Computational optimization of methane yield obtained in semicontiniuous anaerobic digestion

Z avtomatskim sistemom za merjenje metanskega potenciala (AMPTS II) smo izvedli faktorialni semikontinuirani test biometanskega potenciala anaerobne korazgradnje primarnega blata (PB), sirotke (S) in kravje gnojevke (KG) (68 dni, 38 °C). Uporabili smo štiri različne kombinacije substratov pri različnih organskih obremenitvah in hidravličnih zadrževalnih časih. Med testom smo izvajali meritve fizikalno-kemijskih parametrov (pH, električna prevodnost, kratkoverižne maščobne kisline (KMK), KPK, mikroelementi, alkaliteta, amonijski dušik, suha snov) in na koncu optimizirali proces z univariatnimi in multivariatimi statističnimi analizami. Po stabilni 50-dnevni metanski produkciji smo enkrat povečali količino dodane sirotke. Glede na vse analitske metode smo zaznali stabilno produkcijo bioplina iz sirotke pri vseh kombinacijah substratov. Metanski izplen je koreliral s količino dodane kisle sirotke. Sirotka je v takem sistemu glavni vir KMK, kravja gnojevka pa prispeva k stabilnosti procesa s povečanjem puferske kapacitete. V sistemu brez kravje gnojevke smo detektirali več KMK. Z nemetričnim večdimenzionalnim lestvičenjem (NM-MDS) smo pokazali, da so za uspešno vodenje procesa najbolj pomembni pH, KMK in alkaliteta. Potencialno se lahko pojavijo težave zaradi prenizkih koncentracij nekaterih mikroelementov v daljšem časovnem obdobju, ko zaradi izplavljanja dosežejo kritične koncentracije za normalno funkcioniranje metanogenih arhej. Najvišje metanske izplene smo dosegli v paralelkah z volumskim razmerjem substratov PB:S:KG 70:55:10. Po povečanju količine sirotke smo največjo stabilnost zaznali v sistemu z razmerjem 70:70:10.A semicontinuous test of the biomethane potential of primary sludge (PS), cheese whey (CW) and cow manure (CM) has been investigated with automatic methane potential system (AMPTS II) for 68 days (38 °C). Four different combinations of substrates were used at different organic loadings and hydraulic retention times. During the test, we performed measurements of physico-chemical parameters (pH, electrical conductivity, SFACs, COD, microelements, dry matter, alkalinity) and optimized the process with univariate and multivariate statistical analysis. After 50-days of stable methane production, we doubled cheese whey concentrations. According to all analytical methods, stable methane production was observed in all combinations of substrates. The methane yield was correlated with the amount of cheese whey addition. According to our observations, cheese whey was the main source of SCFAs in the system, while cow manure contributed to the stability of the process with increasing buffer capacity. We detected higher concentrations of SCFAs in the process without cow manure addition. pH, alkalinity and SCFAs were the most important parameters according to nonmetric multidimensional scaling analysis. We observed potential problems in process stability in the extension of the process, because of decreasing concentrations of some microelements, because of washing out of the reactors. The highest methane yields in the first 50 days were observed at a PS:CW:CM ratio of 70:55:10. The most stable process after doubling CW addition was observed at a ratio of 70:70:10

No Disillusions in Auditory Extinction: Perceiving a Melody Comprised of Unperceived Notes

The formation of coherent percepts requires grouping together spatio-temporally disparate sensory inputs. Two major questions arise: (1) is awareness necessary for this process; and (2) can non-conscious elements of the sensory input be grouped into a conscious percept? To address this question, we tested two patients suffering from severe left auditory extinction following right hemisphere damage. In extinction, patients are unaware of the presence of left side stimuli when they are presented simultaneously with right side stimuli. We used the ‘scale illusion’ to test whether extinguished tones on the left can be incorporated into the content of conscious awareness. In the scale illusion, healthy listeners obtain the illusion of distinct melodies, which are the result of grouping of information from both ears into illusory auditory streams. We show that the two patients were susceptible to the scale illusion while being consciously unaware of the stimuli presented on their left. This suggests that awareness is not necessary for auditory grouping and non-conscious elements can be incorporated into a conscious percept

Testing the feasibility and acceptability of using the Nintendo Wii in the home to increase activity levels, vitality and well-being in people with multiple sclerosis (Mii-vitaliSe): protocol for a pilot randomised controlled study.

The benefits of physical activity for people with multiple sclerosis (pwMS) have been recognised. However, exercise regimens can be difficult to maintain over the longer term and pwMS may face unique barriers to physical activity engagement. Pilot research suggests the Nintendo Wii can be used safely at home by pwMS with minimal mobility/balance issues and may confer benefits. We have developed a home-based physiotherapist supported Wii intervention ('Mii-vitaliSe') for pwMS that uses commercial software. This is a pilot study to explore the feasibility of conducting a full scale clinical and cost-effectiveness trial of Mii-vitaliSe

How Can We Advance Integrative Biology Research in Animal Science in 21st Century?:Experience at University of Ljubljana from 2002 to 2022

In this perspective analysis, we strive to answer the following question: how can we advance integrative biology research in the 21st century with lessons from animal science? At the University of Ljubljana, Biotechnical Faculty, Department of Animal Science, we share here our three lessons learned in the two decades from 2002 to 2022 that we believe could inform integrative biology, systems science, and animal science scholarship in other countries and geographies. Cultivating multiomics knowledge through a conceptual lens of integrative biology is crucial for life sciences research that can stand the test of diverse biological, clinical, and ecological contexts. Moreover, in an era of the current COVID-19 pandemic, animal nutrition and animal science, and the study of their interactions with human health (and vice versa) through integrative biology approaches hold enormous prospects and significance for systems medicine and ecosystem health

Optics and Quantum Electronics

Contains table of contents for Section 2 and reports on eighteen research projects.National Science Foundation (Grant EET 87-00474)Joint Services Electronics Program (Contract DAAL03-86-K-0002)Joint Services Electronics Program (Contract DAALO3-89-C-0001)Charles Stark Draper Laboratory (Grant DL-H-285408)Charles Stark Draper Laboratory (Grant DL-H-2854018)National Science Foundation (Grant EET 87-03404)National Science Foundation (Grant ECS 84-06290)U.S. Air Force - Office of Scientific Research (Contract F49620-88-C-0089)AT&T Bell FoundationNational Science Foundation (Grant ECS 85-52701)National Institutes of Health (Grant 5-RO1-GM35459)Massachusetts General Hospital (Office of Naval Research Contract N00014-86-K-0117)Lawrence Livermore National Laboratory (Subcontract B048704

Computational framework for high-quality production and large-scale evolutionary analysis of metagenome assembled genomes

Microbial species play important roles in different environments and the production of high-quality genomes from metagenome data sets represents a major obstacle to understanding their ecological and evolutionary dynamics. Metagenome-Assembled Genomes Orchestra (MAGO) is a computational framework that integrates and simplifies metagenome assembly, binning, bin improvement, bin quality (completeness and contamination), bin annotation, and evolutionary placement of bins via detailed maximum-likelihood phylogeny based on multiple marker genes using different amino acid substitution models, next to average nucleotide identity analysis of genomes for delineation of species boundaries and operational taxonomic units. MAGO offers streamlined execution of the entire metagenomics pipeline, error checking, computational resource distribution and compatibility of data formats, governed by usertailored pipeline processing. MAGO is an open-source-software package released in three different ways, as a singularity image and a Docker container for HPC purposes as well as for running MAGO on a commodity hardware, and a virtual machine for gaining a full access to MAGO underlying structure and source code. MAGO is open to suggestions for extensions and is amenable for use in both research and teaching of genomics and molecular evolution of genomes assembled from small single-cell projects or large-scale and complex environmental metagenomes

Bioinformacijska integracija mikrobiomskih in metabolomskih podatkov v translacijskem kontekstu

Human metabolism was studied in three different projects focusing on different levels of inactivity. Urine, liquor and serum metabolomics were used to assess the impact of nusinersen treatment in patients with spinal muscular atrophy. Urine samples were contrasted with samples from matching healthy cohort. In the PreTerm project, metabolomics (fecal and urine) and fecal microbial metagenomics were used to assess the differences between preterm and full-term born adults. In the X-Adapt project, urinary metabolomics was used to evaluate the 10-day training regime and the differences between trained and untrained individuals. In all projects, classification models based on different data sets were developed as a proof of principle and to foster their use in future studies or possibly in medical diagnostics. In addition, two workflows (GUMPP and MAGO tool) and a method to study physicochemical parameters (minimum pressure of piercing strength) were developed to study the microbiome and its environment, respectively. The final work resulted in the creation of the first Slovenian urine 1H-NMR database, which consists of 1200 urine metabolomes from different projects (PlanHab, Spinal Muscular Atrophy, X-Adapt, PreTerm, Healthy males and females) measured by 1H-NMR, outlining the baseline for future extensions. The entire database can be used to build machine-learning models for classification between different diseases or levels of physical activity at a national level.V okviru večih projektov smo preučevali metabolome preiskovancev z različnimi stopnjami neaktivnosti. Za oceno učinka zdravljenja z zdravilom nusinersen pri bolnikih s spinalno mišično atrofijo smo uporabili metabolomiko urina, likvorja in seruma. Dodatne vzorce urina smo primerjali s tistimi iz zdrave kontrolne skupine. V projektu PreTerm smo s kombinacijo metabolomike fecesa in urina ter z metagenomiko fekalnega mikrobioma raziskovali razlike med predčasno in pravočasno rojenimi odraslimi. V projektu X-Adapt smo z metabolomiko urina ocenili učinke 10-dnevnega režima treninga in razlik med treniranimi in netreniranimi posamezniki. V vseh projektih smo na zbranih podatkih razvili modele za razvrščanje skupin z namenom razvoja analitskih poti ter prikaza možnostjo uporabe teh modelov v prihodnjih študijah ali morda v medicinski diagnostiki. Poleg tega sta bila razvita dva cevovoda (orodje GUMPP in MAGO) ter metoda za preučevanje fizikalno-kemijskih parametrov (minimalna prebodna sila) za preučevanje mikrobioma in njegovega okolja. Končni rezultat analize je bila izdelava prve slovenske metabolomske baze podatkov 1H-NMR urina, ki jo sestavlja 1200 metabolomov urina iz različnih projektov (PlanHab, Spinalna mišična atrofija, X-Adapt, PreTerm, Zdravi moški in ženske), merjenih z 1H-NMR, ki predstavljajo osnovo za prihodnje razširitve iz novih projektov. Celotno bazo podatkov je mogoče uporabiti za gradnjo modelov strojnega učenja za razvrščanje med različnimi boleznimi ali stopnjami telesne aktivnosti na nacionalni ravni

The importance of objective stool classificaton in fecal 1H-NMR metabolomics

Past studies strongly connected stool consistency—as measured by Bristol Stool Scale (BSS)—with microbial gene richness and intestinal inflammation, colonic transit time and metabolome characteristics that are of clinical relevance in numerous gastro intestinal conditions. While retention time, defecation rate, BSS but not water activity have been shown to account for BSS-associated inflammatory effects, the potential correlation with the strength of a gel in the context of intestinal forces, abrasion, mucus imprinting, fecal pore clogging remains unexplored as a shaping factor for intestinal inflammation and has yet to be determined. Our study introduced a minimal pressure approach (MP) by probe indentation as measure of stool material crosslinking in fecal samples. Results reported here were obtained from 170 samples collected in two independent projects, including males and females, covering a wide span of moisture contents and BSS. MP values increased exponentially with increasing consistency (i.e., lower BSS) and enabled stratification of samples exhibiting mixed BSS classes. A trade-off between lowest MP and highest dry matter content delineated the span of intermediate healthy density of gel crosslinks. The crossectional transects identified fecal surface layers with exceptionally high MP and of <5 mm thickness followed by internal structures with an order of magnitude lower MP, characteristic of healthy stool consistency. The MP and BSS values reported in this study were coupled to reanalysis of the PlanHab data and fecal 1H-NMR metabolomes reported before. The exponential association between stool consistency and MP determined in this study was mirrored in the elevated intestinal and also systemic inflammation and other detrimental physiological deconditioning effects observed in the PlanHab participants reported before. The MP approach described in this study can be used to better understand fecal hardness and its relationships to human health as it provides a simple, fine scale and objective stool classification approach for the characterization of the exact sampling locations in future microbiome and metabolome studies