Miracle-dz/UniFAR-FTUs huggingface dataset:
Polyunsaturated fatty acid saturation by gut lactic acid bacteria affecting host lipid composition

Significance Microorganisms in the gastrointestinal tract interact with their host in many ways. Lipid metabolism by gastrointestinal microbes generates multiple fatty acid species that can affect host health. In the representative gut bacterium Lactobacillus plantarum, we revealed a fatty acid metabolism, saturation metabolism of polyunsaturated fatty acid, that generates hydroxy fatty acids, oxo fatty acids, conjugated fatty acids, and partially saturated trans-fatty acids as intermediates. Furthermore, fatty acid analysis in mice suggests that the fatty acid metabolism by gastrointestinal microbes modifies fatty acid composition of the host. Therefore, functional investigations of lipid metabolisms of gastrointestinal microbes may provide new methods for improving our health by altering lipid metabolism related to the onset of metabolic syndrome. In the representative gut bacterium Lactobacillus plantarum, we identified genes encoding the enzymes involved in a saturation metabolism of polyunsaturated fatty acids and revealed in detail the metabolic pathway that generates hydroxy fatty acids, oxo fatty acids, conjugated fatty acids, and partially saturated trans-fatty acids as intermediates. Furthermore, we observed these intermediates, especially hydroxy fatty acids, in host organs. Levels of hydroxy fatty acids were much higher in specific pathogen-free mice than in germ-free mice, indicating that these fatty acids are generated through polyunsaturated fatty acids metabolism of gastrointestinal microorganisms. These findings suggested that lipid metabolism by gastrointestinal microbes affects the health of the host by modifying fatty acid composition.
In vitro non-viral gene delivery with nanofibrous scaffolds

Extracellular and intracellular barriers typically prevent non-viral gene vectors from having an effective transfection efficiency. Formulation of a gene delivery vehicle that can overcome the barriers is a key step for successful tissue regeneration. We have developed a novel core-shelled DNA nanoparticle by invoking solvent-induced condensation of plasmid DNA (β-galactosidase or GFP) in a solvent mixture [94% N,N-dimethylformamide (DMF) + 6% 1× TE buffer] and subsequent encapsulation of the condensed DNA globule in a triblock copolymer, polylactide-poly(ethylene glycol)-polylactide (L8E78L8), in the same solvent environment. The polylactide shell protects the encapsulated DNA from degradation during electrospinning of a mixture of encapsulated DNA nanoparticles and biodegradable PLGA (a random copolymer of lactide and glycolide) to form a nanofibrous non-woven scaffold using the same solution mixture. The bioactive plasmid DNA can then be released in an intact form from the scaffold with a controlled release rate and transfect cells in vitro.
Accuracy of SRTM-X and ASTER Elevation Data and its Influence on Topographical and Hydrological Modeling: Case Study of the Pieniny Mts. in Poland

Satellite sensors provide currently reliable elevation data over large areas, with spatial resolutions below 100 m and reported accuracies of approximately 10 m. However, the vertical accuracy of these quasi-global digital elevation models (DEM) varies depending on the terrain and land cover, decreasing in mountain areas, and may influence the quality of products derived from these data, like stream channel network or relief forms. In this paper, we investigated two global elevation data sets: SRTM-X DEM and ASTER GDEM, assessing their vertical accuracy and reliability of terrain features extracted automatically from the elevation data. The research was carried out in the Pieniny Mts. , a small mountain range in southern Poland, with elevations ranging from about 400 m to 1000 m a.s. l. One particular attribute of this mountain range that may create several problems in deriving accurate terrain features is a deep, narrow and windy gorge of the Dunajec river. We found that the vertical accuracy of SRTM-X DEM is significantly better than of the ASTER GDEM (Root Mean Square errors of 12.05 m and 17.43 m, respectively). Both DEMs allow to extract terrain features with a similar accuracy in areas of moderately steep and gentle slopes, yet fail to properly represent the floor of the Dunajec gorge as relative vertical errors along the river may exceed 100 m. Therefore, we conclude that while both models provide statistically reliable description of the terrain surface, they require additional corrections for hydrological or terrain modeling.
Finding Loop Invariants for Programs over Arrays Using a Theorem Prover

Invariants with quantifiers are important for verification and static analysis of programsover arrays due to the unbounded nature of arrays. Such invariants can expressrelationships among array elements and properties involving array and scalar variablesof the loop.This talk presents how quantified loop invariants of programs over arrayscan be automatically inferred using a first order theorem prover,reducing the burden of annotating loops with complete invariants.Unlike all previously known methods, our method is ableto generate loop invariants containing quantifier alternations
Earthquake processes of the Himalayan collision zone in eastern Nepal and the southern Tibetan Plateau

SUMMARY Focal mechanisms determined from moment tensor inversion and first motion polarities of the Himalayan Nepal Tibet Seismic Experiment (HIMNT) coupled with previously published solutions show the Himalayan continental collision zone near eastern Nepal is deforming by a variety of styles of deformation. These styles include strike-slip, thrust and normal faulting in the upper and lower crust, but mostly strike-slip faulting near or below the crust‐mantle boundary (Moho). One normal faulting earthquake from this experiment accommodates east‐ west extension beneath the Main Himalayan Thrust of the Lesser Himalaya while three upper crustal normal events on the southern Tibetan Plateau are consistent with east‐west extension of the Tibetan crust. Strike-slip earthquakes near the Himalayan Moho at depths >60 km also absorb this continental collision. Shallow plunging P-axes and shallow plunging EW trending T-axes, proxies for the predominant strain orientations, show active shearing at focal depths ∼60‐90 km beneath the High Himalaya and southern Tibetan Plateau. Beneath the southern Tibetan Plateau the plunge of the P-axes shift from vertical in the upper crust to mostly horizontal near the crust‐mantle boundary, indicating that body forces may play larger role at shallower depths than at deeper depths where plate boundary forces may dominate.
Skeletal Muscle Depletion and Markers for Cancer Cachexia Are Strong Prognostic Factors in Epithelial Ovarian Cancer

Objective Tumor cachexia is an important prognostic parameter in epithelial ovarian cancer (EOC). Tumor cachexia is characterized by metabolic and inflammatory disturbances. These conditions might be reflected by body composition measurements (BCMs) ascertained by pre-operative computed tomography (CT). Thus, we aimed to identify the prognostically most relevant BCMs assessed by pre-operative CT in EOC patients. Methods We evaluated muscle BCMs and well established markers of nutritional and inflammatory status, as well as clinical-pathological parameters in 140 consecutive patients with EOC. Furthermore, a multiplexed inflammatory marker panel of 25 cytokines was used to determine the relationship of BCMs with inflammatory markers and patient’s outcome. All relevant parameters were evaluated in uni- and multivariate survival analysis. Results Muscle attenuation (MA)—a well established BCM parameter—is an independent prognostic factor for survival in multivariate analysis (HR 2.25; p = 0.028). Low MA—reflecting a state of cachexia—is also associated with residual tumor after cytoreductive surgery (p = 0.046) and with an unfavorable performance status (p = 0.015). Moreover, MA is associated with Eotaxin and IL-10 out of the 25 cytokine multiplex marker panel in multivariate linear regression analysis (p = 0.021 and p = 0.047, respectively). Conclusion MA—ascertained by routine pre-operative CT—is an independent prognostic parameter in EOC patients. Low MA is associated with the inflammatory, as well as the nutritional component of cachexia. Therefore, the clinical value of pre-operative CT could be enhanced by the assessment of MA.
Genome-Wide Survey of the Soybean GATA Transcription Factor Gene Family and Expression Analysis under Low Nitrogen Stress

GATA transcription factors are transcriptional regulatory proteins that contain a characteristic type-IV zinc finger DNA-binding domain and recognize the conserved GATA motif in the promoter sequence of target genes. Previous studies demonstrated that plant GATA factors possess critical functions in developmental control and responses to the environment. To date, the GATA factors in soybean (Glycine max) have yet to be characterized. Thus, this study identified 64 putative GATA factors from the entire soybean genomic sequence. The chromosomal distributions, gene structures, duplication patterns, phylogenetic tree, tissue expression patterns, and response to low nitrogen stress of the 64 GATA factors in soybean were analyzed to further investigate the functions of these factors. Results indicated that segmental duplication predominantly contributed to the expansion of the GATA factor gene family in soybean. These GATA proteins were phylogenetically clustered into four distinct subfamilies, wherein their gene structure and motif compositions were considerably conserved. A comparative phylogenetic analysis of the GATA factor zinc finger domain sequences in soybean, Arabidopsis (Arabidopsis thaliana), and rice (Oryza sativa) revealed four major classes. The GATA factors in soybean exhibited expression diversity among different tissues; some of these factors showed tissue-specific expression patterns. Numerous GATA factors displayed upregulation or downregulation in soybean leaf in response to low nitrogen stress, and two GATA factors GATA44 and GATA58 were likely to be involved in the regulation of nitrogen metabolism in soybean. Overexpression of GmGATA44 complemented the reduced chlorophyll phenotype of the Arabidopsis ortholog AtGATA21 mutant, implying that GmGATA44 played an important role in modulating chlorophyll biosynthesis. Overall, our study provides useful information for the further analysis of the biological functions of GATA factors in soybean and other crops.
Evolved distal tail carbohydrate binding modules of Lactobacillus phage J‐1: a novel type of anti‐receptor widespread among lactic acid bacteria phages

Bacteriophage replication requires specific host‐recognition. Some siphophages harbour a large complex, the baseplate, at the tip of their non‐contractile tail. This baseplate holds receptor binding proteins (RBPs) that can recognize the host cell‐wall polysaccharide (CWPS) and specifically attach the phage to its host. While most phages possess a dedicated RBP, the phage J‐1 that infects Lactobacillus casei seemed to lack one. It has been shown that the phage J‐1 distal tail protein (Dit) plays a role in host recognition and that its sequence comprises two inserted modules compared with ‘classical’ Dits. The first insertion is similar to carbohydrate‐binding modules (CBMs), whereas the second insertion remains undocumented. Here, we determined the structure of the second insertion and found it also similar to several CBMs. Expressed insertion CBM2, but not CBM1, binds to L. casei cells and neutralize phage attachment to the bacterial cell wall and the isolated and purified CWPS of L. casei BL23 prevents CBM2 attachment to the host. Electron microscopy single particle reconstruction of the J‐1 virion baseplate revealed that CBM2 is projected at the periphery of Dit to optimally bind the CWPS receptor. Taken together, these results identify J‐1 evolved Dit as the phage RBP.
An inverse-modelling approach to assess the impacts of climate change in the Seyhan River basin, Turkey / Une approche de modélisation inverse pour évaluer les impacts du changement climatique dans le bassin versant de la Rivière Seyhan, Turquie

Abstract One of the most significant anticipated consequences of global climate change is the change in frequency of hydrological extremes. Predictions of climate change impacts on the regime of hydrological extremes have traditionally been conducted by a top-down approach that involves a high degree of uncertainty associated with the temporal and spatial characteristics of general circulation model (GCM) outputs and the choice of downscaling technique. This study uses the inverse approach to model hydrological risk and vulnerability to changing climate conditions in the Seyhan River basin, Turkey. With close collaboration with the end users, the approach first identifies critical hydrological exposures that may lead to local failures in the Seyhan River basin. The Hydro-BEAM hydrological model is used to inversely transform the main hydrological exposures, such as floods and droughts, into corresponding meteorological conditions. The frequency of critical meteorological conditions is investigated under present and future climate scenarios by means of a weather generator based on the improved K-nearest neighbour algorithm. The weather generator, linked with the output of GCMs in the last step of the proposed methodology, allows for the creation of an ensemble of scenarios and easy updating when improved GCM outputs become available. Two main conclusions were drawn from the application of the inverse approach to the Seyhan River basin. First, floods of 100-, 200- and 300-year return periods under present conditions will have 102-, 293- and 1370-year return periods under the future conditions; that is, critical flood events will occur much less frequently under the changing climate conditions. Second, the drought return period will change from 5.3 years under present conditions to 2.0 years under the future conditions; that is, critical drought events will occur much more frequently under the changing climate conditions.
Characterizing long‐time scale hydrological effects on gravity for improved distinction of tectonic signals

The influence of the hydrological noise on repeated gravity measurements has been investigated on the basis of the time series of 18 superconducting gravimeters (SGs) and on predictions inferred from the Land Dynamics (LaD) world-Gascoyne land water-energy balances model. Presently, the global hydrologic models are not precise enough to fulfill the geodetic requirements and are not efficient enough to separate the hydrology from tectonic motion in the land-based gravity time series. However, although the LaD model predictions and the gravity observations present significant differences in the time domain, it is shown that they have similar amplitudes in the frequency domain in most of the cases. The time series of the Global Geodynamics Project make it possible to investigate phenomena of a few years in the best case. Given the similarity between the power spectral densities (PSDs) of the LaD model predictions and the SG measurements when taken at the same epoch, it makes sense to use the LaD model to study the spectral behavior of the hydrological effects down to the decadal time scale, which is not yet possible with land-based measurements. It is shown that the PSDs of the hydrological effects flattens at low frequency and is characterized by a generalized Gauss-Markov structure. With such a noise level, the time necessary to measure a gravity rate of change of 1 nm/s(2)/a, at the 1 sigma level should not extend any longer than 17 years at the locations where the hydrological effects play a major role
MicroRNA profiling associated with non-small cell lung cancer: next generation sequencing detection, experimental validation, and prognostic value

Background The average five-year survival for non-small cell lung cancer (NSCLC) patients is approximately 15%. Emerging evidence indicates that microRNAs (miRNAs) constitute a new class of gene regulators in humans that may play an important role in tumorigenesis. Hence, there is growing interest in studying their role as possible new biomarkers whose expression is aberrant in cancer. Therefore, in this study we identified dysregulated miRNAs by next generation sequencing (NGS) and analyzed their prognostic value. Methods Sequencing by oligo ligation detection technology was used to identify dysregulated miRNAs in a training cohort comprising paired tumor/normal tissue samples (N = 32). We validated 22 randomly selected differentially-expressed miRNAs by quantitative real time PCR in tumor and adjacent normal tissue samples (N = 178). Kaplan-Meier survival analysis and Cox regression were used in multivariate analysis to identify independent prognostic biomarkers. Results NGS analysis revealed that 39 miRNAs were dysregulated in NSCLC: 28 were upregulated and 11 were downregulated. Twenty-two miRNAs were validated in an independent cohort. Interestingly, the group of patients with high expression of both miRNAs (miR-21high and miR-188high) showed shorter relapse-free survival (RFS) and overall survival (OS) times. Multivariate analysis confirmed that this combined signature is an independent prognostic marker for RFS and OS (p = 0.001 and p < 0.0001, respectively). Conclusions NGS technology can specifically identify dysregulated miRNA profiles in resectable NSCLC samples. MiR-21 or miR-188 overexpression correlated with a negative prognosis, and their combined signature may represent a new independent prognostic biomarker for RFS and OS.
Sociocultural aspects of transitions from assisted living for residents with dementia.

PURPOSE Negotiating transitions and residential relocation are especially difficult for residents with dementia and their families. This article examined the decision-making process regarding retention or transfer of persons with dementia in assisted living facilities. DESIGN AND METHODS Using an ethnographic approach, this study observed residents and facility life, and interviewed residents, staff, and family members in three assisted living facilities. RESULTS Facility managers and administrators are pivotal figures in determining the timing of transitions and transitional care. Operating within the context of care requirements of dementia, they, the facility culture, and the family members' involvement in resident care mediate interpretations of and responses to change and decline, and ultimately influence decision making regarding retention or transfer. IMPLICATIONS Transfer or retention may occur differently depending on whether managers are on- or off-site, the assisted living culture is dementia-friendly, and families are involved in care. Sensitizing assisted living managers and educating potential residents and family members to the importance of these factors may affect the eventual likelihood and timing of discharge.
Decadal‐to‐interdecadal fluctuations of arctic sea‐ice cover and the atmospheric circulation during 1954–1994

Abstract The relationship between the Arctic and subarctic sea‐ice concentration (SIC) anomalies, particularly those associated with the decadal‐scale Greenland and Labrador Seas “Ice and Salinity Anomalies (ISAs) “, and the overlying atmospheric circulation fluctuations is investigated using the singular value decomposition (SVD) and composite map analysis methods. The data analyzed are monthly SIC and sea level pressure (SLP) anomalies, which cover the northern hemisphere poleward of 45°N and extend over the 41‐year period 1954–1994. The SVD1 (first) mode of the coupled variability, which accounts for 57% of the square covariance, is for the most part an atmosphere‐to‐ice forcing mode characterized by the decadal timescale. The aforementioned ISA anomalies are clearly captured by this mode whose SIC anomalies are dominated by a strong dipole across Greenland. However, as part of the same mode, there is also a weaker SIC dipole in the northern North Pacific which has opposite‐signed anomalies in the Sea .
Bloodless Liver Resection Using Radiofrequency Energy

Background: Liver surgery carries the risk of intraoperative bleeding. In order to avoid bleeding, transection of the liver can be performed after coagulating the parenchyma by using monoplolar or bipolar radiofrequency energy. Methods: 236 consecutive patients underwent liver resection with the radiofrequency-assisted technique using either a monopolar or a bipolar device. Data were collected prospectively to assess the outcome including, intraoperative blood loss, blood transfusion requirement, morbidity and mortality rates. Results: There were 41 major hepatectomies and 195 minor resections. Overall mean intraoperative blood loss was 157 ± 240 ml, while mean blood loss during liver transection was 90 ± 105 ml. 10 patients (4%) received blood transfusion. 50 patients (21%) developed postoperative complications including 5 bile leaks (2%). The mortality rate was 2.1%. No patient was reoperated for postoperative haemorrhage or bile leak. The mean postoperative stay was 11 ± 10 days. Conclusion: The radiofrequency-assisted liver resection technique offers hepatobiliary surgeons an additional method for performing liver resections with minimal blood loss, low transfusion requirement, and low morbidity and mortality rates.
A cooling rate bias in paleointensity determination from volcanic glass: An experimental demonstration

[1] The suitability of volcanic glass for paleointensity determinations is the basis of many studies. The dominant single domain (SD) magnetic remanence carriers, the pristine character of volcanic glass, and the possibility to correct paleointensity data for cooling rate dependence using relaxation geospeedometry are all arguments that have been made in favor of this technique. In the present study the validity of cooling rate correction is tested using remelted volcanic glass. To obtain a stable multicomponent glass, with ideal magnetic properties, a natural phonolitic glass from Tenerife was remelted in air to avoid heterogeneity and degassing in later experiments. Further, it was tempered for altogether 10 hours at 900°C to yield a sufficient concentration of magnetic remanence carriers. To exclude nucleation or crystallization, six samples were then heated to about 60°C above the calorimetric glass transition temperature (≈660°C) and quenched at different rates from 0.1 to 15 K/min. Rock magnetic measurements show that low titanium titanomagnetite in the SD range is the main remanence carrier. After performing paleointensity experiments using a modified Thellier method, the dependence of the thermoremanence on cooling rate was investigated. Using the synthesis cooling rates and the experimentally determined magnetic cooling rate dependencies we were able to correct the data and obtained a mean paleointensity of 46.9 ± 1. 3μT, which reflects the ambient field of 48μT within error. The uncorrected mean paleointensity corresponds to a 18% larger value of 56.5 ± 0. 9μT. Therefore, application of a cooling rate correction is essential to obtain the correct ancient magnetic field intensity from SD assemblages in volcanic glass.
Macromycetes of the proposed nature reserve Wilcze Uroczysko-Olszanka in the Odra estuary

The paper presents a characterisation of the mycoflora on the cupola-type rised bog in the Odra river valley. The characteristic of each species includes: type of substrate and plant community, date of fruitbody occurence, and the forest unit, where the species was observed. Systematic, ecological and sociological analyses of the mycoflora have been performed and the protected and endangered species singled out.