Inheritance of feed intake-based resilience traits and their correlation with production traits in Finnish pig breeds.

High resilience against diseases, changing environmental conditions, and other stress factors and the ability to efficiently recover to normal status, is becoming increasingly important in pig production. Finding new phenotypes that relate to resilience is a crucial step for improving the resilience of pigs through selection. The objective of this study was to extract resilience-related phenotypes based on fluctuations in daily feed intake (DFI, g) and time spent in feeding per day (TPD, min) and to estimate the heritability of these traits and genetic correlations with production traits (PT). Resilience-related traits with high enough heritability and with either favorable or neutral genetic correlation with PT could be used in the selection program to improve the productivity and welfare of pigs. In this study, we used data from 7,347 Finnish Yorkshire, Landrace, and crossbred pigs raised at the test station. Six pig-specific resilience-related phenotypes were extracted from the individual DFI and TPD: root mean square error (RMSE), quantile regression (QR), and coefficient of variation (CV). RMSE was calculated from the differences between the actual DFI (or TPD) and the pig-specific predicted values. QR was based on the number of days that a pig belonged to the group with the lowest 5% of pigs based on DFI (or TPD), and CV was calculated over the daily observations of DFI (or TPD). PT included average daily gain (ADG, g), backfat thickness (BF, mm), and feed conversion rate (FCR, g/g). The heritability estimates for resilience-related traits varied between 0.07 ±â€…0.02 (QRDFI) and 0.20 ±â€…0.03 (RMSETPD). The genetic correlations between resilience-related traits and PT were mostly neutral, but for example, RMSEDFI had a favorable genetic correlation with FCR and BF but an unfavorable correlation with ADG. Lastly, we observed that pigs belonging to the lowest 10% group based on their breeding value (BV) for QRTPD had a lower proportion (10% incidence) of sick days compared to the highest 10% BV group (30% incidence). Therefore, pigs exhibiting small TPD variation (related to high resilience) tend to be less susceptible to sickness than pigs with large TPD variation (related to low resilience). Given its moderate heritability, neutral genetic correlation with PT, and positive effect on health, QRTPD can be considered the most promising resilience-related trait in the Finnish production system.

Improving resilience, i.e., the capacity to respond to the impacts of stressors and to effectively recover to normal status, is a promising approach to enhancing the well-being of pigs and the productivity of the pig industry. Animals with high resilience can maintain their performance under challenging conditions. However, obtaining heritable measurements and indicators of resilience is challenging. One indicator of resilience is fluctuation in daily feed intake (DFI) and time spent in feeding per day (TPD). In our study, the proportion of days during which a particular pig belongs to the lowest 5% of pigs based on TPD (QRTPD) turned out to be the most promising resilience-related trait. This trait is moderately inheritable and has only a weak genetic correlation with production traits (PTs). Pigs with the most favorable breeding values (BVs) for QRTPD had four times fewer sick days than pigs with less favorable BVs for QRTPD. Overall, selecting QRTPD would improve pig resilience and health without negative effects on PTs.

Real-time visualisation of ion exchange in molecularly confined spaces where electric double layers overlap.

Ion interactions with interfaces and transport in confined spaces, where electric double layers overlap, are essential in many areas, ranging from crevice corrosion to understanding and creating nano-fluidic devices at the sub 10 nm scale. Tracking the spatial and temporal evolution of ion exchange, as well as local surface potentials, in such extreme confinement situations is both experimentally and theoretically challenging. Here, we track in real-time the transport processes of ionic species (LiClO4) confined between a negatively charged mica surface and an electrochemically modulated gold surface using a high-speed in situ sensing Surface Forces Apparatus. With millisecond temporal and sub-micrometer spatial resolution we capture the force and distance equilibration of ions in the confinement of D ≈ 2-3 nm in an overlapping electric double layer (EDL) during ion exchange. Our data indicate that an equilibrated ion concentration front progresses with a velocity of 100-200 µm s-1 into a confined nano-slit. This is in the same order of magnitude and in agreement with continuum estimates from diffusive mass transport calculations. We also compare the ion structuring using high resolution imaging, molecular dynamics simulations, and calculations based on a continuum model for the EDL. With this data we can predict the amount of ion exchange, as well as the force between the two surfaces due to overlapping EDLs, and critically discuss experimental and theoretical limitations and possibilities.

Machine Learning Insights Into Uric Acid Elevation With Thiazide Therapy Commencement and Intensification.

Background Elevated serum uric acid, associated with cardiovascular conditions such as atherosclerotic heart disease, hypertension, and heart failure, can be elevated by thiazide or thiazide-like drugs (THZ), essential in hypertension management. Identifying clinical determinants affecting THZ-related uric acid elevation is critical. Methods In this retrospective cross-sectional study, we explored the clinical determinants influencing uric acid elevation related to THZ, focusing on patients where THZ was initiated or the dose escalated. A cohort of 143 patients was analyzed, collecting baseline and control uric acid levels, alongside basic biochemical studies and clinical data. Feature selection was conducted utilizing criteria based on mean squared error increase and enhancement in node purity. Four machine learning algorithms - Random Forest, Neural Network, Support Vector Machine, and Gradient Boosting regressions - were applied to pinpoint clinical influencers. Results Significant features include uncontrolled diabetes, index estimated Glomerular Filtration Rate (eGFR) level, absence of insulin, action of indapamide, and absence of statin treatment, with absence of Sodium-glucose cotransporter 2 inhibitors (SGLT2i), low dose aspirin exposure, and older age also being noteworthy. Among the applied models, the Gradient Boosting regression model outperformed the others, exhibiting the lowest Mean Absolute Error (MAE), Mean Squared Error (MSE), Root Mean Squared Error (RMSE) values, and the highest R2 value (0.779). While Random Forest and Neural Network regression models were able to fit the data adequately, the Support Vector Machine demonstrated inferior metrics. Conclusions Machine learning algorithms are adept at accurately identifying the factors linked to uric acid fluctuations caused by THZ. This proficiency aids in customizing treatments more effectively, reducing the need to unnecessarily avoid THZ, and providing guidance on its use to prevent instances where uric acid levels could become problematic.

The Minimum Effective Analgesic Volume of 0.5% Bupivacaine for Ultrasound-Guided Anterior Suprascapular Nerve Block.

Objective The interscalene brachial plexus block (ISBB) constitutes the gold standard for analgesia after shoulder procedures. Ipsilateral phrenic nerve block remains the most common adverse effect after ISBB. Alternative nerve blocks are performed in shoulder surgery in order to prevent hemi-diaphragmatic paralysis (HDP). The purpose of the present study was to investigate the minimum effective local anesthetic volume of 0.5% bupivacaine for postoperative analgesia with an anterior suprascapular nerve block (ASSB). The secondary aim was to investigate diaphragm functions with the local anesthetic doses used while conducting effective volume research. Method This prospective observational study was conducted at the American Hospital of Istanbul, Turkey, from March to July 2022. The initial injected volume of 0.5% bupivacaine was 10 ml. Our clinical experience indicates that this yields a complete sensory block of the anterior suprascapular nerve. In accordance with the up-and-down method, the volume of 0.5% bupivacaine used for a particular patient was determined by the outcome of the preceding block, which represented block success. In case of effective ASSB being achieved, the volume of 0.5% bupivacaine to be administered to the next patient was lowered by 1 ml. In case of block failure, however, the volume of 0.5% bupivacaine to be applied in the subsequent case was increased by 1 ml. Ipsilateral hemi-diaphragmatic movement measurements were taken before (baseline) and 30 minutes after the block. General anesthesia was induced 60 minutes after the completion of the block performance by means of a standardized protocol. Results Sixty-seven patients were included in the study. The ED50 and ED95 calculated for anterior suprascapular nerve block using probit transformation and logistic regression analysis were 2.646 (95% CI, 0.877-2.890) and 3.043 ml (95% CI, 2.771-4.065), respectively. When complete paralysis was defined as 75% or above, partial paralysis as 25-50%, and no paralysis as 25% or less, volumes of 6 ml or lower appeared to cause no paralysis for the anterior suprascapular nerve block. Conclusion We, therefore, recommend using a volume of 6 ml or less in order to achieve diaphragm-sparing features for anterior suprascapular nerve blocks.

Mussel adhesion: A fundamental perspective on factors governing strong underwater adhesion.

Protein-based underwater adhesives of marine organisms exhibit extraordinary binding strength in high salinity based on utilizing a variety of molecular interaction mechanisms. These include acid-base interactions, bidentate bindings or complex hydrogen bonding interactions, and electrochemical manipulation of interfacial bonding. In this Perspective, we briefly review recent progress in the field, and we discuss how interfacial electrochemistry can vary interfacial forces by concerted tuning of surface charging, hydration forces, and tuning of the interfacial ion concentration. We further discuss open questions, controversial findings, and new paths into understanding and utilizing redox-proteins and derived polymers for enhancing underwater adhesion in a complex salt environment.

How sensitive are physical properties of choline chloride-urea mixtures to composition changes: Molecular dynamics simulations and Kirkwood-Buff theory.

Deep eutectic solvents (DESs) have emerged as a cheaper and greener alternative to conventional organic solvents. Choline chloride (ChCl) mixed with urea at a molar ratio of 1:2 is one of the most common DESs for a wide range of applications such as electrochemistry, material science, and biochemistry. In this study, molecular dynamics simulations are performed to study the effect of urea content on the thermodynamic and transport properties of ChCl and urea mixtures. With increased mole fraction of urea, the number of hydrogen bonds (HBs) between cation-anion and ion-urea decreases, while the number of HBs between urea-urea increases. Radial distribution functions (RDFs) for ChCl-urea and ChCl-ChCl pairs shows a significant decrease as the mole fraction of urea increases. Using the computed RDFs, Kirkwood-Buff Integrals (KBIs) are computed. KBIs show that interactions of urea-urea become stronger, while interactions of urea-ChCl and ChCl-ChCl pairs become slightly weaker with increasing mole fraction of urea. All thermodynamic factors are found larger than one, indicating a non-ideal mixture. Our results also show that self- and collective diffusivities increase, while viscosities decrease with increasing urea content. This is mainly due to the weaker interactions between ions and urea, resulting in enhanced mobilities. Ionic conductivities exhibit a non-monotonic behavior. Up to a mole fraction of 0.5, the ionic conductivities increase with increasing urea content and then reach a plateau.

Thermodynamic, transport, and structural properties of hydrophobic deep eutectic solvents composed of tetraalkylammonium chloride and decanoic acid.

With the emergence of hydrophobic deep eutectic solvents (DESs), the scope of applications of DESs has been expanded to include situations in which miscibility with water is undesirable. Whereas most studies have focused on the applications of hydrophobic DESs from a practical standpoint, few theoretical works exist that investigate the structural and thermodynamic properties at the nanoscale. In this study, Molecular Dynamics (MD) simulations have been performed to model DESs composed of tetraalkylammonium chloride hydrogen bond acceptor and decanoic acid hydrogen bond donor (HBD) at a molar ratio of 1:2, with three different cation chain lengths (4, 7, and 8). After fine-tuning force field parameters, densities, viscosities, self-diffusivities, and ionic conductivities of the DESs were computed over a wide temperature range. The liquid structure was examined using radial distribution functions (RDFs) and hydrogen bond analysis. The MD simulations reproduced the experimental density and viscosity data from the literature reasonably well and were used to predict diffusivities and ionic conductivities, for which experimental data are scarce or unavailable. It was found that although an increase in the cation chain length considerably affected the density and transport properties of the DESs (i.e., yielding smaller densities and slower dynamics), no significant influence was observed on the RDFs and the hydrogen bonds. The self-diffusivities showed the following order for the mobility of the various components: HBD > anion > cation. Strong hydrogen bonds between the hydroxyl and carbonyl groups of decanoic acid and between the hydroxyl group of decanoic acid and chloride were observed to dominate the intermolecular interactions.

Brick-CFCMC: Open Source Software for Monte Carlo Simulations of Phase and Reaction Equilibria Using the Continuous Fractional Component Method.

We present a new molecular simulation code, Brick-CFCMC, for performing Monte Carlo simulations using state-of-the-art simulation techniques. The Continuous Fractional Component (CFC) method is implemented for simulations in the NVT/NPT ensembles, the Gibbs Ensemble, the Grand-Canonical Ensemble, and the Reaction Ensemble. Molecule transfers are facilitated by the use of fractional molecules which significantly improve the efficiency of the simulations. With the CFC method, one can obtain phase equilibria and properties such as chemical potentials and partial molar enthalpies/volumes directly from a single simulation. It is possible to combine trial moves from different ensembles. This enables simulations of phase equilibria in a system where also a chemical reaction takes place. We demonstrate the applicability of our software by investigating the esterification of methanol with acetic acid in a two-phase system.

Structural, Thermodynamic, and Transport Properties of Aqueous Reline and Ethaline Solutions from Molecular Dynamics Simulations.

Deep eutectic solvents (DESs) are a new generation of green solvents, which are considered an environmentally friendly alternative to ionic liquids and volatile organic compounds. The addition of controlled amounts of water to DESs has a significant effect on their microscopic structure and thus on their thermodynamic and transport properties. In this way, DESs can be modified, leading to solvents with improved characteristics. In this work, molecular dynamics (MD) simulations are performed to obtain a better understanding of the relation between the microscopic structure, molecular interactions, and thermophysical properties of aqueous reline and ethaline solutions at temperatures ranging from 303.15 to 363.15 K. For both reline and ethaline solutions, the hydrogen bond (HB) networks disappear with increasing mass fraction of water, and the intensity of radial distribution function (RDF) peaks decreases. For a mass fraction of water of 40%, most of the HBs between the compounds of reline and ethaline are broken, and DESs are fully dissolved in water. Consequently, a monotonic decrease in viscosities and an increase in self-diffusion coefficients are observed. Ionic conductivities show a nonmonotonic behavior with increasing water content. Up to 60% water mass fraction, the ionic conductivities increase with increasing water content. A further increase in the mass fraction of water decreases conductivities. For all studied systems, the HB network and the peaks of RDFs show relatively small changes for water mass fractions below 5% and beyond 40%. The MD results show that viscosities decrease with temperature, while diffusivities and ionic conductivities increase. The effect of the temperature on the structure of DES-water mixtures is negligible.

Estimation of heritability of feeding behaviour traits and their correlation with production traits in Finnish Yorkshire pigs.

A major proportion of the costs of pork production is related to feed. The feed conversion rate (FCR) or residual feed intake (RFI) is thus commonly included in breeding programmes. Feeding behaviour traits do not directly have economic value but, if correlated with production traits, can be used as auxiliary traits. The aim of this study was to estimate the heritability of feeding behaviour traits and their genetic correlations with production traits in the Finnish Yorkshire pig population. The data were available from 3,235 pigs. Feeding behaviour was measured as the number of visits per day (NVD), time spent in feeding per day (TPD), daily feed intake (DFI), time spent feeding per visit (TPV), feed intake per visit (FPV) and feed intake rate (FR). The test station phase was divided into five periods. Estimates of heritabilities of feeding behaviour traits varied from 0.17 to 0.47. Strong genetic correlations were obtained between behaviour traits in all periods. However, only DFI was strongly correlated with the production traits. Interestingly, a moderate positive genetic correlation was obtained between FR and backfat thickness (0.1-0.5) and between FR and average daily gain (0.3-0.4), depending on the period. Based on the results, there is no additional benefit from including feeding-related traits other than those commonly used (FCR and RFI) in the breeding programme. However, if correlated with animal welfare, the feeding behaviour traits could be valuable in the breeding programme.

A phenomenological continuum model for force-driven nano-channel liquid flows.

A phenomenological continuum model is developed using systematic molecular dynamics (MD) simulations of force-driven liquid argon flows confined in gold nano-channels at a fixed thermodynamic state. Well known density layering near the walls leads to the definition of an effective channel height and a density deficit parameter. While the former defines the slip-plane, the latter parameter relates channel averaged density with the desired thermodynamic state value. Definitions of these new parameters require a single MD simulation performed for a specific liquid-solid pair at the desired thermodynamic state and used for calibration of model parameters. Combined with our observations of constant slip-length and kinematic viscosity, the model accurately predicts the velocity distribution and volumetric and mass flow rates for force-driven liquid flows in different height nano-channels. Model is verified for liquid argon flow at distinct thermodynamic states and using various argon-gold interaction strengths. Further verification is performed for water flow in silica and gold nano-channels, exhibiting slip lengths of 1.2 nm and 15.5 nm, respectively. Excellent agreements between the model and the MD simulations are reported for channel heights as small as 3 nm for various liquid-solid pairs.

Convolutive bounded component analysis algorithms for independent and dependent source separation.

Bounded component analysis (BCA) is a framework that can be considered as a more general framework than independent component analysis (ICA) under the boundedness constraint on sources. Using this framework, it is possible to separate dependent as well as independent components from their mixtures. In this paper, as an extension of a recently introduced instantaneous BCA approach, we introduce a family of convolutive BCA criteria and corresponding algorithms. We prove that the global optima of the proposed criteria, under generic BCA assumptions, are equivalent to a set of perfect separators. The algorithms introduced in this paper are capable of separating not only the independent sources but also the sources that are dependent/correlated in both component (space) and sample (time) dimensions. Therefore, under the condition that the sources are bounded, they can be considered as extended convolutive ICA algorithms with additional dependent/correlated source separation capability. Furthermore, they have potential to provide improvement in separation performance, especially for short data records. This paper offers examples to illustrate the space-time correlated source separation capability through a copula distribution-based example. In addition, a frequency-selective Multiple Input Multiple Output equalization example demonstrates the clear performance advantage of the proposed BCA approach over the state-of-the-art ICA-based approaches in setups involving convolutive mixtures of digital communication sources.

TRAINER: a general-purpose trainable short biosequence classifer.

Classifying sequences is one of the central problems in computational biosciences. Several tools have been released to map an unknown molecular entity to one of the known classes using solely its sequence data. However, all of the existing tools are problem-specific and restricted to an alphabet constrained by relevant biological structure. Here, we introduce TRAINER, a new online tool designed to serve as a generic sequence classification platform to enable users provide their own training data with any alphabet therein defined. TRAINER allows users to select among several feature representation schemes and supervised machine learning methods with relevant parameters. Trained models can be saved for future use without retraining by other users. Two case studies are reported for effective use of the system for DNA and protein sequences; candidate effector prediction and nucleolar localization signal prediction. Biological relevance of the results is discussed.

Nano-positioning system for structural analysis of functional homomeric proteins in multiple conformations.

Proteins may undergo multiple conformational changes required for their function. One strategy used to estimate target-site positions in unknown structural conformations involves single-pair resonance energy transfer (RET) distance measurements. However, interpretation of inter-residue distances is difficult when applied to three-dimensional structural rearrangements, especially in homomeric systems. We developed a positioning method using inverse trilateration/triangulation to map target sites within a homomeric protein in all defined states, with simultaneous functional recordings. The procedure accounts for probe diffusion to accurately determine the three-dimensional position and confidence region of lanthanide LRET donors attached to a target site (one per subunit), relative to a single fluorescent acceptor placed in a static site. As first application, the method is used to determine the position of a functional voltage-gated potassium channel's voltage sensor. Our results verify the crystal structure relaxed conformation and report on the resting and active conformations for which crystal structures are not available.

Video-based tracking of single molecules exhibiting directed in-frame motion.

Trajectories of individual molecules moving within complex environments such as cell cytoplasm and membranes or semiflexible polymer networks provide invaluable information on the organization and dynamics of these systems. However, when such trajectories are obtained from a sequence of microscopy images, they can be distorted due to the fact that the tracked molecule exhibits appreciable directed motion during the single-frame acquisition. We propose a new model of image formation for mobile molecules that takes the linear in-frame motion into account and develop an algorithm based on the maximum likelihood approach for retrieving the position and velocity of the molecules from single-frame data. The position and velocity information obtained from individual frames are further fed into a Kalman filter for interframe tracking of molecules that allows prediction of the trajectory of the molecule and further improves the precision of the position and velocity estimates. We evaluate the performance of our algorithm by calculations of the Cramer-Rao Lower Bound, simulations, and model experiments with a piezo-stage. We demonstrate tracking of molecules moving as fast as 7 pixels/frame (12.6 µm/s) within a mean error of 0.42 pixel (37.43 nm).

Primary carcinoma of the neovagina: a case report.

We present a case of squamous cell carcinoma arising in the neovagina of a woman in whom we performed vaginoplasty 20 years before. To the best of our knowledge, this is the 23rd case of total carcinoma arising in the neovagina constructed because of vaginal agenesis, and the 3nd case of carcinoma arising in the neovagina performed without using a graft.

Cutaneous rhinosporidiosis presents with recurrent nasal philtrum mass in southern Turkey.

We report a case of cutaneous rhinosporidiosis localized in the nasal philtrum. The patient's complaints started 3 months prior to being seen in our clinics. Ear, nose, and throat examination showed the presence of a polypoid lesion filling the right nostril. Complete surgical resection of the polypoid lesion provided a temporary relief as the patient developed the same lesion atin 6 weeks post-operation. The appearance and the recurrence pattern have led us to determine whether this lesion was rhinosporidiosis. Histopathological examination confirmed rhinosporidiosis. Finally, we performed complete resection followed by cauterization of the base of the mass. The infection has been reported in hot, tropical climates, and endemic zones of India and Sri Lanka. To our knowledge there is no reported case of rhinosporidiosis from southern Turkey within the subtropical Mediterranean climatic area.

Validation of the Gifted Rating Scales-School Form in China.

The Gifted Rating Scales-School Form (GRS-S), a teacher-completed rating scale, is designed to identify five types of giftedness and motivation. This study examines the reliability and validity of a Chinese-translated version of the GRS-S with a sample of Chinese elementary and middle school students (N = 499). The Chinese GRSS was found to have high internal consistency. Results of the confirmatory factor analysis corroborated the six-factor solution of the original GRS-S. Comparison of the GRS-S scores and measures of academic performance provide preliminary support for the criterion validity of the Chinese-translated GRS-S. Significant age and gender differences on the Chinese GRS-S were found. Results provide preliminary support for the Chinese version of the GRS-S as a reliable and valid measure of giftedness for Chinese students.

Detection of micrometastatic tumor cells in head and neck squamous cell carcinoma. A possible predictor of recurrences?

OBJECTIVE: To evaluate the presence of micrometastatic tumor cells in the peripheral blood samples of the patients with head and neck squamous cell carcinoma (HNSCC) and to determine whether the presence of micrometastatic cells had any biological relevance in terms of local recurrences or metastasis during a follow-up period of 3 years. METHODS: We included 21 consecutive patients with untreated primary HNSCC admitted to the Ear Nose and Throat Department of Akdeniz University Medical School, Antalya, Turkey between February and October 2002. Squamous carcinoma cells in peripheral blood samples of these patients prior to surgery were detected via a magnetic cell separation technique using anti-epithelial cell adhesion molecule antibody, and thereafter evaluated by light microscopy with hematoxylin and eosin staining. RESULTS: Seven out of 21 patients showed squamous carcinoma cells in peripheral blood samples. Patients with stage III and IV tumors were nearly 5 times more likely to show micrometastatic cells compared with those with stage I and II tumors (6/12 versus 1/9). During the follow-up, 2 patients out of 7 with micrometastasis had recurrences. None in the micrometastasis negative group relapsed. CONCLUSION: We suggest that HNSCC patients with detectable tumor cells in peripheral blood represent a subset of patients who should be followed up more closely for possible recurrences.