Miracle-dz/UniFAR-FTUs huggingface dataset:
State of the Art in the Culture of the Human Microbiota: New Interests and Strategies

The last 5 years have seen a turning point in the study of the gut microbiota with a rebirth of culture-dependent approaches to study the gut microbiota. High-throughput methods have been developed to study bacterial diversity with culture conditions aimed at mimicking the gut environment by using rich media such as YCFA (yeast extract, casein hydrolysate, fatty acids) and Gifu anaerobic medium in an anaerobic workstation, as well as media enriched with rumen and blood and coculture, to mimic the symbiosis of the gut microbiota. SUMMARY The last 5 years have seen a turning point in the study of the gut microbiota with a rebirth of culture-dependent approaches to study the gut microbiota. High-throughput methods have been developed to study bacterial diversity with culture conditions aimed at mimicking the gut environment by using rich media such as YCFA (yeast extract, casein hydrolysate, fatty acids) and Gifu anaerobic medium in an anaerobic workstation, as well as media enriched with rumen and blood and coculture, to mimic the symbiosis of the gut microbiota. Other culture conditions target phenotypic and metabolic features of bacterial species to facilitate their isolation. Preexisting technologies such as next-generation sequencing and flow cytometry have also been utilized to develop innovative methods to isolate previously uncultured bacteria or explore viability in samples of interest. These techniques have been applied to isolate CPR (Candidate Phyla Radiation) among other, more classic approaches. Methanogenic archaeal and fungal cultures present different challenges than bacterial cultures. Efforts to improve the available systems to grow archaea have been successful through coculture systems. For fungi that are more easily isolated from the human microbiota, the challenge resides in the identification of the isolates, which has been approached by applying matrix-assisted laser desorption ionization–time of flight mass spectrometry technology to fungi. Bacteriotherapy represents a nonnegligible avenue in the future of medicine to correct dysbiosis and improve health or response to therapy. Although great strides have been achieved in the last 5 years, efforts in bacterial culture need to be sustained to continue deciphering the dark matter of metagenomics, particularly CPR, and extend these methods to archaea and fungi.
Short Run and Long Run Association of Macro-Economic Indicators with Stock Market: Evidence from Pakistan Stock Market

Stock markets are of prime importance for the stability and boosting of an economy; its development and formation of capital. An active and stable stock market induces effective and successful organizations. The stability of stock markets is always disturbed by fluctuations in certain macroeconomic variables. This study is an endeavor to find out the effect of these variables on the Pakistan stock exchange index both on long term as well as short term bases. Statistical tests were applied on the quarterly time series data from January 2004 to December 2018. The results of the study show that there is negative association among the rate of inflation and share price while the stock prices have positive association with exchange rate and rate of interest. Findings of this study could help the investors to gain positive returns from investment in stock market.
Induction of callogenesis and organogenesis of different melon genotypes

The effect of different concentration of BA and Kinetin on regeneration of cotyledons, hypocotyls and leaves of four melon genotypes was studied. It was established that cotyledons and leaf segments were more effective as explants for bud induction and subsequent plant regeneration than hypocotyls. In the studied melon genotypes, the better regeneration was obtained in medium variants supplemented with growth regulator BA. The best response was observed in true leaves (70.0%) and cotyledons (53.3%) from line 5-1-2 in medium variant containing 1.0 mgL-1 BA. On medium variants containing Kinetin the regeneration efficiency was lower. Data from three-way analysis of variance confirmed that regeneration ability is strongly influenced by explant type and interaction of both factors - genotype and explant type. The highest number of plantlets/explant was registered in leaf segments from line K052 (0.9%), followed by cotyledons and true leaves from line 5-1-2 (0.7%) in medium variant contained 1.0 mgL-1 BA.
Microsecond Interaural Time Difference Discrimination Restored by Cochlear Implants After Neonatal Deafness

Cochlear implants (CIs) can restore a high degree of functional hearing in deaf patients but enable only poor spatial hearing or hearing in noise. Early deaf CI users are essentially completely insensitive to interaural time differences (ITDs). A dearth of binaural experience during an early critical period is often blamed for these shortcomings. However, here we show that neonatally deafened rats which are fitted with binaural CIs in early adulthood are highly sensitive to ITDs immediately after implantation. Under binaural synchronized stimulation they can be trained to localize ITDs with essentially normal behavioral thresholds near 50 μs. This suggests that the deficits seen in human patients are unlikely to be caused by lack of experience during their period of deafness. It may instead be due to months or years of CI stimulation with inappropriate binaural parameters provided by CI processors which do not provide sub-millisecond temporal fine structure of sounds.
Tobacco Smoke Carcinogens Induce DNA Repair Machinery Function Loss: Protection by Carbon Nanotubes

Purpose: DNA damage is a continuous process occurring within the cells caused by intrinsic and extrinsic factors, but it gets repaired regularly. If the DNA repair process is faulty, the incidences of damages/mutations can accumulate in cells resulting in cell transformation. It is hypothesized that the negative variations in DNA repair pathways in even at one point viz. genetic, translational or posttranslational stage may fairly be crucial for the beginning and development of carcinogenesis. Therefore, we investigated the potential of tobacco specific nitrosamines (TSNs) related carcinogens to interact with the enzymes involved in DNA repair mechanisms in the current study. Methods: The derivatives of cigarettes’ smoke like NNK and NNAL are very well known and recognized carcinogens. Therefore, almost 120 enzymes playing crucial role in the DNA repair process have been analysed for their reactivity with NNK and NNAL. Results: The molecular docking study helped to screen out, 07 possible DNA repair enzyme targets for NNK, and 12for NNAL. Present study revealed the loss of activity of DNA repair enzymes in the presence of NNK and NNAL, and this accumulation may induce the tendency of DNA damage which can lead the transformation of exposed normal cells in to cancerous cells. This study also demonstrated the protective potential of nanoparticles like SWCNTs/MWCNTs against TSN’s induced toxicity; here SWCNT against NNK (-17.16 Kcal/Mol) and MWCNT against NNK -17.01 Kcal/Mol were showing maximum binding affinities than the known biomolecular target of NNK 1UGH (Uracil-DNA glycosylase,-7.82Kcal/Mol). Conclusion: CNTs can be applied as chemo-preventive agents against environmental and tobacco induced carcinogens owing to their scavenging potential and warrants for in vivo and in vitro experimental validation of the results obtained from the present study.
Implantation technique and optimal subcutaneous defibrillator chest position: a PRAETORIAN score-based study.

AIMS The traditional technique for subcutaneous implantable cardioverter-defibrillator (S-ICD) implantation involves three incisions and a subcutaneous pocket. Recently, a two-incision and intermuscular (IM) technique has been adopted. The PRAETORIAN score is a chest radiograph-based tool that predicts S-ICD conversion testing. We assessed whether the S-ICD implantation technique affects optimal position of the defibrillation system according to the PRAETORIAN score. METHODS AND RESULTS We analysed consecutive patients undergoing S-ICD implantation. The χ2 test and regression analysis were used to determine the association between the PRAETORIAN score and implantation technique. Two hundred and thirteen patients were enrolled. The S-ICD generator was positioned in an IM pocket in 174 patients (81.7%) and the two-incision approach was adopted in 199 (93.4%). According to the PRAETORIAN score, the risk of conversion failure was classified as low in 198 patients (93.0%), intermediate in 13 (6.1%), and high in 2 (0.9%). Patients undergoing the two-incision and IM technique were more likely to have a low (<90) PRAETORIAN score than those undergoing the three-incision and subcutaneous technique (two-incision: 94.0% vs. three-incision: 78.6%; P = 0.004 and IM: 96.0% vs. subcutaneous: 79.5%; P = 0.001). Intermuscular plus two-incision technique was associated with a low-risk PRAETORIAN score (hazard ratio 3.76; 95% confidence interval 1.01-14.02; P = 0.04). Shock impedance was lower in PRAETORIAN low-risk patients than in intermediate-/high-risk categories (66 vs. 96 Ohm; P = 0.001). The PRAETORIAN score did not predict shock failure at 65 J. CONCLUSION In this cohort of S-ICD recipients, combining the two-incision technique and IM generator implantation yielded the lowest PRAETORIAN score values, indicating optimal defibrillation system position. CLINICAL TRIAL REGISTRATION http://clinicaltrials.gov/ Identifier: NCT02275637.
The Cell Envelope Stress Response of Bacillus subtilis towards Laspartomycin C

Cell wall antibiotics are important tools in our fight against Gram-positive pathogens, but many strains become increasingly resistant against existing drugs. Laspartomycin C is a novel antibiotic that targets undecaprenyl phosphate (UP), a key intermediate in the lipid II cycle of cell wall biosynthesis. While laspartomycin C has been thoroughly examined biochemically, detailed knowledge about potential resistance mechanisms in bacteria is lacking. Here, we use reporter strains to monitor the activity of central resistance modules in the Bacillus subtilis cell envelope stress response network during laspartomycin C attack and determine the impact on the resistance of these modules using knock-out strains. In contrast to the closely related UP-binding antibiotic friulimicin B, which only activates ECF σ factor-controlled stress response modules, we find that laspartomycin C additionally triggers activation of stress response systems reacting to membrane perturbation and blockage of other lipid II cycle intermediates. Interestingly, none of the studied resistance genes conferred any kind of protection against laspartomycin C. While this appears promising for therapeutic use of laspartomycin C, it raises concerns that existing cell envelope stress response networks may already be poised for spontaneous development of resistance during prolonged or repeated exposure to this new antibiotic.
Optical OFDM for SiPM-Based Underwater Optical Wireless Communication Links

Underwater optical wireless systems have dual requirements of high data rates and long ranges in harsh scattering and attenuation conditions. In this paper, we investigate the advantages and limitations of optical orthogonal frequency-division multiplexing (O-OFDM) signaling when a silicon photo-multiplier (SiPM) is used at the receiver in order to ensure high sensitivity. Considering a light-emitting diode (LED) transmitter and taking into account the limited dynamic range imposed by the transmitter and the SiPM receiver, we study the performance of three popular O-OFDM schemes, i.e., DC-biased, asymmetrically-clipped, and layered asymmetrically-clipped O-OFDM (DCO-, ACO-, and LACO-OFDM, respectively). We consider a constraint on transmit electrical power PTxe and take into account the required DC bias for the three considered schemes in practice, showing the undeniable advantage of ACO- and LACO-OFDM in terms of energy efficiency. For instance, for the considered SiPM and LED components, a spectral efficiency of ∼1 bps/Hz with a data rate of 20 Mbps, a link range of 70 m, and a target bit-error-rate (BER) of 10−3, ACO and LACO allow a reduction of about 10 and 6 mW, respectively, in the required PTxe, compared to DCO-OFDM. Meanwhile, we show that when relaxing the PTxe constraint, DCO-OFDM offers the largest operational link range within which a target BER can be achieved. For instance, for a target BER of 10−3 and a data rate of 20 Mbps, and considering PTxe of 185, 80, and 50 mW for DCO-, LACO-, and ACO-OFDM, respectively, the corresponding intervals of operational link range are about 81, 74.3, and 73.8 m. Lastly, we show that LACO-OFDM makes a good compromise between energy efficiency and operational range flexibility, although requiring a higher computational complexity and imposing a longer latency at the receiver.
Molecular Manipulation of MicroRNA397 Abundance Influences the Development and Salt Stress Response of Arabidopsis thaliana

Arabidopsis thaliana (Arabidopsis) has been used extensively as a heterologous system for molecular manipulation to genetically characterize both dicotyledonous and monocotyledonous plant species. Here, we report on Arabidopsis transformant lines molecularly manipulated to over-accumulate the small regulatory RNA microRNA397 (miR397) from the emerging C4 monocotyledonous grass model species Setaria viridis (S. viridis). The generated transformant lines, termed SvMIR397 plants, displayed a range of developmental phenotypes that ranged from a mild, wild-type-like phenotype, to a severe, full dwarfism phenotype. Reverse transcriptase quantitative polymerase chain reaction (RT-qPCR)-based profiling of the SvMIR397 transformant population revealed a strong correlation between the degree of miR397 over-accumulation, repressed LACCASE (LAC) target gene expression, reduced lignin content, and the severity of the developmental phenotype displayed by SvMIR397 transformants. Further, exposure of SvMIR397 transformants to a 7-day regime of salt stress revealed the SvMIR397 transformant lines to be more sensitive to the imposed stress than were wild-type Arabidopsis plants. Taken together, the findings reported here via the use of Arabidopsis as a heterologous system show that the S. viridis miR397 small regulatory RNA is able to repress the expression of three Arabidopsis LAC genes which led to reduced lignin content and increased salt stress sensitivity.
Synthesis of Oxide Iron Nanoparticles Using Laser Ablation for Possible Hyperthermia Applications

In this work, iron oxide nanoparticles produced using the laser ablation technique were studied in order to determine the characteristics of these nanoparticles as a function of the laser energy for the possible application in magnetic hyperthermia. Nanoparticles were obtained by varying the power of the laser considering values of 90, 173, 279 and 370 mJ. The morphology of these nanoparticles was determined using the dynamic light scattering (DLS) and scattering transmission electron microscopy (STEM) techniques, confirming that the size of the particles was in the order of nanometers. A great influence of the laser power on the particle size was also observed, caused by the competition between the energy and the temperature. The composition was determined by X-ray diffraction and Raman spectroscopy, showing the presence of magnetite, maghemite and hematite. The hyperthermia measurements showed that the temperature rise of the iron oxide nanoparticles was not greatly influenced by the energy change, the heating capacity of magnetic NPs is quantified by the specific absorption rate (SAR), that tends to decrease with increasing energy, which indicates a dependence of these values on the nanoparticles concentration.
Systemically Delivered Magnetic Hyperthermia for Prostate Cancer Treatment

Herein, we report a novel therapy for prostate cancer based on systemically delivered magnetic hyperthermia. Conventional magnetic hyperthermia is a form of thermal therapy where magnetic nanoparticles delivered to cancer sites via intratumoral administration produce heat in the presence of an alternating magnetic field (AMF). To employ this therapy for prostate cancer tumors that are challenging to inject intratumorally, we designed novel nanoclusters with enhanced heating efficiency that reach prostate cancer tumors after systemic administration and generate desirable intratumoral temperatures upon exposure to an AMF. Our nanoclusters are based on hydrophobic iron oxide nanoparticles doped with zinc and manganese. To overcome the challenges associated with the poor water solubility of the synthesized nanoparticles, the solvent evaporation approach was employed to encapsulate and cluster them within the hydrophobic core of PEG-PCL (methoxy poly(ethylene glycol)-b-poly(ε-caprolactone))-based polymeric nanoparticles. Animal studies demonstrated that, following intravenous injection into mice bearing prostate cancer grafts, the nanoclusters efficiently accumulated in cancer tumors within several hours and increased the intratumoral temperature above 42 °C upon exposure to an AMF. Finally, the systemically delivered magnetic hyperthermia significantly inhibited prostate cancer growth and did not exhibit any signs of toxicity.
Fabrication routes via projection stereolithography for 3D-printing of microfluidic geometries for nucleic acid amplification

Digital Light Processing (DLP) stereolithography (SLA) as a high-resolution 3D printing process offers a low-cost alternative for prototyping of microfluidic geometries, compared to traditional clean-room and workshop-based methods. Here, we investigate DLP-SLA printing performance for the production of micro-chamber chip geometries suitable for Polymerase Chain Reaction (PCR), a key process in molecular diagnostics to amplify nucleic acid sequences. A DLP-SLA fabrication protocol for printed micro-chamber devices with monolithic micro-channels is developed and evaluated. Printed devices were post-processed with ultraviolet (UV) light and solvent baths to reduce PCR inhibiting residuals and further treated with silane coupling agents to passivate the surface, thereby limiting biomolecular adsorption occurences during the reaction. The printed devices were evaluated on a purpose-built infrared (IR) mediated PCR thermocycler. Amplification of 75 base pair long target sequences from genomic DNA templates on fluorosilane and glass modified chips produced amplicons consistent with the control reactions, unlike the non-silanized chips that produced faint or no amplicon. The results indicated good functionality of the IR thermocycler and good PCR compatibility of the printed and silanized SLA polymer. Based on the proposed methods, various microfluidic designs and ideas can be validated in-house at negligible costs without the requirement of tool manufacturing and workshop or clean-room access. Additionally, the versatile chemistry of 3D printing resins enables customised surface properties adding significant value to the printed prototypes. Considering the low setup and unit cost, design flexibility and flexible resin chemistries, DLP-SLA is anticipated to play a key role in future prototyping of microfluidics, particularly in the fields of research biology and molecular diagnostics. From a system point-of-view, the proposed method of thermocycling shows promise for portability and modular integration of funcitonalitites for diagnostic or research applications that utilize nucleic acid amplification technology.
Application of a thyroid cartilage window technique for transoral resection of early glottic cancer involving the anterior commissure

Abstract Background Management of early stage glottic carcinoma involving the anterior commissure is challenging. Aims/objectives This study aimed to evaluate the efficacy of a thyroid cartilage window (TCW) technique for transoral laser resection of early glottic cancer with involvement of the anterior commissure. Material and methods Twenty-one patient who underwent a TCW technique for transoral resection early glottic carcinoma involving the anterior commissure, were retrospectively analyzed. The technical nuances, organ preservation rate and voice outcomes, local and regional recurrence, and perioperative comorbidities, were assessed. Results All 21 patients underwent a TCW technique for resection, both the organ preservation rate and negative margin achieved 100%. The local control rate achieved 100%, and the 5 years recurrence free survival was 90.5%. For two patients with subglottic involvement (9.5%), regional recurrence with confirmation of a positive pre-laryngeal lymph node was observed. Postoperative granuloma was detected in all 21 patients, 13 of whom spontaneously disappeared (61.9%); whereas the remaining 8 patients (38.1%) demonstrated a consistent presence of granuloma more than 12 weeks, and they accepted surgical extirpation of granuloma under surface anesthesia. The laryngeal web developed in all 21 patients, while no dyspnea and local recurrence were present. By comparison with preoperative baseline, postoperative self-assessment voice demonstrated a significant improvement (p = .01), while objective voice indices were not significantly altered (p > .05). Conclusions and significance TCW technique is a valuable means for transoral resection of early glottic laryngeal cancer involving the anterior commissure, with acceptable voice quality and seemingly low comorbidities.
Metabolic and Cardiorespiratory Responses of Semiprofessional Football Players in Repeated Ajax Shuttle Tests and Curved Sprint Tests, and Their Relationship with Football Match Play

In this study, the Ajax Shuttle Test (AST) and the Curved Sprint Test (CST) were conducted on semiprofessional football players to evaluate (1) their test performance, (2) the extent of anaerobic glycolysis by measuring blood lactate, (3) performance decrement and onset of fatigue, and (4) the correlation between selected physiological variables and test performance. Thirty-two semiprofessional Polish football players participated in this study. Both AST and CST were conducted on an outdoor football ground and were conducted in two sets; each set had six repetitions. In the case of AST, the total duration for 6 repetitions of the exercise in Sets 1 and 2 were 90.63 ± 3.71 and 91.65 ± 4.24 s, respectively, whereas, in the case of CST, the respective values were 46.8 ± 0.56 and 47.2 ± 0.66 s. Peak blood lactate concentration [La] after Sets 1 and 2 of AST were 14.47 ± 3.77 and 15.00 ± 1.85 mmol/L, and in the case of CST, the values were 8.17 ± 1.32 and 9.78 ± 1.35 mmol/L, respectively. Performance decrement in AST was more than in CST, both after Set 1 (4.32 ± 1.43 and 3.31 ± 0.96 in AST and CST, respectively) and Set 2 (7.95 ± 3.24 and 3.71 ± 1.02 in AST and CST, respectively). Only in a few of the repetitions, pulmonary ventilation (VE) and oxygen uptake (VO2) were found to be significantly correlated with the performance of the volunteers in both AST and CST. Respiratory exchange ratio (RER) was significantly correlated with most of the repetitions of AST, but not with CST. The study concludes that (1) AST shows more dependence on the anaerobic glycolytic system than shorter repetitive sprints (as in CST), (2) there is more performance decrement and fatigue in AST than in CST, and (3) early decrease in performance and fatigue in the semiprofessional football players in AST and CST may be due to the insufficiency of their aerobic energy system.
In vivo investigation of the multi‐exponential T2 decay in human white matter at 7 T: Implications for myelin water imaging at UHF

Multi‐component T2 mapping using a gradient‐ and spin‐echo (GraSE) acquisition has become standard for myelin water imaging at 3 T. Higher magnetic field strengths promise signal‐to‐noise ratio benefits but face specific absorption rate limits and shortened T2 times. This study investigates compartmental T2 times in vivo and addresses advantages and challenges of multi‐component T2 mapping at 7 T.