Miracle-dz/UniFAR-FTUs huggingface dataset:
Urban Air Pollution Inference : A Neural Network Ensemble Approach

Air pollution maps can help people to plan outdoor activities and environmental scientists to evaluate new policies. Urban air is filled with ultrafine particles (UFPs) that can have a severe impact on human health. Therefore, UFP concentration maps with high spatio-temporal resolution are of great importance to control air pollution. An extensive amount of UFP data is provided over more than three years by sensors mounted on trams of Zurich as part of the OpenSense project. However, the locations of these measurements are only sparsely distributed over the city area as the mobility of the trams is limited. Air quality information at locations without any measurements can be inferred by annotating measurement data with information about factors that have an impact on air pollution like weather, traffic and land use. In this thesis, an air pollution prediction approach based on neural networks is proposed and tested on the OpenSense dataset. Timely dynamic weather and traffic features are aggregated in order to improve the temporal resolution of urban air pollution maps. In order to check the performance of the model at locations where no UFP measurements are available, two approaches that quantify the uncertainty of air pollution predictions from neural networks based on ensembles and dropout are proposed and evaluated. The comparison of the neural network with a generalized additive model showed that similar or better performance in terms of the error metrics is achieved. However, unrealistic pollution concentrations are predicted at locations that differ a lot in terms of environmental conditions from the training dataset. This observation is confirmed by the generated uncertainty maps.
Dream Recall Frequency Is Associated With Medial Prefrontal Cortex White-Matter Density

Recent findings indicate that dream recall frequency (DRF) is associated with neurophysiological traits, and notably the regional cerebral blood flow at rest within the medial prefrontal cortex (MPFC) and the temporo-parietal junction (TPJ). To test whether, such physiological traits are rooted in anatomical specificities, we used voxel-based morphometry to compare the white matter and gray matter density in regions related to dream recall (either at the experimental or theoretical level, MPFC, TPJ, hippocampus and amygdala) between 46 high dream recallers (HR, DRF = 5.98 ± 1.25 days per week with a dream report) and 46 low dream recallers (LR, DRF = 0.34 ± 0.29). We found an increased medial prefrontal cortex white-matter density in HR compared to LR but no other significant difference between the two groups. These results are consistent with previous studies showing that lesions within the white matter of medial prefrontal cortex are associated with a partial or total cessation of dream reporting and suggest an implication of this region in dream recall or, more likely, in dream production.
BacDive in 2019: bacterial phenotypic data for High-throughput biodiversity analysis

Abstract The bacterial metadatabase BacDive (http://bacdive.dsmz.de) has become a comprehensive resource for structured data on the taxonomy, morphology, physiology, cultivation, isolation and molecular data of prokaryotes. With its current release (7/2018) the database offers information for 63 669 bacterial and archaeal strains including 12 715 type strains. During recent developments of BacDive, the enrichment of information on existing strains was prioritized. This has resulted in a 146% increase of database content over the past three years. Especially rich datasets were integrated from 4782 manual annotated species descriptions in the International Journal of Systematic and Evolutionary Microbiology which yielded standardized phenotypic data for 5468 type strains. Another important improvement of content was achieved through the mobilization of 8977 Analytical Profile Index (API®) test results that constitute physiological data for the identification of 5237 strains. BacDive offers a unique API® data collection with respect to size and diversity. In addition, data on fatty acid profiles and antibiotic susceptibility tests were integrated. A revised graphical user interface and new search tools such as the API® test finder, the TAXplorer, or the Microbial Isolation Source Search significantly improve the user experience.
Dietary Management of Blood Glucose in Medical Critically Ill Overweight and Obese Patients: An Open‐Label Randomized Trial

Abstract Background: Enteral nutrition (EN) increases hyperglycemia due to high carbohydrate concentrations while providing insufficient protein. The study tested whether an EN formula with very high‐protein‐ and low‐carbohydrate‐facilitated glucose control delivered higher protein concentrations within a hypocaloric protocol. Methods: This was a multicenter, randomized, open‐label clinical trial with parallel design in overweight/obese mechanically ventilated critically ill patients prescribed 1.5 g protein/kg ideal body weight/day. Patients received either an experimental very high‐protein (37%) and low‐carbohydrate (29%) or control high‐protein (25%) and conventional‐carbohydrate (45%) EN formula. Results: A prespecified interim analysis was performed after enrollment of 105 patients (52 experimental, 53 control). Protein and energy delivery for controls and experimental groups on days 1–5 were 1.2 ± 0.4 and 1.1 ± 0.3 g/kg ideal body weight/day (P = .83), and 18.2 ± 6.0 and 12.5 ± 3.7 kcals/kg ideal body weight/day (P < .0001), respectively. The combined rate of glucose events outside the range of >110 and ≤150 mg/dL were not different (P = .54, primary endpoint); thereby the trial was terminated. The mean blood glucose for the control and the experimental groups were 138 (−SD 108, +SD 177) and 126 (−SD 99, +SD 160) mg/dL (P = .004), respectively. Mean rate of glucose events >150 mg/dL decreased (Δ = −13%, P = .015), whereas that of 80–110 mg/dL increased (Δ = 14%, P = .0007). Insulin administration decreased 10.9% (95% CI, −22% to 0.1%; P = .048) in the experimental group relative to the controls. Glycemic events ≤80 mg/dL and rescue dextrose use were not different (P = .23 and P = .53). Conclusions: A very high‐protein and low‐carbohydrate EN formula in a hypocaloric protocol reduces hyperglycemic events and insulin requirements while increasing glycemic events between 80–110 mg/dL.
New frequency-domain ℓ2-stability criteria for nonlinear MIMO discrete-time systems with constant and varying time delays

Abstract New frequency-domain -stability criteria are derived for nonlinear discrete-time MIMO systems, having a linear time-invariant block with the transfer function , in negative feedback with an aperiodic matrix gain , and a linear combination of a vector of certain classes of (generalised) first-and-third-quadrant non-monotone nonlinearities , having arguments with constant and time-varying delays, but without restrictions on their slopes. The framework does not employ Lyapunov–Krasovskii functionals involving linear matrix inequalities (LMIs) or their equivalent. The new stability criteria seem to be the most general for nonlinear and time variying time-delay systems, and have the following structure: (1) positive definiteness of the real part (as evaluated on ) of the product of and an algebraic sum of general causal and anticausal matrix multiplier functions of z. (2) An upper bound on the -norm of the inverse Fourier transform of the multiplier function, the -norm being weighted by certain novel, quantitative characteristic parameters (CPs) of the nonlinearities without the asumptions of monotonicity, slope restrictions and the like. And (3) constraints on certain global averages of the generalised eigenvalues of , that are expressed in terms of (i) CPs of the nonlinearities, (ii) their coefficients, and, in general, (iii) time-delays in their arguments, a trade-off among all the three being possible. These global averages imply a restriction on the rate of variation of in a new sense. The literature results turn out to be special cases of the results of the present paper. Examples illustrate the stability theorems.
Inter-hospital transfer and patient outcomes: a retrospective cohort study

Background Inter-hospital transfer (IHT, the transfer of patients between hospitals) occurs regularly and exposes patients to risks of discontinuity of care, though outcomes of transferred patients remains largely understudied. Objective To evaluate the association between IHT and healthcare utilisation and clinical outcomes. Design Retrospective cohort. Setting CMS 2013 100 % Master Beneficiary Summary and Inpatient claims files merged with 2013 American Hospital Association data. Participants Beneficiaries≥age 65 enrolled in Medicare A and B, with an acute care hospitalisation claim in 2013 and 1 of 15 top disease categories. Main outcome measures Cost of hospitalisation, length of stay (LOS) (of entire hospitalisation), discharge home, 3 -day and 30- day mortality, in transferred vs non-transferred patients. Results The final cohort consisted of 53 420 transferred patients and 53 420 propensity-score matched non-transferred patients. Across all 15 disease categories, IHT was associated with significantly higher costs, longer LOS and lower odds of discharge home. Additionally, IHT was associated with lower propensity-matched odds of 3-day and/or 30- day mortality for some disease categories (acute myocardial infarction, stroke, sepsis, respiratory disease) and higher propensity-matched odds of mortality for other disease categories (oesophageal/gastrointestinal disease, renal failure, congestive heart failure, pneumonia, renal failure, chronic obstructivepulmonary disease, hip fracture/dislocation, urinary tract infection and metabolic disease). Conclusions In this nationally representative study of Medicare beneficiaries, IHT was associated with higher costs, longer LOS and lower odds of discharge home, but was differentially associated with odds of early death and 30 -day mortality depending on patients’ disease category. These findings demonstrate heterogeneity among transferred patients depending on the diagnosis, presenting a nuanced assessment of this complex care transition.
Comparative analysis of cardiac cycle length during exercise in healthy people and cardiac patients.

Arterio-venous oxygen difference is very high at rest (70-80%) and is the main determinant to set an increase in coronary blood flow as the major mechanism to meet myocardial oxygen requirements during exercise. Coronary blood flow is not evenly distributed throughout the myocardium during cardiac cycle: it is higher in the subepicardium during systole and higher in the subendocardium during diastole and mainly depends on two factors: heart rate (HR) and blood pressure. The increase in coronary blood flow during exercise is produced by the increment of HR, as the increased contractility entails an increase of the compression of intramural vessels, while an increment of myocardial relaxation occurs during diastole. However, the increased HR produces a decrease of cardiac cycle times, specifically diastole time, resulting in a reduction of blood flow to the subendocardium. All this has led to think about the existence of a subcritical coronary stenosis, which can result in a selective subendocardial hypoperfusion during exercise. Therefore, diastolic time is considered a major determinant of oxygen delivery to myocardium. Our main objective was to study the variation in the duration of cardiac cycle phases in two different groups: healthy people and patients with exercise-induced cardiac ischemia. As diastole is the cardiac cycle phase where a larger increase in coronary blood flow occurs, we hypothesized that the behavior of variations of diastolic time was different between patients and healthy subjects. Twenty three healthy asymptomatic males, and twenty four sedentary male subjects who had an exerciseinduced ischemia when undergoing a stress test. The study was approved by the local ethical committee of the Polytechnic University of Madrid, complying with the Declaration of Helsinki. All subjects were informed in detail about the tests they were going to undergo, and gave written consent to have them done. Healthy subjects were screened obtaining a 12 lead electrocardiogram (EKG) at rest, and underwent an incremental (increasing 5 watts every 12 seconds) ergoespirometry test on cycle-ergometer with real time HR and 12 lead EKG continuous monitoring. The group of patients, who had previously shown positive EKG signs of exercise-induced ischemia following a Bruce protocol, underwent a second stress test based on nuclear imaging procedures with radioisotopes.
Effective Sequential Combined Chemotherapy with Trifluridine/Tipiracil and Regorafenib in Human Colorectal Cancer Cells

Salvage chemotherapy for refractory metastatic colorectal cancer using trifluridine/tipiracil (FTD/TPI) and regorafenib has shown survival benefits. We evaluated the antitumor effects of FTD or FTD/TPI combined with regorafenib in vitro and in vivo. SW620, HCT 116, and HT-29 human colorectal cancer cell lines were treated with FTD and regorafenib simultaneously and sequentially. Cell death, incorporation of FTD into DNA, and molecules related to FTD and regorafenib-associated cell death were investigated. The antitumor effects of FTD combined with regorafenib in SW620 and COLO205 xenografts were also evaluated. Cell death was greater after sequential treatment with FTD followed by regorafenib in SW620 cells, but not in HCT 116 and HT-29 cells, than after treatment with FTD alone, which was attributable to thymidylate synthase reduction with the induction of apoptosis. In contrast, simultaneous and sequential exposure to regorafenib followed by FTD, but not FTD alone, attenuated the cell death effect. Furthermore, combined FTD/TPI treatment followed by regorafenib had greater antitumor activity than either monotherapy in SW620 and COLO205 xenograft models. Treatment results following regorafenib administration subsequent to FTD or FTD/TPI suggest that sequential therapy with FTD/TPI prior to regorafenib may be effective in a clinical setting.
Evaluating the validity and reliability of a visual dental scale for detection of periodontal disease (PD) in non-anesthetized dogs (Canis familiaris)

Periodontal disease is one of the most common conditions affecting companion dogs. The objectives of this cross-sectional study were: to determine 1) the agreement between visual assessments (VA) of periodontal disease (PD) performed on awake dogs and the reference standard (RS) of a dental examination and radiographs performed with the dog under general anesthesia, and 2) inter-rater reliability (IRR) for two individuals performing VAs of PD on the same dogs. One hundred and eight dogs were recruited from three veterinary practices. An oral examination and visual PD staging based on the American Veterinary Dental College’s (AVDC) 5-point scale was performed by the investigators prior to general anesthesia and the dental procedure. After the anesthetic evaluation and radiographs, the attending veterinarian staged each dog based on the AVDC’s 5-point scale. Agreement between the VA and RS as well as IRR were determined using percent agreement and a weighted kappa statistic. Eighty-nine dogs received a complete oral examination under general anesthesia with periodontal probing and full-mouth radiographs. Fifty-nine dogs received a VA by both raters. VA agreed with the RS 41.57% of the time with a weighted kappa of 0.42 (95% confidence interval 0.29–0.55), indicating moderate agreement. Between raters, VA agreed 61.02% of the time with a weighted kappa of 0.63 (95% confidence interval 0.49–0.76), indicating substantial IRR. The results of this study reinforce the idea that an oral examination in an awake dog can be a helpful screening tool, but should not be considered a comprehensive evaluation of periodontal health. In facilities housing large numbers of dogs such as shelters, breeding kennels, and research facilities, use of a VA can aid in identifying and prioritizing dogs most in need of procedures such as professional cleaning, periodontal treatment, including closed root planing, or surgical care.
Genomic organization, gene expression and activity profile of Marinobacter hydrocarbonoclasticus denitrification enzymes

Background Denitrification is one of the main pathways of the N-cycle, during which nitrate is converted to dinitrogen gas, in four consecutive reactions that are each catalyzed by a different metalloenzyme. One of the intermediate metabolites is nitrous oxide, which has a global warming impact greater then carbon dioxide and which atmospheric concentration has been increasing in the last years. The four denitrification enzymes have been isolated and biochemically characterized from Marinobacter hydrocarbonoclasticus in our lab. Methods Bioinformatic analysis of the M. hydrocarbonoclasticus genome to identify the genes involved in the denitrification pathway. The relative gene expression of the gene encoding the catalytic subunits of those enzymes was analyzed during the growth under microoxic conditions. The consumption of nitrate and nitrite, and the reduction of nitric oxide and nitrous oxide by whole-cells was monitored during anoxic and microoxic growth in the presence of 10 mM sodium nitrate at pH 7.5. Results The bioinformatic analysis shows that genes encoding the enzymes and accessory factors required for each step of the denitrification pathway are clustered together. An unusual feature is the co-existence of genes encoding a q- and a c-type nitric oxide reductase, with only the latter being transcribed at similar levels as the ones encoding the catalytic subunits of the other denitrifying enzymes, when cells are grown in the presence of nitrate under microoxic conditions. Using either a batch- or a closed system, nitrate is completely consumed in the beginning of the growth, with transient formation of nitrite, and whole-cells can reduce nitric oxide and nitrous oxide from mid-exponential phase until being collected (time-point 50 h). Discussion M. hydrocarbonoclasticus cells can reduce nitric and nitrous oxide in vivo, indicating that the four denitrification steps are active. Gene expression profile together with promoter regions analysis indicates the involvement of a cascade regulatory mechanism triggered by FNR-type in response to low oxygen tension, with nitric oxide and nitrate as secondary effectors, through DNR and NarXL, respectively. This global characterization of the denitrification pathway of a strict marine bacterium, contributes to the understanding of the N-cycle and nitrous oxide release in marine environments.
Pathways of Pathogenicity: Transcriptional Stages of Germination in the Fatal Fungal Pathogen Rhizopus delemar

Germination is key to the growth of many organisms, including fungal spores. Mucormycete spores exist abundantly within the environment and germinate to form hyphae. These spores are capable of infecting immunocompromised individuals, causing the disease mucormycosis. Germination from spore to hyphae within patients leads to angioinvasion, tissue necrosis, and often fatal infections. This study advances our understanding of how spore germination occurs in the mucormycetes, identifying processes we may be able to inhibit to help prevent or treat mucormycosis. ABSTRACT Rhizopus delemar is an invasive fungal pathogen responsible for the frequently fatal disease mucormycosis. Germination, a crucial mechanism by which infectious spores of Rhizopus delemar cause disease, is a key developmental process that transforms the dormant spore state into a vegetative one. The molecular mechanisms that underpin this transformation may be key to controlling mucormycosis; however, the regulation of germination remains poorly understood. This study describes the phenotypic and transcriptional changes that take place over the course of germination. This process is characterized by four distinct stages: dormancy, isotropic swelling, germ tube emergence, and hyphal growth. Dormant spores are shown to be transcriptionally unique, expressing a subset of transcripts absent in later developmental stages. A large shift in the expression profile is prompted by the initiation of germination, with genes involved in respiration, chitin, cytoskeleton, and actin regulation appearing to be important for this transition. A period of transcriptional consistency can be seen throughout isotropic swelling, before the transcriptional landscape shifts again at the onset of hyphal growth. This study provides a greater understanding of the regulation of germination and highlights processes involved in transforming Rhizopus delemar from a single-cellular to multicellular organism. IMPORTANCE Germination is key to the growth of many organisms, including fungal spores. Mucormycete spores exist abundantly within the environment and germinate to form hyphae. These spores are capable of infecting immunocompromised individuals, causing the disease mucormycosis. Germination from spore to hyphae within patients leads to angioinvasion, tissue necrosis, and often fatal infections. This study advances our understanding of how spore germination occurs in the mucormycetes, identifying processes we may be able to inhibit to help prevent or treat mucormycosis.
Chemical composition and antimicrobial activity of Gannan navel orange (Citrus sinensis Osbeck cv. Newhall) peel essential oils

Abstract The present investigation reported the chemical composition of cold pressed Gannan navel orange peel essential oil (EO) and its molecular distillation fraction (light phase EO), and examined their antimicrobial activity against spoiling and pathogenic microorganisms. Gas chromatography‐mass spectrometry analysis identified 27 and 20 different chemical constituents in cold pressed EO and light phase EO, respectively. Limonene was the major constituent, accounting for 85.32% of cold pressed EO and 60.44% of light phase EO. Both EOs and some of their constituents showed good antimicrobial activity. Compared to cold pressed EO, light phase EO exhibited the better antimicrobial activity under weak acidic and neutral conditions. The light phase EO presented a higher antimicrobial activity after thermo‐treatment at 60–100°C for 20 min than cold pressed EO. These results demonstrated that light phase EO had a potential to be used as a novel antimicrobial agent for food preservation and food processing.