An unsupervised machine learning method for assessing quality of tandem mass spectra

<p>Abstract</p> <p>Background</p> <p>In a single proteomic project, tandem mass spectrometers can produce hundreds of millions of tandem mass spectra. However, majority of tandem mass spectra are of poor quality, it wastes time to search them for peptides. Therefore, the quality assessment (before database search) is very useful in the pipeline of protein identification via tandem mass spectra, especially on the reduction of searching time and the decrease of false identifications. Most existing methods for quality assessment are supervised machine learning methods based on a number of features which describe the quality of tandem mass spectra. These methods need the training datasets with knowing the quality of all spectra, which are usually unavailable for the new datasets.</p> <p>Results</p> <p>This study proposes an unsupervised machine learning method for quality assessment of tandem mass spectra without any training dataset. This proposed method estimates the conditional probabilities of spectra being high quality from the quality assessments based on individual features. The probabilities are estimated through a constraint optimization problem. An efficient algorithm is developed to solve the constraint optimization problem and is proved to be convergent. Experimental results on two datasets illustrate that if we search only tandem spectra with the high quality determined by the proposed method, we can save about 56 % and 62% of database searching time while losing only a small amount of high-quality spectra.</p> <p>Conclusions</p> <p>Results indicate that the proposed method has a good performance for the quality assessment of tandem mass spectra and the way we estimate the conditional probabilities is effective.</p

Is exponential gravity a viable description for the whole cosmological history?

Here we analysed a particular type of $F(R)$ gravity, the so-called exponential gravity which includes an exponential function of the Ricci scalar in the action. Such term represents a correction to the usual Hilbert-Einstein action. By using Supernovae Ia, Barionic Acoustic Oscillations, Cosmic Microwave Background and $H(z)$ data, the free parameters of the model are well constrained. The results show that such corrections to General Relativity become important at cosmological scales and at late-times, providing an alternative to the dark energy problem. In addition, the fits do not determine any significant difference statistically with respect to the $\Lambda$CDM model. Finally, such model is extended to include the inflationary epoch in the same gravitational Lagrangian. As shown in the paper, the additional terms can reproduce the inflationary epoch and satisfy the constraints from Planck data.Comment: 20 pages, 6 figures, analysis extended, version published in EPJ

Decoupled Iterative Refinement Framework for Interacting Hands Reconstruction from a Single RGB Image

Reconstructing interacting hands from a single RGB image is a very challenging task. On the one hand, severe mutual occlusion and similar local appearance between two hands confuse the extraction of visual features, resulting in the misalignment of estimated hand meshes and the image. On the other hand, there are complex spatial relationship between interacting hands, which significantly increases the solution space of hand poses and increases the difficulty of network learning. In this paper, we propose a decoupled iterative refinement framework to achieve pixel-alignment hand reconstruction while efficiently modeling the spatial relationship between hands. Specifically, we define two feature spaces with different characteristics, namely 2D visual feature space and 3D joint feature space. First, we obtain joint-wise features from the visual feature map and utilize a graph convolution network and a transformer to perform intra- and inter-hand information interaction in the 3D joint feature space, respectively. Then, we project the joint features with global information back into the 2D visual feature space in an obfuscation-free manner and utilize the 2D convolution for pixel-wise enhancement. By performing multiple alternate enhancements in the two feature spaces, our method can achieve an accurate and robust reconstruction of interacting hands. Our method outperforms all existing two-hand reconstruction methods by a large margin on the InterHand2.6M dataset.Comment: Accepted to ICCV 2023 (Oral

Continual Exposure to Cigarette Smoke Extracts Induces Tumor-Like Transformation of Human Nontumor Bronchial Epithelial Cells in a Microfluidic Chip

IntroductionHeavy cigarette smoking-related chronic obstructive pulmonary disease is an independent risk factor for lung squamous carcinoma. However, the mechanisms underlying the malignant transformation of bronchial epithelial cells are unclear.MethodsIn our study, human tumor-adjacent bronchial epithelial cells were obtained from 10 cases with smoking-related chronic obstructive pulmonary disease and lung squamous carcinoma and cultured in an established microfluidic chip for continual exposure to cigarette smoke extracts (CSE) to investigate the potential tumor-like transformation and mechanisms. The integrated microfluidic chip included upstream concentration gradient generator and downstream cell culture chambers supplied by flowing medium containing different concentrations of CSE.ResultsOur results showed that continual exposure to low doses of CSE promoted cell proliferation whereas to high doses of CSE triggered cell apoptosis. Continual exposure to CSE promoted reactive oxygen species production in human epithelial cells in a dose-dependent manner. More importantly, continual exposure to low dose of CSE promoted the epithelial-to-mesenchymal transition process and anchorage-independent growth, and increased chromosome instability in bronchial epithelial cells, accompanied by activating the GRP78, NF-κB, and PI3K pathways.ConclusionsThe established microfluidic chip is suitable for primary culture of human tumor-adjacent bronchial epithelial cells to investigate the malignant transformation. Continual exposure to low doses of CSE promoted tumor-like transformation of human nontumor bronchial epithelial cells by inducing reactive oxygen species production and activating the relevant signaling

Characterization of Human Coronavirus Etiology in Chinese Adults with Acute Upper Respiratory Tract Infection by Real-Time RT-PCR Assays

BACKGROUND: In addition to SARS associated coronaviruses, 4 non-SARS related human coronaviruses (HCoVs) are recognized as common respiratory pathogens. The etiology and clinical impact of HCoVs in Chinese adults with acute upper respiratory tract infection (URTI) needs to be characterized systematically by molecular detection with excellent sensitivity. METHODOLOGY/PRINCIPAL FINDINGS: In this study, we detected 4 non-SARS related HCoV species by real-time RT-PCR in 981 nasopharyngeal swabs collected from March 2009 to February 2011. All specimens were also tested for the presence of other common respiratory viruses and newly identified viruses, human metapneumovirus (hMPV) and human bocavirus (HBoV). 157 of the 981 (16.0%) nasopharyngeal swabs were positive for HCoVs. The species detected were 229E (96 cases, 9.8%), OC43 (42 cases, 4.3%), HKU1 (16 cases, 1.6%) and NL63 (11 cases, 1.1%). HCoV-229E was circulated in 21 of the 24 months of surveillance. The detection rates for both OC43 and NL63 were showed significantly year-to-year variation between 2009/10 and 2010/11, respectively (P<0.001 and P = 0.003), and there was a higher detection frequency of HKU1 in patients aged over 60 years (P = 0.03). 48 of 157(30.57%) HCoV positive patients were co-infected. Undifferentiated human rhinoviruses and influenza (Flu) A were the most common viruses detected (more than 35%) in HCoV co-infections. Respiratory syncytial virus (RSV), human parainfluenza virus (PIV) and HBoV were detected in very low rate (less than 1%) among adult patients with URTI. CONCLUSIONS/SIGNIFICANCE: All 4 non-SARS-associated HCoVs were more frequently detected by real-time RT-PCR assay in adults with URTI in Beijing and HCoV-229E led to the most prevalent infection. Our study also suggested that all non-SARS-associated HCoVs contribute significantly to URTI in adult patients in China

High‐Efficiency Graphene‐Oxide/Silicon Solar Cells with an Organic‐Passivated Interface

A breakthrough in graphene-oxide/silicon heterojunction solar cells is presented in which edge-oxidized graphene and an in-plane charge transfer dopant (Nafion) are combined to form a high-quality passivating contact scheme. A graphene oxide (GO):Nafion ink is developed and an advanced back-junction GO:Nafion/n-Si solar cell with a high-power conversion efficiency (18.8%) and large area (5.5 cm2) is reported. This scalable solution-based processing technique has the potential to enable low-cost carbon/silicon heterojunction photovoltaic devices

Analiza genskih varijacija rekombinantnog soja dobivenog iz triju linija virusa-2 reproduktivnog i respiratornog sindroma svinja

Since the rise of the porcine reproductive and respiratory syndrome virus (PRRSV) in China, gene mutations have frequently occurred. To understand the current prevalence and evolution of PRRSV in Shandong Province, 1,528 samples suspected of PRRSV were collected from local pig farms of different sizes. The complete genome sequence of the PRRSV strain SDLY-27 was determined by next-generation sequencing (NGS) technology. The genomic sequence of SDLY-27 was 15,363 nucleotides (nt) in length, comparative analysis of the whole genome sequence suggested that the homology between SDLY 27 and 81 PRRSV strains from China and other countries in genbank was 61.9 ~ 96.4%. This study is the first to detect recombinants from multiple recombination events among the Lineage 8 (JXA1-like strains), Lineage 5 (RespPRRSV-MLV and VR2332 strains) and Sublineage 1.5 (NADC34-like strains) in Shandong, China, and provides new data for the epidemiological study of PRRSV in China. This study enriches the epidemiological data on PRRSV in Shandong Province, China. It provides an important reference for the development of new vaccines and for the prevention and control of PRRSV in China.Usporedno sa širenjem virusa reproduktivnog i respiratornog sindroma svinja (PRRSV) u Kini, sve su češće bile i njegove genske mutacije. Kako bi se ustanovila trenutačna prevalencija i evolucija PRRSV-a u pokrajini Shandong, s lokalnih farmi prikupljeno je 1528 uzoraka svinja različitih kategorija za koje je postojala sumnja na zarazu PRRSVom. Kompletan genomski slijed soja SDLY-27 PRRSV-a određen je tehnologijom sekvenciranja sljedeće generacije (NGS). Slijed je imao dužinu od 15 363 nukleotida (nt), a komparativna analiza cijeloga genomskog slijeda uputila je na to da je homolognost između sojeva SDLY 27 i 81 PRRSV-a iz Kine i uzoraka u banci gena iz drugih zemalja 61,9~96,4%. Ovo je prvo istraživanje koje je otkrilo rekombinantne sojeve iz višestrukih rekombinacija među linijama 8 (sojevi nalik na JXA1), 5 (sojevi RespPRRSV-MLV i VR2332) i podlinije 1,5 (sojevi nalik na NADC34) u Shandongu, Kina.Kao takvo, istraživanje pruža nove podatke o epidemiologiji PRRSV-a u Kini, posebno u pokrajini Shandong, a ujedno predstavlja i važnu referenciju za razvoj novih cjepiva te prevenciju i kontrolu bolesti uzrokovane navedenim virusom

A Multi-Body Dynamics based numerical modelling tool for solving aquatic biomimetic problems

In this paper, a versatile Multi-Body Dynamic (MBD) algorithm is developed to integrate an incompressible fluid flow with a bio-inspired multibody dynamic system. Of particular interest to the biomimetic application, the algorithm is developed via four properly selected benchmark verifications. The present tool has shown its powerful capability for solving a variety of biomechanics fish swimming problems, including self-propelled multiple degrees of freedom with a rigid undulatory body, multiple deformable fins and an integrated system with both undulatory fish body and flexible fins. The established tool has paved the way for future investigation on more complex bio-inspired robots and live fish, for either propulsion or manoeuvring purposes