Miracle-dz/UniFAR-FTUs huggingface dataset:
Calcium Prevents Biofilm Dispersion in Bacillus subtilis

Bacteria growing as biofilms are notoriously difficult to eradicate and sometimes pose serious threats to public health. Bacteria escape from biofilms by degrading them when biofilm conditions deteriorate. ABSTRACT Biofilm dispersion is the final stage of biofilm development, during which biofilm cells actively escape from biofilms in response to deteriorating conditions within the biofilm. Biofilm dispersion allows cells to spread to new locations and form new biofilms in better locations. However, dispersal mechanisms have been elucidated only in a limited number of bacteria. Here, we investigated biofilm dispersion in Bacillus subtilis. Biofilm dispersion was clearly observed when B. subtilis was grown under static conditions in modified LB medium containing glycerol and manganese. Biofilm dispersion was synergistically caused by two mechanisms: decreased expression of the epsA operon encoding exopolysaccharide synthetases and the induction of sporulation. Indeed, constitutive expression of the epsA operon in the sporulation-defective ΔsigK mutant prevented biofilm dispersion. The addition of calcium to the medium prevented biofilm dispersion without significantly affecting the expression of the epsA operon and sporulation genes. In synthetic medium, eliminating calcium did not prevent the expression of biofilm matrix genes and, thereby, biofilm formation, but it attenuated biofilm architecture. These results indicate that calcium structurally stabilizes biofilms and causes resistance to biofilm dispersion mechanisms. Sporulation-dependent biofilm dispersion required the spoVF operon, encoding dipicolinic acid (DPA) synthase. During sporulation, an enormous amount of DPA is synthesized and stored in spores as a chelate with calcium. We speculate that, during sporulation, calcium bound to biofilm matrix components may be transported to spores as a calcium-DPA complex, which weakens biofilm structure and leads to biofilm dispersion. IMPORTANCE Bacteria growing as biofilms are notoriously difficult to eradicate and sometimes pose serious threats to public health. Bacteria escape from biofilms by degrading them when biofilm conditions deteriorate. This process, called biofilm dispersion, has been studied as a promising strategy for safely controlling biofilms. However, the regulation and mechanism of biofilm dispersion has been elucidated only in a limited number of bacteria. Here, we identified two biofilm dispersion mechanisms in the Gram-positive, spore-forming bacterium Bacillus subtilis. The addition of calcium to the medium stabilized biofilms and caused resistance to dispersal mechanisms. Our findings provide new insights into biofilm dispersion and biofilm control.
Influence of Sintering Temperature of Kaolin, Slag, and Fly Ash Geopolymers on the Microstructure, Phase Analysis, and Electrical Conductivity

This paper clarified the microstructural element distribution and electrical conductivity changes of kaolin, fly ash, and slag geopolymer at 900 °C. The surface microstructure analysis showed the development in surface densification within the geopolymer when in contact with sintering temperature. It was found that the electrical conductivity was majorly influenced by the existence of the crystalline phase within the geopolymer sample. The highest electrical conductivity (8.3 × 10−4 Ωm−1) was delivered by slag geopolymer due to the crystalline mineral of gehlenite (3Ca2Al2SiO7). Using synchrotron radiation X-ray fluorescence, the high concentration Ca boundaries revealed the appearance of gehlenite crystallisation, which was believed to contribute to development of denser microstructure and electrical conductivity.
Measuring how two proteins affect each other's net charge in a crowded environment

Theory predicts that the net charge (Z) of a protein can be altered by the net charge of a neighboring protein as the two approach one another below the Debye length. This type of charge regulation suggests that a protein's charge and perhaps function might be affected by neighboring proteins without direct binding. Charge regulation during protein crowding has never been directly measured due to analytical challenges. Here, we show that lysine specific protein crosslinkers (NHS ester‐Staudinger pairs) can be used to mimic crowding by linking two non‐interacting proteins at a maximal distance of ~7.9 Å. The net charge of the regioisomeric dimers and preceding monomers can then be determined with lysine‐acyl “protein charge ladders” and capillary electrophoresis. As a proof of concept, we covalently linked myoglobin (Zmonomer = −0.43 ± 0.01) and α‐lactalbumin (Zmonomer = −4.63 ± 0.05). Amide hydrogen/deuterium exchange and circular dichroism spectroscopy demonstrated that crosslinking did not significantly alter the structure of either protein or result in direct binding (thus mimicking crowding). Ultimately, capillary electrophoretic analysis of the dimeric charge ladder detected a change in charge of ΔZ = −0.04 ± 0.09 upon crowding by this pair (Zdimer = −5.10 ± 0.07). These small values of ΔZ are not necessarily general to protein crowding (qualitatively or quantitatively) but will vary per protein size, charge, and solvent conditions.
Comprehensive Enhancement in Thermomechanical Performance of Melt-Extruded PEEK Filaments by Graphene Incorporation

A simple and scalable fabrication process of graphene nanoplatelets (GnPs)-reinforced polyether ether ketone (PEEK) filaments with enhanced mechanical and thermal performance was successfully demonstrated in this work. The developed PEEK–GnP nanocomposite filaments by a melt-extrusion process showed excellent improvement in storage modulus at 30 °C (61%), and significant enhancement in tensile strength (34%), Young’s modulus (25%), and elongation at break (37%) when GnP content of 1.0 wt. % was used for the neat PEEK. Moreover, the GnPs addition to the PEEK enhanced the thermal stability of the polymer matrix. Improvement in mechanical and thermal properties was attributed to the improved dispersion of GnP inside PEEK, which could form a stronger/robust interface through hydrogen bonding and π–π* interactions. The obtained mechanical properties were also correlated to the mechanical reinforcement models of Guth and Halpin–Tsai. The GnP layers could form agglomerates as the GnP content increases (>1 wt.%), which would decline neat PEEK’s crystallinity and serve as stress concentration sites inside the composite, leading to a deterioration of the mechanical performance. The results demonstrate that the developed PEEK–GnP nanocomposites can be used in highly demanding engineering sectors like 3D printing of aerospace and automotive parts and structural components of humanoid robots and biomedical devices.
Prognostic Impact of APOBEC3B Expression in Metastatic Urothelial Carcinoma and Its Association with Tumor-Infiltrating Cytotoxic T Cells

APOBEC3B enzymes are endogenous carcinogenic mutagens. Metastatic urothelial carcinomas often harbor APOBEC3B-mediated mutations in which tCw to T or G substitution occurs. Here, we evaluated patient survival and CD8+ T-cell density according to APOBEC3B expression in patients with metastatic urothelial carcinoma who underwent cytotoxic chemotherapy. We performed a retrospective study on 94 patients with urothelial carcinoma who were treated with first line palliative chemotherapy. APOBEC3B expression and CD8+/CD3+ ratio of tumor-infiltrating lymphocytes were evaluated using immunohistochemistry. Kaplan–Meier survival curves were generated and the log-rank test was employed. The association between APOBEC3B expression and tumor-infiltrating lymphocytes was analyzed using Pearson’s chi-squared test. High APOBEC3B expression was detected in 71 of the 94 patients (75.5%). The median overall survival was longer in patients with high APOBEC3B expression (15 months) than in those with low expression (p = 0.045). The hazard ratio obtained based on the Cox regression analysis was 0.292 (95% confidence interval 0.118–0.723, p = 0.008). APOBEC3B expression was associated with the CD8+/CD3+ ratio (2.914, 95% confidence interval 1.030–8.249, p = 0.039). Collectively, APOBEC3B expression was an independent prognostic factor in patients with metastatic urothelial carcinoma treated with platinum-based chemotherapy. Tumor-infiltrating cytotoxic T cells were associated with APOBEC3B expression.
Effects of slaughter age on carcass traits and meat quality of crossbred (Duroc × Landrace × Yorkshire) finishing pigs

Abstract Thirty castrated Duroc × Landrace × Yorkshire (DLY) pigs were randomly divided into three groups and slaughtered at 180, 210, and 240 days of age, respectively. Here, we found that the live weight, carcass weight, carcass length, dressing percentage, eye muscle area, backfat deposit, muscle yellowness b* value, drip loss, and cooking loss increased significantly, and the muscle pH 45 min value decreased dramatically as the slaughter age of DLY pigs extended. Moreover, increasing the slaughter age of DLY pigs could obtain higher n-3 polyunsaturated fatty acid (PUFA) percentage, crude protein, essential amino acids (EAA) contents and EAA/NEAA level, and lower n-6/n-3 PUFA level and antioxidant capacity. Together, this study suggests that the older slaughter age improves the carcass traits and nutritional value of pork, but leads to a significant decrease in pork sensory quality in DLY finishing pigs.
Device Modeling and Design of Inverted Solar Cell Based on Comparative Experimental Analysis between Effect of Organic and Inorganic Hole Transport Layer on Morphology and Photo-Physical Property of Perovskite Thin Film

It is crucial to find a good material as a hole transport layer (HTL) to improve the performance of perovskite solar cells (PSCs), devices with an inverted structure. Polyethylene dioxythiophene-poly (styrene sulfonate) (PEDOT:PSS) and inorganic nickel oxide (NiOx) have become hotspots in the study of hole transport materials in PSCs on account of their excellent properties. In our research, NiOx and PEDOT: PSS, two kinds of hole transport materials, were prepared and compared to study the impact of the bottom layer on the light absorption and morphology of perovskite layer. By the way, some experimental parameters are simulated by wx Analysis of Microelectronic and Photonic Structures (wxAMPS). In addition, thin interfacial layers with deep capture levels and high capture cross sections were inserted to simulate the degradation of the interface between light absorption layer and PEDOT:PSS. This work realizes the combination of experiment and simulation. Exploring the mechanism of the influence of functional layer parameters plays a vital part in the performance of devices by establishing the system design. It can be found that the perovskite film growing on NiOx has a stronger light absorption capacity, which makes the best open-circuit voltage of 0.98 V, short-circuit current density of 24.55 mA/cm2, and power conversion efficiency of 20.01%.
Surface-Mounted Bare and Packaged Fiber Bragg Grating Sensors for Measuring Rock Strain in Uniaxial Testing

The paper explores the possibility of using high-resolution fiber Bragg grating (FBG) sensing technology for on-specimen strain measurement in the laboratory. The approach provides a means to assess the surface deformation of the specimen, both the axial and radial, through a chain of FBG sensor (C-FBG), in a basic setup of a uniaxial compression test. The method is cost-effective, straightforward and can be commercialized. Two C-FBG; one was applied directly to the sample (FBGBare), and the other was packaged (FBGPack) for ease of application. The approach measures the local strain with high-resolution and accuracy levels that match up to the existing local strain measuring sensors. The approach enables the evaluation of small-strain properties of the specimen intelligently. The finite element model analysis deployed has proven the adaptability of the technique for measuring material deformation. The adhesive thickness and packaging technique have been shown to influence the sensitivity of the FBG sensors. Owing to the relative ease and low-cost of instrumentation, the suggested method has a great potential to be routinely applied for elemental testing in the laboratory.
Mechanisms of High-Grade Serous Carcinogenesis in the Fallopian Tube and Ovary: Current Hypotheses, Etiologic Factors, and Molecular Alterations

Ovarian high-grade serous carcinomas (HGSCs) are a heterogeneous group of diseases. They include fallopian-tube-epithelium (FTE)-derived and ovarian-surface-epithelium (OSE)-derived tumors. The risk/protective factors suggest that the etiology of HGSCs is multifactorial. Inflammation caused by ovulation and retrograde bleeding may play a major role. HGSCs are among the most genetically altered cancers, and TP53 mutations are ubiquitous. Key driving events other than TP53 mutations include homologous recombination (HR) deficiency, such as BRCA 1/2 dysfunction, and activation of the CCNE1 pathway. HR deficiency and the CCNE1 amplification appear to be mutually exclusive. Intratumor heterogeneity resulting from genomic instability can be observed at the early stage of tumorigenesis. In this review, I discuss current carcinogenic hypotheses, sites of origin, etiologic factors, and molecular alterations of HGSCs.
Virulence Determinants and Antimicrobial Profiles of Pasteurella multocida Isolated from Cattle and Humans in Egypt

Pasteurella multocida is a Gram-negative bacterium that causes drastic infections in cattle and humans. In this study, 55 isolates were recovered from 115 nasal swabs from apparently healthy and diseased cattle and humans in Minufiya and Qalyubia, Egypt. These isolates were confirmed by kmt1 existence, and molecular classification of the capsular types showed that types B, D, and E represented 23/55 (41.8%), 21/55 (38.1%), and 11/55 (20.0%), respectively. The isolates were screened for five virulence genes with hgbA, hgbB, and ptfA detected in 28/55 (50.9%), 30/55 (54.5%), and 25/55 (45.5%), respectively. We detected 17 capsular and virulence gene combinations with a discriminatory power (DI) of 0.9286; the most prevalent profiles were dcbF type D and dcbF type D, hgbA, hgbB, and ptfA, which represented 8/55 (14.5%) each. These strains exhibited high ranges of multiple antimicrobial resistance indices; the lowest resistances were against chloramphenicol, ciprofloxacin, amoxicillin/clavulanic acid, and levofloxacin. The macrolide–lincosamide–streptogramin B methylase gene erm(Q), with erm(42) encoding MLSB monomethyltransferase, mph(E) encoding a macrolide efflux pump, and msr(E) encoding macrolide-inactivating phosphotransferase were present. The class 1 and 2 integrons and extended-spectrum β-lactamase genes intl1, intl2, blaCTX-M, blaCTX-M-1, and blaTEM were detected. It is obvious to state that co-occurrence of resistance genes resulted in multiple drug-resistant phenotypes. The identified isolates were virulent, genetically diverse, and resistant to antimicrobials, highlighting the potential risk to livestock and humans.
High-Pressure Processing for the Production of Added-Value Claw Meat from Edible Crab (Cancer pagurus)

High-pressure processing (HPP) in a large-scale industrial unit was explored as a means for producing added-value claw meat products from edible crab (Cancer pagurus). Quality attributes were comparatively evaluated on the meat extracted from pressurized (300 MPa/2 min, 300 MPa/4 min, 500 MPa/2 min) or cooked (92 °C/15 min) chelipeds (i.e., the limb bearing the claw), before and after a thermal in-pack pasteurization (F9010 = 10). Satisfactory meat detachment from the shell was achieved due to HPP-induced cold protein denaturation. Compared to cooked or cooked–pasteurized counterparts, pressurized claws showed significantly higher yield (p < 0.05), which was possibly related to higher intra-myofibrillar water as evidenced by relaxometry data, together with lower volatile nitrogen levels. The polyunsaturated fatty acids content was unaffected, whereas the inactivation of total viable psychrotrophic and mesophilic bacteria increased with treatment pressure and time (1.1–1.9 log10 CFU g−1). Notably, pressurization at 300 MPa for 4 min resulted in meat with no discolorations and, after pasteurization, with high color similarity (ΔE* = 1.2–1.9) to conventionally thermally processed samples. Following further investigations into eating quality and microbiological stability, these HPP conditions could be exploited for producing uncooked ready-to-heat or pasteurized ready-to-eat claw meat products from edible crab.
Detection of the Anaerobic Threshold in Endurance Sports: Validation of a New Method Using Correlation Properties of Heart Rate Variability

Past attempts to define an anaerobic threshold (AnT) have relied upon gas exchange kinetics, lactate testing and field-based evaluations. DFA a1, an index of heart rate (HR) variability (HRV) fractal correlation properties, has been shown to decrease with exercise intensity. The intent of this study is to investigate whether the AnT derived from gas exchange is associated with the transition from a correlated to uncorrelated random HRV pattern signified by a DFA a1 value of 0.5. HRV and gas exchange data were obtained from 15 participants during an incremental treadmill run. Comparison of the HR reached at the second ventilatory threshold (VT2) was made to the HR reached at a DFA a1 value of 0.5 (HRVT2). Based on Bland–Altman analysis and linear regression, there was strong agreement between VT2 and HRVT2 measured by HR (r = 0.78, p < 0.001). Mean VT2 was reached at a HR of 174 (±12) bpm compared to mean HRVT2 at a HR of 171 (±16) bpm. In summary, the HR associated with a DFA a1 value of 0.5 on an incremental treadmill ramp was closely related to that of the HR at the VT2 derived from gas exchange analysis. A distinct numerical value of DFA a1 representing an uncorrelated, random interbeat pattern appears to be associated with the VT2 and shows potential as a noninvasive marker for training intensity distribution and performance status.
Performance and serum parameters of calves (Bos taurus) subject to milk restriction associated with supplementation with 2-hydroxy-4-(methylthio)butanoic acid

Abstract Our aim with this study was to evaluate the consumption, performance, quantitative characteristics of carcasses, biochemical profile, plasma levels of ghrelin and leptin, expression of the receptor for ghrelin (GHS-R1a) in the hypothalamus and duodenum, and the number of goblet cells in the duodenum of calves subjected to milk volume restriction and supplemented with 2-hydroxy-4-(methylthio)butanoic acid (HMTBa). We used 21 Holstein mixed-breed calves, aged between 3 and 15 d with an average weight of 36.8 kg, and housed in pens with troughs for hay, concentrate, and water. The study included two consecutive experimental periods (first period [P1] and second period [P2]) of 21 d each, with 7 d of adaptation to the diet and facilities. The calves were distributed in a completely randomized design in three treatments with seven repetitions. 1) Control: 6 liters of milk/d during P1 and 6 liters of milk/day during P2; 2) RES (milk restriction): 3 liters of milk/day during P1 and 6 liters of milk/day during P2; and 3) RES + HMTBa: 3 liters of milk/day during P1 and 6 liters of milk/day during P2 + 3.3 g of HMTBa/day in both periods. HMTBa was supplied in milk, and the amount of concentrated ration and hay provided and leftovers were recorded daily to estimate dry matter (DM) and crude protein consumption. Mean daily weight gain (DWG), final weight (FW), and feed conversion (FC) were obtained at the beginning and at the end of each 21-d period. Plasma concentrations of ghrelin and leptin, triglycerides, total protein, urea, lactate, creatinine, alkaline phosphatase, and cholesterol were measured for P1 and P2 at the end of each 21-d period. At the end of P2, animals were slaughtered; sections of the duodenum were collected to evaluate the expression of GHS-R1a and quantity of goblet cells; hypothalamus was used to evaluate the expression of GHS-R1a; rumen was used to evaluate the thickness of epithelium and keratin and the density, height, and width of ruminal papillae. In P1, total DM consumption, FW, DWG, glucose, and triglycerides were lower in the RES and RES + HMTBa groups (P < 0.001). In P2, there was an improvement in the FC of the RES + HMTBa group (compared with Control and RES groups) and a lower urea concentration in the RES group (compared with Control and RES + HMTBa groups) (P < 0.001). No differences were observed among groups regarding hormonal concentrations, histological parameters, and GHS-R1a expression in the duodenum and hypothalamus. Therefore, milk restriction combined with HMTBa supplementation promoted greater compensatory gain by a mechanism independent of changes in GHS-R1a expression and hormone levels of ghrelin and leptin.
Pathophysiology of Mitochondrial Dysfunction in Human Spermatozoa: Focus on Energetic Metabolism, Oxidative Stress and Apoptosis

The dogma of mitochondria as the major source of energy in supporting sperm motility should be critically reconsidered in the light of several experimental data pointing to a major role of glycolysis in mammalian spermatozoa. In this light, the reported positive correlation between the mitochondrial membrane potential (ΔΨm) and motility of ejaculated spermatozoa cannot be explained convincingly by an impaired mitochondrial ATP generation only. Evidence has been produced suggesting that, in human sperm, dysfunctional mitochondria represent the main site of generation of reactive oxygen species (ROS). Furthermore, in these organelles, a complex bidirectional relationship could exist between ROS generation and apoptosis-like events that synergize with oxidative stress in impairing sperm biological integrity and functions. Despite the activity of enzymatic and non-enzymatic antioxidant factors, human spermatozoa are particularly vulnerable to oxidative stress, which plays a major role in male factor infertility. The purpose of this article is to provide an overview of metabolic, oxidative and apoptosis-like inter-linkages of mitochondrial dysfunction and their reflections on human sperm biology.
Standardization of the [68Ga]Ga-PSMA-11 Radiolabeling Protocol in an Automatic Synthesis Module: Assessments for PET Imaging of Prostate Cancer

Prostate-specific membrane antigen (PSMA) is a glycoprotein present in the prostate, that is overexpressed in prostate cancer (PCa). Recently, PSMA-directed radiopharmaceuticals have been developed, allowing the pinpointing of tumors with the Positron Emission Tomography (PET) or Single Photon Emission Computed Tomography (SPECT) imaging techniques. The aim of the present work was to standardize and validate an automatic synthesis module-based radiolabeling protocol for [68Ga]Ga-PSMA-11, as well as to produce a radiopharmaceutical for PET imaging of PCa malignancies. [68Ga]Ga-PSMA-11 was evaluated to determine the radiochemical purity (RCP), stability in saline solution and serum, lipophilicity, affinity to serum proteins, binding and internalization to lymph node carcinoma of the prostate (LNCaP) cells, and ex vivo biodistribution in mice. The radiopharmaceutical was produced with an RCP of 99.06 ± 0.10%, which was assessed with reversed-phase high-performance liquid chromatography (RP-HPLC). The product was stable in saline solution for up to 4 h (RCP > 98%) and in serum for up to 1 h (RCP > 95%). The lipophilicity was determined as −3.80 ± 0.15, while the serum protein binding (SPB) was <17%. The percentages of binding to LNCaP cells were 4.07 ± 0.51% (30 min) and 4.56 ± 0.46% (60 min), while 19.22 ± 2.73% (30 min) and 16.85 ± 1.34% (60 min) of bound material was internalized. High accumulation of [68Ga]Ga-PSMA-11 was observed in the kidneys, spleen, and tumor, with a tumor-to-contralateral-muscle ratio of >8.5 and a tumor-to-blood ratio of >3.5. In conclusion, an automatic synthesis module-based radiolabeling protocol for [68Ga]Ga-PSMA-11 was standardized and the product was evaluated, thus verifying its characteristics for PET imaging of PCa tumors in a clinical environment.