Miracle-dz/UniFAR-FTUs huggingface dataset:
The effect of multi-strain probiotics as feed additives on performance, immunity, expression of nutrient transporter genes and gut morphometry in broiler chickens

Objective This study was conducted to investigate the effects of dietary multi-strain probiotic (MSP) (Bacillus coagulans Unique IS2 + Bacillus subtillis UBBS14 + Saccharomyces boulardii Unique 28) on performance, gut morphology and expression of nutrient transporter related genes in broiler chickens. Methods A total of 256 (4×8×8) day-old CARIBRO Vishal commercial broiler chicks of uniform body weight were randomly distributed into four treatments with 8 replicates each and having eight chicks in each replicate. Four dietary treatments were T1 (negative control-basal diet), T2 (positive control-antibiotic bacitracin methylene disalicylate at 20 mg/kg diet), T3 (MSP at 107 colony-forming unit [CFU]/g feed), and T4 (MSP at 108 CFU/g feed). Results During 3 to 6 weeks and 0 to 6 weeks, the body weight gain increased significantly (p<0.05) in T3 and T4 groups. The feed intake significantly (p<0.05) reduced from T1 to T3 during 0 to 3 weeks and the feed conversion ratio also significantly (p<0.05) improved in T3 and T4 during 0 to 6 weeks. The humoral and cell mediated immune response and the weight of immune organs were also significantly (p<0.05) improved in T3 and T4. However, significant (p<0.05) dietary effects were observed on intestinal histo-morphometry of ileum in T3 followed by T4 and T2. At 14 d post hatch, the relative gene expression of glucose transporter (GLUT5), sodium-dependent glucose transporter (SGLT1) and peptide transporter (PepT1) showed a significant (p<0.05) up-regulating pattern in T2, T3, and T4. Whereas, at 21 d post hatch, the gene expression of SGLT1 and PepT1 was significantly (p<0.05) down-regulated in MSP supplemented treatments T3 and T4. Conclusion The supplementation of MSP at 107 CFU/g diet showed significant effects with improved performance, immune response, gut morphology and expression of nutrient transporter genes. Thus, the MSP could be a suitable alternative to antibiotic growth promoters in chicken diets.
Synergistic effects of D-arginine, D-methionine and D-histidine against Porphyromonas gingivalis biofilms

Abstract Porphyromonas gingivalis biofilms are implicated in the pathology of peri-implantitis and periodontitis. In this study, D-arginine (R), D-methionine (M), D-histidine (H), and a mixture of these D-amino acids (D-AAs) were investigated as an effective therapeutic strategy against P. gingivalis biofilms. The bacterial growth activity and minimum inhibitory concentrations were determined for each D-AA, along with the effects of the D-AAs mixture on biofilm development, morphology, structure, extracellular polysaccharides (EPS), cytotoxicity towards commensals, and bacterial structure. The D-AA mixture delayed the proliferation of P. gingivalis, changed its membrane structure, and decreased biofilm thickness and integrity, as compared with individual D-AAs. The EPS content increased with the concentration of D-AAs. The present study shows that a 4 mM RMH, triple D-AA mixture, enhanced deleterious effects on P. gingivalis biofilms without any cytotoxicity compared with individual D-AAs, thus providing a new strategy for the treatment of peri-implantitis and periodontitis.
The Effect of Anodal Transcranial Direct Current Stimulation on Quadriceps Maximal Voluntary Contraction, Corticospinal Excitability, and Voluntary Activation Levels

Abstract Kristiansen, M, Thomsen, MJ, Nørgaard, J, Aaes, J, Knudsen, D, and Voigt, M. The effect of anodal transcranial direct current stimulation on quadriceps maximal voluntary contraction, corticospinal excitability, and voluntary activation levels. J Strength Cond Res 36(6): 1540–1547, 2022—Anodal transcranial direct current stimulation (a-tDCS) has previously been shown to improve maximal isometric voluntary contraction (MVIC), possibly through an upregulation of corticospinal excitability. Because muscle strength is an essential part of the performance of many sports, any ergogenic effect of a-tDCS on this parameter could potentially increase performance outcomes. The purpose of this study was to investigate the effect of a-tDCS on MVIC, voluntary activation levels (VALs), and corticospinal excitability, assessed by eliciting motor-evoked potentials (MEPs), in untrained subjects. Thirteen subjects completed 2 test sessions in which they received either a-tDCS or sham stimulation for 3 consecutive intervals of 10 minutes, separated by 5-minute breaks. Before and after each stimulation session, transcranial magnetic stimulation was used to elicit MEPs, and femoral nerve stimulation was used to assess VAL by measuring twitch torque during an MVIC test and in a relaxed state. Two-way analyses of variance with statistical significance set at p ≤ 0.05 were used to test for differences. A significant main effect was identified, as the MVIC pre-test (271.2 ± 56.6 Nm) was on average 4.1% higher compared to the post-test (260.6 ± 61.4 Nm) (p = 0.05). No significant differences were found in MEP, MVIC, or VAL as a result of stimulation type or time. In healthy subjects, the potential for improvement in corticospinal excitability may be negligible, which may in turn explain the lack of improvements in MEP, MVIC, and VAL after a-tDCS. The small decrease in MVIC for both conditions and nonsignificant changes in MEP and VAL do not justify the use of a-tDCS in combination with sporting performance in which the intent is to increase maximal isometric strength performance in the quadriceps muscle of healthy subjects.
The Role of πσ* Excited States in the Photodissociation of Heteroaromatic Molecules

High-resolution measurements of the kinetic energies of hydrogen atom fragments formed during ultraviolet photolysis of imidazole, pyrrole, and phenol in the gas phase confirm that N(O)–H bond fission is an important nonradiative decay process from their respective 1πσ* excited states. The measurements also reveal that the respective cofragments (imidazolyl, pyrrolyl, and phenoxyl) are formed in very limited subsets of their available vibrational states. Identification of these product states yields uniquely detailed insights into the vibronic couplings involved in the photoinduced evolution from parent molecule to ultimate fragments.
Seasonal dynamics of dimethylarsinic-acid-decomposing bacteria dominating in Lake Kahokugata

Decomposition processes of organoarsenic compounds significantly influence arsenic cycles in aquatic environments, and such processes depend on bacterial activity. However, the bacterial characteristics in these environments are obscure. Accordingly, we observed seasonal variations of arsenic species and the bacterial population decomposing dimethylarsinic acid (DMAA) in Lake Kahokugata from April 2002 to January 2003. Monitoring of bacterial biomass involving DMAA decomposition using the most probable number procedure showed that the bacterial cell densities ranged from 36 to 3600 ml -1 . On the other hand, methylated arsenic was not detected during the experimental period, although the inorganic arsenic concentration was over 4 nM. This suggests that bacteria remineralized methylated arsenic species to inorganic arsenic. Furthermore, the composition of bacterial communities involving DMAA decomposition was examined by restriction-fragment-length polymorphism analysis of the 16S rDNA nucleotide. As a result, a total of 49 isolates were classified into 10 type groups, and 32 of these isolates belonged to three dominant type groups. Phylogenetic analysis using 16S rDNA partial sequences (ca 320 bp) suggests that the representative isolates of the dominant type groups are specific to the summer or winter season. Moreover, as a result of the culture experiments to examine DMAA decomposition activity, the representative isolates decomposed 1 μM DMAA at a decomposition percentage of below 80%. In conclusion, some bacterial communities in a specific season can decompose DMAA to varying degrees, contributing to the annual cycle of arsenic species.
The Study of Molecular Interactions by AFM Force Spectroscopy

Recent progress in atomic force microscopy (AFM) technology has allowed the measurement of inter- and intramolecular forces at the level of individual molecules. The mechanical manipulation of single polymer chains immobilized on solid substrates has become possible in solution, as they are spanned and stretched between the tip of an AFM cantilever and the substrate surface. This investigation of polymer chains far from their maximum entropy configurations has stimulated the refinement of existing polymer theories. From the measured force-distance curves quantitative information can be obtained on the elasticity of single macromolecules in solution, on conformational transitions along the chains, about the mechanical stability of chemical bonds and on secondary structures, as well as on the desorption of individual polymer molecules from solid substrates. Recent applications of AFM single molecule force spectroscopy reach from the study of dynamic processes in complex biological systems and intermolecular forces in colloidal systems to the investigation of new functional materials capable of performing energy transductions on the level of individual macromolecules. In this article, we present a detailed description of the experimental procedure, followed by an overview of the development, the success and the current challenges of this technique during the past five years, in which it has rapidly evolved from the first proof of principle to a highly active field of research.
Molecular cytogenetic analysis of a triploid population of the human broad tapeworm, Dibothriocephalus latus (Diphyllobothriidea)

Abstract Abstract The large-sized tapeworm Dibothriocephalus latus is known as the broad or fish-borne cestode of mammals that is capable to infect humans and cause diphyllobothriosis. Recently, molecular data on D. latus has been accumulating in the literature and a complete genome sequence has been published; however, little is known about the karyotype and chromosome architecture. In this study, an in-depth karyological analysis of 2 D. latus specimens was carried out. The plerocercoids originated from a perch caught in subalpine Lake Iseo (Italy) and the tapeworms were reared in hamsters. Both specimens contained cells with a highly variable number of chromosomes ranging from18 to 27. Nevertheless, the largest portion of mitotic figures (47%) showed a number corresponding to the triploid set, 3n = 27. Accordingly, the karyotype of the analyzed specimens consisted of 9 triplets of metacentric chromosomes. Fluorescence in situ hybridization (FISH) with the 18S rDNA probe clearly demonstrated the presence of 3 clusters of hybridization signals on the triplet of chromosome 7, thus confirming the triploid status of the specimens. FISH with a telomeric (TTAGGG)n probe confined hybridization signals exclusively to the terminal chromosomal regions, supporting the earlier findings that this repetitive motif is a conserved feature of tapeworm telomeres.
Different co‐occurring bacteria enhance or decrease the growth of the microalga Nannochloropsis sp. CCAP211/78

Marine photosynthetic microalgae are ubiquitously associated with bacteria in nature. However, the influence of these bacteria on algal cultures in bioreactors is still largely unknown. In this study, eighteen different bacterial strains were isolated from cultures of Nannochloropsis sp. CCAP211/78 in two outdoor pilot‐scale tubular photobioreactors. The majority of isolates was affiliated with the classes Alphaproteobacteria and Flavobacteriia. To assess the impact of the eighteen strains on the growth of Nannochloropsis sp. CCAP211/78, 24‐well plates coupled with custom‐made LED boxes were used to simultaneously compare replicate axenic microalgal cultures with addition of individual bacterial isolates. Co‐culturing of Nannochloropsis sp. CCAP211/78 with these strains demonstrated distinct responses, which shows that the technique we developed is an efficient method for screening the influence of harmful/beneficial bacteria. Two of the tested strains, namely a strain of Maritalea porphyrae (DMSP31) and a Labrenzia aggregata strain (YP26), significantly enhanced microalgal growth with a 14% and 12% increase of the chlorophyll concentration, respectively, whereas flavobacterial strain YP206 greatly inhibited the growth of the microalga with 28% reduction of the chlorophyll concentration. Our study suggests that algal production systems represent a ‘natural’ source to isolate and study microorganisms that can either benefit or harm algal cultures.
A Joint Model for Macular Edema Analysis in Optical Coherence Tomography Images Based on Image Enhancement and Segmentation

Optical coherence tomography (OCT) provides the visualization of macular edema which can assist ophthalmologists in the diagnosis of ocular diseases. Macular edema is a major cause of vision loss in patients with retinal vein occlusion (RVO). However, manual delineation of macular edema is a laborious and time-consuming task. This study proposes a joint model for automatic delineation of macular edema in OCT images. This model consists of two steps: image enhancement using a bioinspired algorithm and macular edema segmentation using a Gaussian-filtering regularized level set (SBGFRLS) algorithm. We then evaluated the delineation efficiency using the following parameters: accuracy, precision, sensitivity, specificity, Dice's similarity coefficient, IOU, and kappa coefficient. Compared with the traditional level set algorithms, including C-V and GAC, the proposed model had higher efficiency in macular edema delineation as shown by reduced processing time and iteration times. Moreover, the accuracy, precision, sensitivity, specificity, Dice's similarity coefficient, IOU, and kappa coefficient for macular edema delineation could reach 99.7%, 97.8%, 96.0%, 99.0%, 96.9%, 94.0%, and 96.8%, respectively. More importantly, the proposed model had comparable precision but shorter processing time compared with manual delineation. Collectively, this study provides a novel model for the delineation of macular edema in OCT images, which can assist the ophthalmologists for the screening and diagnosis of retinal diseases.
Light-Induced Change of Arginine Conformation Modulates the Rate of Adenosine Triphosphate to Cyclic Adenosine Monophosphate Conversion in the Optogenetic System Containing Photoactivated Adenylyl Cyclase

We report the first computational characterization of an optogenetic system composed of two photosensing BLUF (blue light sensor using flavin adenine dinucleotide) domains and two catalytic adenylyl cyclase (AC) domains. Conversion of adenosine triphosphate (ATP) to the reaction products, cyclic adenosine monophosphate (cAMP) and pyrophosphate (PPi), catalyzed by ACs initiated by excitation in photosensing domains has emerged in the focus of modern optogenetic applications because of the request in photoregulated enzymes that modulate cellular concentrations of signaling messengers. The photoactivated AC from the soil bacterium Beggiatoa sp. (bPAC) is an important model showing a considerable increase in the ATP to cAMP conversion rate in the catalytic domain after the illumination of the BLUF domain. The 1 μs classical molecular dynamics simulations reveal that the activation of the BLUF domain leading to tautomerization of Gln49 in the chromophore-binding pocket results in switching of the position of the side chain of Arg278 in the active site of AC. Allosteric signal transmission pathways between Gln49 from BLUF and Arg278 from AC were revealed by the dynamical network analysis. The Gibbs energy profiles of the ATP → cAMP + PPi reaction computed using QM(DFT(ωB97X-D3/6-31G**))/MM(CHARMM) molecular dynamics simulations for both Arg278 conformations in AC clarify the reaction mechanism. In the light-activated system, the corresponding arginine conformation stabilizes the pentacoordinated phosphorus of the α-phosphate group in the transition state, thus lowering the activation energy. Simulations of the bPAC system with the Tyr7Phe replacement in the BLUF demonstrate occurrence of both arginine conformations in an equal ratio, explaining the experimentally observed intermediate catalytic activity of the bPAC-Y7F variant as compared with the dark and light states of the wild-type bPAC.
Hepatoprotection of Lycii Fructus Polysaccharide against Oxidative Stress in Hepatocytes and Larval Zebrafish

Scavenging of oxidative stress by antioxidants may provide a therapeutic strategy for nonalcoholic fatty liver disease (NAFLD). Increasing evidence is supporting the potential application of natural resourced polysaccharides as promising prevention or treatment strategies against NAFLD. In the current study, an acidic heteropolysaccharide, LFP-a1, was isolated and purified from Lycii fructus with successively hot water refluxing extraction, alcohol precipitation, protein removal, and DEAE-52 cellulose chromatographic separation. LFP-a1 was a complicated structured polysaccharide with an average MW of 4.74 × 104 Da and composed of 6 monosaccharides and 1 uronic acid. Preexposure of LFP-a1 could increase the cell viability and reverse the abnormal oxidative stress though inhibition of mitochondrial-mediated apoptotic pathway and correction of cell cycle progression against H2O2 hepatoxicity in NAFLD model L02 cells. Consistently, in vivo study in thioacetamide- (TAA-) induced NAFLD model zebrafish larvae showed LFP-a1 preserved the liver integrity and alleviated TAA-induced oxidative stress through downregulation of abnormal apoptosis. These observations indicated the hepatoprotective activity of LFP-a1, which may be applied for the prevention or treatment of NAFLD or other oxidative stress-related diseases.
Evolution of the structure, microstructure and physical properties of RuSr2GdCu2O8 as a function of the thermal treatment

The crystal structure of RuSr2GdCu2O8 was successfully refined in the orthorhombic system (Pbam space group) using synchrotron powder diffraction data collected on a high purity and low defect containing sample. The microstructures of selected samples submitted to different thermal treatments were investigated by means of TEM analysis: the progressive annealing in an O2 atmos phere suppresses the formation of nano-domains and extended planar defects, whereas annealing under vacuum favours the formation of extended planar defects and nano-domains as well. Lattice parameters increase with the anneling time, whereas an abrupt decrease of the c parameter occurs after de-oxygenation. A dependence of magnetization and superconductivity on the thermal treatment was evidenced and related to the structural and microstructural changes.
Estimating counterfactuals for evaluation of ecological and conservation impact: an introduction to matching methods

Matching methods encompass non‐parametric approaches to estimating counterfactual states through a rigorous selection of control units with similar characteristics to units submitted to an intervention. These methods enable comparisons between treated and control units in a way that facilitates understanding of causal relationships between interventions and outcomes. Matching methods have been used only recently in ecology and conservation biology, where such applications changed the way the field investigates causal questions, for example, in impact‐evaluation studies. However, the strengths and limitations of matching methods are not well understood by most ecologists and environmental scientists. Herein, we review state‐of‐the‐art matching methods aiming to help fill this gap in understanding. First, we present relevant theoretical concepts related to matching methods and related subjects such as counterfactual states and causation. Next, we propose guidelines and strategies for the application of matching methods in ecology and conservation biology. Finally, we discuss the possibilities for future applications of matching methods in the environmental sciences.
Financial Impact of Inaccurate Coding Plus Cost-Effectiveness Analysis for Surgically Managed Patients With Periprosthetic Fractures

Background An upward trend is seen in a number of periprosthetic fractures. Their management often requires complex surgical intervention, expert skills and expensive equipment. Hospitals get paid according to Healthcare Resource Group (HRG) tariffs. HRG gets generated once diagnoses, Charlson comorbidity (CC) index score, surgical procedures, investigations and length of stay have been coded for. Coding departments consist of non-clinicians. Although auditing systems are in and made of internal and external auditors, we hypothesized that multiple errors can still occur which may result in significant financial losses. Objectives To assess the accuracy of coding for management of periprosthetic fractures. To identify causes for inaccurate coding and assess the financial impact of highly complex trauma in a district general hospital (DGH). Methods Retrospective comparative analysis of case notes for patients with an M966 diagnosis code (periprosthetic fracture) between 1st November 2017 and 1st November 2018. All cases were analysed and data for primary procedure, primary diagnosis, secondary procedures and secondary diagnosis, comorbidities and length of stay were extrapolated and re-coded using the same software in use by the coding team. Costs incurred for each surgically managed patient were calculated using a rough estimate of cost of each procedure. Finally, cost-effectiveness analysis was carried out by comparing our calculated figures to the actual final claim by our institution. Results Twenty-nine patients with the diagnosis of periprosthetic fracture were identified by the coding team using M966 code. A further case was identified by reviewing operating software (Operating Room Management Information System [ORMIS®]). In four cases (13.3 %), the primary diagnosis was coded incorrectly by the coding team. Overall coders accuracy for surgically managed patients (n=21) was 52% (n=11). This resulted in an estimated incurred loss of £25,000. Wrong/omitted site of surgery was found to be the most influential coder error with up to £8000 loss in one case (P<0.05). Cost-effectiveness analysis demonstrated the stark differences in costs for HRG tariffs when used in trauma setting vs non-trauma setting. Open reduction and internal fixation (ORIF) was associated with less financial loss to our trust with closer procedural costs to HRG tariff (average cost of £9200 for ORIF vs £22,030 for a massive endoprosthesis). Conclusions Surgeons should carefully review codes for such complex procedures before or soon after surgery. Wrong/omitted site of surgery is the key cause for losses in our cohort, followed by inadequate recording of comorbidities. Coders can only code for what is documented. Following cost-effectiveness analysis our study highlights the need for HRG tariffs to be revised for such procedures. The cost of ORIF vs massive endoprosthesis should be noted, signifying the implant costs when such specialised revision surgery performed over less expensive ORIF surgery.