in petri dishes (static condition); 2- the two cell lines separately seeded under flow (dynamic condition); 3- the two lines, seeded in dynamic conditions, connected, each maintaining its own medium, with a membrane as interface for biohumoral changes between the two mediums, and then treated. We detected that only in condition 3 there was a synergic AngII-dependent VEGF production in SH-SY5Y cells coupled to an AngII-dependent PKCβII/HuR/VEGF pathway activation in HCASMC, consistent with the observed physiological response in vivo. HCASMC response to AngII seems therefore to be generated by/derived from the reciprocal cell crosstalk under the dynamic inter-connection ensured by the dual flow LiveBox 2 bioreactor. This system can represent a useful tool for studying the crosstalk between organs, helpful for instance in rehabilitation research or when investigating chronic diseases; further, it offers the advantageous opportunity of cultivating each cell line in its own medium, thus mimicking, at least in part, distinct tissue milieu.
Fourier transform infrared spectroscopy of milk samples as a tool to estimate energy balance, energy- and dry matter intake in lactating dairy cows

Abstract The objective of the study was to evaluate the potential of Fourier transform infrared spectroscopy (FTIR) analysis of milk samples to predict body energy status and related traits (energy balance (EB), dry matter intake (DMI) and efficient energy intake (EEI)) in lactating dairy cows. The data included 2371 milk samples from 63 Norwegian Red dairy cows collected during the first 105 days in milk (DIM). To predict the body energy status traits, calibration models were developed using Partial Least Squares Regression (PLSR). Calibration models were established using split-sample (leave-one cow-out) cross-validation approach and validated using an external test set. The PLSR method was implemented using just the FTIR spectra or using the FTIR together with milk yield (MY) or concentrate intake (CONCTR) as predictors of traits. Analyses were conducted for the entire first 105 DIM and separately for the two lactation periods: 5 ≤ DIM ≤ 55 and 55 < DIM ≤ 105. To test the models, an external validation using an independent test set was performed. Predictions depending on the parity (1st, 2nd and 3rd-to 6th parities) in early lactation were also investigated. Accuracy of prediction (r) for both cross-validation and external test set was defined as the correlation between the predicted and observed values for body energy status traits. Analyzing FTIR in combination with MY by PLSR, resulted in relatively high r-values to estimate EB (r = 0.63), DMI (r = 0.83), EEI (r = 0.84) using an external validation. Only moderate correlations between FTIR spectra and traits like EB, EEI and dry matter intake (DMI) have so far been published. Our hypothesis was that improvements in the FTIR predictions of EB, EEI and DMI can be obtained by (1) stratification into different stages of lactations and different parities, or (2) by adding additional information on milking and feeding traits. Stratification of the lactation stages improved predictions compared with the analyses including all data 5 ≤ DIM ≤105. The accuracy was improved if additional data (MY or CONCTR) were included in the prediction model. Furthermore, stratification into parity groups, improved the predictions of body energy status. Our results show that FTIR spectral data combined with MY or CONCTR can be used to obtain improved estimation of body energy status compared to only using the FTIR spectra in Norwegian Red dairy cattle. The best prediction results were achieved using FTIR spectra together with MY for early lactation. The results obtained in the study suggest that the modeling approach used in this paper can be considered as a viable method for predicting an individual cow's energy status.
Long-Term Clinical Outcome of Cardiogenic Shock Patients Undergoing Impella CP Treatment vs. Standard of Care

The number of patients treated with the mechanical circulatory support device Impella Cardiac Power (CP) for cardiogenic shock is steadily increasing. The aim of this study was to investigate long-term survival and complications related to this modality. Patients undergoing Impella CP treatment for cardiogenic shock were retrospectively enrolled and matched with cardiogenic shock patients not treated with mechanical circulatory support between 2010 and 2020. Data were collected from the cardiogenic shock registry of the university hospital of Munich (DRKS00015860). 70 patients with refractory cardiogenic shock without mechanical circulatory support were matched with 70 patients treated with Impella CP. At presentation, the mean age was 67 ± 15 years with 80% being male in the group without support and 67 ± 14 years (p = 0.97) with 76% being male (p = 0.68) in the group with Impella. There was no significant difference in the rate of cardiac arrest (47% vs. 51%, p = 0.73) and myocardial infarction was the predominant cause of cardiogenic shock in both groups (70% vs. 77%). A total of 41% of patients without cardiocirculatory support and 54% of patients with Impella support died during the first month (p = 0.17). After one year, mortality rates were similar in both groups (55% in conventional vs. 59% in Impella CP group, p = 0.30) as was mortality rate at long-term 5-years follow-up (64% in conventional vs. 73% in Impella CP group, p = 0.33). The rate of clinically significant bleedings during ICU stay was lower in the conventional group than in the Impella support group (15% vs. 43%, p = 0.002). In this small observational and non-randomized analysis no difference in long-term outcome between patients treated with Impella CP vs. guideline directed cardiogenic shock therapy without mechanical circulatory support could be detected. Care must be taken regarding the high rate of bleeding and vascular complications when using Impella CP. Large, adequately powered studies are urgently needed to investigate the efficacy and safety of Impella CP in cardiogenic shock.
Stem Cell-Derived Exosomes and Nanovesicles: Promotion of Cell Proliferation, Migration, and Anti-Senescence for Treatment of Wound Damage and Skin Ageing

Extracellular vesicles (EVs), such as exosomes, are nano-sized vesicles derived from endocytic membranes and contain biomolecules such as proteins, lipids, RNAs, and DNAs for the transfer of signals to recipient cells, playing significant roles in cell-to-cell communication. Discovery of exosomes has attracted attention for possible use as next generation therapies in clinical applications; however, several studies suggest that cells secrete exosomes that perform as mediators in the tumor niche and play several roles in tumorigenesis, angiogenesis, and metastasis. Recently, stem cell-derived exosomes have been suggested as a desirable source for regenerative medicine due to their roles in the promotion of angiogenesis via migratory and proliferative mechanisms. This review is aimed at demonstrating the present knowledge of stem cell-derived exosomes and cell-engineered nanovesicles (CNVs) as proliferative, migratory, and anti-senescent therapeutic biomaterial for use in tissue regeneration; wound healing and anti-ageing are explained. We conclude this review by discussing the future perspectives of stem cell-derived exosomes and CNVs as a platform in therapeutic strategies for treatment of wound damage and skin aging.