Miracle-dz/UniFAR-FTUs huggingface dataset:
Factors Associated with Mortality in Immunocompetent Patients with Hospital-acquired Pneumonia

Aim: The aim of the study is to determine the factors associated with 28-day mortality in immunocompetent patients with hospital-acquired pneumonia (HAP). Methods: This was a 42-month retrospective cohort study in Chiang Kham Hospital. Patients with HAP diagnosed between January 2013 and June 2016 who did not have an immunocompromised status were recruited into the study. Statistical Analysis Used: Univariable and multivariable binary logistic regression analyses were performed to determine the factors associated with mortality in patients with HAP. Results: A total of 181 HAP patients. The most causative pathogens were nonfermenting Gram-negative bacilli. Fifty-two (28.7%) patients had died within 28 days after HAP diagnosis. Multivariable analysis demonstrated that mechanical ventilation (MV) dependency (adjusted odds ratio [OR] = 3.58, 95% confidence interval [CI] 1.53–8.37, P = 0.003), antibiotic duration (adjusted OR = 0.79, 95% CI 0.70–0.88, P < 0.001), acute kidney injury (adjusted OR = 5.93, 95% CI 1.29–27.22, P = 0.022), and hematologic diseases (adjusted OR = 11.45, 95% CI 1.61–81.50, P = 0.015) were the significant factors associated with 28-day mortality. Conclusions: The factors associated with mortality were MV dependency, HAP duration of treatment, acute kidney injury, and hematologic disease. Early recognition of these factors in immunocompetent patients with HAP and treatment with intensive care may improve the outcome.
Cryo-EM structure of phosphodiesterase 6 reveals insights into the allosteric regulation of type I phosphodiesterases

We report the cryo-EM structure of rod photoreceptor phosphodiesterase 6. Cyclic nucleotide phosphodiesterases (PDEs) work in conjunction with adenylate/guanylate cyclases to regulate the key second messengers of G protein–coupled receptor signaling. Previous attempts to determine the full-length structure of PDE family members at high-resolution have been hindered by structural flexibility, especially in their linker regions and N- and C-terminal ends. Therefore, most structure-activity relationship studies have so far focused on truncated and conserved catalytic domains rather than the regulatory domains that allosterically govern the activity of most PDEs. Here, we used single-particle cryo–electron microscopy to determine the structure of the full-length PDE6αβ2γ complex. The final density map resolved at 3.4 Å reveals several previously unseen structural features, including a coiled N-terminal domain and the interface of PDE6γ subunits with the PDE6αβ heterodimer. Comparison of the PDE6αβ2γ complex with the closed state of PDE2A sheds light on the conformational changes associated with the allosteric activation of type I PDEs.
PKAD: a database of experimentally measured pKa values of ionizable groups in proteins

Abstract Ionizable residues play key roles in many biological phenomena including protein folding, enzyme catalysis and binding. We present PKAD, a database of experimentally measured pKas of protein residues reported in the literature or taken from existing databases. The database contains pKa data for 1350 residues in 157 wild-type proteins and for 232 residues in 45 mutant proteins. Most of these values are for Asp, Glu, His and Lys amino acids. The database is available as downloadable file as well as a web server (http://compbio.clemson.edu/pkad). The PKAD database can be used as a benchmarking source for development and improvement of pKa’s prediction methods. The web server provides additional information taken from the corresponding structures and amino acid sequences, which allows for easy search and grouping of the experimental pKas according to various biophysical characteristics, amino acid type and others.
Integrative diagnosis, biological observations, and histopathology of the fig cyst nematode Heteroderafici Kirjanova (1954) associated with Ficuscarica L. in southern Italy

Abstract Morpho-biological notes and histopathology, based on LM and SEM observations, of the fig cyst nematode Heteroderafici isolated from Ficuscarica roots, collected in home and public gardens of Apulia region, southern Italy, are described and illustrated. Seventy-five localities throughout the Apulia region were sampled and one-quarter of the sampled localities had fig roots infested with H.fici, with population densities ranging from 44 to 180 cysts/100 ml of soil. All attempts to detect H.fici on ornamental Ficus spp. as well as on imported bonsai in Italy were unsuccessful. Morphometric characters of the Italian population conform to those of the type and re-description populations reported for H.fici. Molecular analysis using ITS, D2–D3 expansion domains of the 28S rRNA, and the partial 18S rRNA sequences of H.fici newly obtained in this study matched well with the corresponding sequences of H.fici present in the GenBank database. Phylogenetic trees confirmed and supported the grouping of H.fici in the Humuli group. Heteroderafici completes its embryogenic development in 14–16 days at 25 °C. Post-invasion development and maturity in the roots of F.carica seedlings is completed in 64–68 days at 25–28 °C with juveniles and adults showing different parasitic habits, being endoparasitic and semi-endoparasitic respectively. The establishment of permanent feeding sites that consist of the formation of large syncytia causes anatomical modification of vascular elements and general disorder in the root stelar structures. Syncytia structures associated with mature females showed different degrees of vacuolisation, numbers of syncytial cells, and contained nuclei and nucleoli which were constantly hypertrophied.
Stochastic vertex corrections: linear scaling methods for accurate quasiparticle energies.

New stochastic approaches for the computation of electronic excitations are developed within the many-body perturbation theory. Three approximations to the electronic self-energy are considered: G0W0, G0W0tc, and G0W0tcΓx. All three methods are formulated in the time domain and the latter two incorporate non-local vertex corrections. In case of G0W0tcΓx, the vertex corrections are included both in the screened Coulomb interaction and in the expression for the self-energy. The implementation of the three approximations is verified by comparison to deterministic results for a set of small molecules. The performance fully stochastic implementation is tested on acene molecules, C60 and PC60BM. The vertex correction appears crucial for the description of unoccupied states. Unlike conventional (deterministic) approaches, all three stochastic methods scale linearly with the number of electrons.
Species‐level biodiversity assessment using marine environmental DNA metabarcoding requires protocol optimization and standardization

Abstract DNA extraction from environmental samples (environmental DNA; eDNA) for metabarcoding‐based biodiversity studies is gaining popularity as a noninvasive, time‐efficient, and cost‐effective monitoring tool. The potential benefits are promising for marine conservation, as the marine biome is frequently under‐surveyed due to its inaccessibility and the consequent high costs involved. With increasing numbers of eDNA‐related publications have come a wide array of capture and extraction methods. Without visual species confirmation, inconsistent use of laboratory protocols hinders comparability between studies because the efficiency of target DNA isolation may vary. We determined an optimal protocol (capture and extraction) for marine eDNA research based on total DNA yield measurements by comparing commonly employed methods of seawater filtering and DNA isolation. We compared metabarcoding results of both targeted (small taxonomic group with species‐level assignment) and universal (broad taxonomic group with genus/family‐level assignment) approaches obtained from replicates treated with the optimal and a low‐performance capture and extraction protocol to determine the impact of protocol choice and DNA yield on biodiversity detection. Filtration through cellulose‐nitrate membranes and extraction with Qiagen's DNeasy Blood & Tissue Kit outperformed other combinations of capture and extraction methods, showing a ninefold improvement in DNA yield over the poorest performing methods. Use of optimized protocols resulted in a significant increase in OTU and species richness for targeted metabarcoding assays. However, changing protocols made little difference to the OTU and taxon richness obtained using universal metabarcoding assays. Our results demonstrate an increased risk of false‐negative species detection for targeted eDNA approaches when protocols with poor DNA isolation efficacy are employed. Appropriate optimization is therefore essential for eDNA monitoring to remain a powerful, efficient, and relatively cheap method for biodiversity assessments. For seawater, we advocate filtration through cellulose‐nitrate membranes and extraction with Qiagen's DNeasy Blood & Tissue Kit or phenol‐chloroform‐isoamyl for successful implementation of eDNA multi‐marker metabarcoding surveys.
Getting the Dried Whey Protein Concentrate and Its Effect on Pan Bread Evaluation

The aim of study is to obtain dried whey protein concentrate and to study the functional properties and physical, chemical properties. It was incorporated into pan bread made using different levels of dried whey protein concentrate. Pan bread samples were analyzed for sensory, physical and chemical attributes. The results revealed that sweet cheese whey contain 93.14% water, 4.85% lactose, 0.7% soluble protein, 0.11% fat and 0.9% ash contents. While, the produced dried whey protein concentrate contained 7.04% water 92.96% total solids, 10.47% lactose, 66.87% protein, 3.65% fat and 5.63% ash contents and contained higher levels of essential amino acids especially lysine, threonine and valine. Functional properties of dried whey protein concentrate were 4.8%, 2.2%, 50%, 80% and 0.52 g/cm for water absorption capacity, oil absorption capacity, foam capacity, foam stability and bulk density, respectively. Sensory, physical and chemical evaluation revealed that pan bread made using 20% dried whey protein concentrate had the best quality compared with control and other levels of dried whey protein concentrate.
Independent Neural Activity Patterns for Sensory- and Confidence-Based Information Maintenance during Category-Selective Visual Processing

Abstract Several influential theories of consciousness attempt to explain how, when and where conscious perception arises in the brain. The extent of conscious perception of a stimulus is often probed by asking subjects to provide confidence estimations in their choices in challenging perceptual decision-making tasks. Here, we aimed to dissociate neural patterns of “cognitive” and “sensory” information maintenance by linking category selective visual processes to decision confidence using multivariate decoding techniques on human EEG data. Participants discriminated at-threshold masked face versus house stimuli and reported confidence in their discrimination performance. Three distinct types of category-selective neural activity patterns were observed, dissociable by their timing, scalp topography, relationship with decision confidence, and generalization profile. An early (∼150–200 ms) decoding profile was unrelated to confidence and quickly followed by two distinct decodable patterns of late neural activity (350–500 ms). One pattern was on-diagonal, global and highly related to decision confidence, likely indicating cognitive maintenance of consciously reportable stimulus representations. The other pattern however was off-diagonal, restricted to posterior electrode sites (local), and independent of decision confidence, and therefore may reflect sensory maintenance of category-specific information, possibly operating via recurrent processes within visual cortices. These results highlight that two functionally independent neural processes are operating in parallel, only one of which is related to decision confidence and conscious access.
In vitro assessment of the antifungal effects of neem powder added to polymethyl methacrylate denture base material

Background Denture with antimicrobial activities is desirable to prevent Candida albican adhesion subsequently decreasing the susceptibility of denture stomatitis incidence. Azadirachta Indica, commonly known as Neem powder has antimicrobial effect but the effect of its addition to acrylic denture base on C. albicans adhesion has not been investigated. The aim of this study was determine whether adding neem powder to acrylic denture base materials could reduce Candida albicansadhesion. Material and Methods One hundred and twenty acrylic resin denture specimens were fabricated and divided into heat-polymerized (n=60) and auto-polymerized (n=60) groups. Each group was further divided into 6 groups (n=10) based on the neem concentration: 0, 0.5, 1, 1.5, 2 and 2.5 wt% of the polymer. After polymerization, the specimens were polished, stored in distilled water, sonicated, sterilized, submerged in artificial saliva containing C. albicans, and finally, placed in an incubator at 37°C. Slide counting and direct culture methods were used to assess the antifungal effects of the neem addition. An analysis of variance and post hoc Tukey’s test were performed for the data analysis (p≤0.05 was statistically significant). Results Based on the results, the neem addition significantly decreased the C. albicans count when compared to the control group (p≤0.05). Moreover, the count decreased as the neem concentration increased (lowest count with 2.5 wt%). Conclusions The results suggest that adding neem powder to acrylic resin denture base materials reduces the adhesion of C. albicans; therefore, the incorporation of neem could be a possible denture stomatitis prevention method. Key words:Denture stomatitis, Candida albicans, Azadirachta indica, neem powder, denture base.
Effect of cooling water temperature on the temperature changes in pulp chamber and at handpiece head during high-speed tooth preparation

Objectives It was the aim of this study to evaluate the effect of cooling water temperature on the temperature changes in the pulp chamber and at the handpiece head during high-speed tooth preparation using an electric handpiece. Materials and Methods Twenty-eight intact human molars received a standardized occlusal preparation for 60 seconds using a diamond bur in an electric handpiece, and one of four treatments were applied that varied in the temperature of cooling water applied (control, with no cooling water, 10°C, 23°C, and 35°C). The temperature changes in the pulp chamber and at the handpiece head were recorded using K-type thermocouples connected to a digital thermometer. Results The average temperature changes within the pulp chamber and at the handpiece head during preparation increased substantially when no cooling water was applied (6.8°C and 11.0°C, respectively), but decreased significantly when cooling water was added. The most substantial drop in temperature occurred with 10°C water (−16.3°C and −10.2ºC), but reductions were also seen at 23°C (−8.6°C and −4.9°C). With 35°C cooling water, temperatures increased slightly, but still remained lower than the no cooling water group (1.6°C and 6.7ºC). Conclusions The temperature changes in the pulp chamber and at the handpiece head were above harmful thresholds when tooth preparation was performed without cooling water. However, cooling water of all temperatures prevented harmful critical temperature changes even though water at 35°C raised temperatures slightly above baseline.
Deletion of Ripk3 Prevents Motor Neuron Death In Vitro but not In Vivo

Abstract Increasing evidence suggests that necroptosis, a form of programmed cell death (PCD), contributes to neurodegeneration in several disorders, including ALS. Supporting this view, investigations in both in vitro and in vivo models of ALS have implicated key molecular determinants of necroptosis in the death of spinal motor neurons (MNs). Consistent with a pathogenic role of necroptosis in ALS, we showed increased mRNA levels for the three main necroptosis effectors Ripk1, Ripk3, and Mlkl in the spinal cord of mutant superoxide dismutase-1 (SOD1G93A) transgenic mice (Tg), an established model of ALS. In addition, protein levels of receptor-interacting protein kinase 1 (RIPK1; but not of RIPK3, MLKL or activated MLKL) were elevated in spinal cord extracts from these Tg SOD1G93A mice. In postmortem motor cortex samples from sporadic and familial ALS patients, no change in protein levels of RIPK1 were detected. Silencing of Ripk3 in cultured MNs protected them from toxicity associated with SOD1G93A astrocytes. However, constitutive deletion of Ripk3 in Tg SOD1G93A mice failed to provide behavioral or neuropathological improvement, demonstrating no similar benefit of Ripk3 silencing in vivo. Lastly, we detected no genotype-specific myelin decompaction, proposed to be a proxy of necroptosis in ALS, in either Tg SOD1G93A or Optineurin knock-out mice, another ALS mouse model. These findings argue against a role for RIPK3 in Tg SOD1G93A-induced neurodegeneration and call for further preclinical investigations to determine if necroptosis plays a critical role in the pathogenesis of ALS.
Growth Kinetics of the Rat Mesenchymal Stem Cells from the Bone Marrow and Adipose Tissue. A Comparative Study

ABSTRACTBackground: The bone marrow has been considered as a main source for isolation of multipotent mesenchymal stem cells (MSCs). They are still the most frequently investigated cell type and often identified as the gold standard. However, a similar cell population has been also isolated from other tissues such as adipose tissue. Unlike bone marrow, the adipose tissue is abundantly accessible source of stem cell that can give a good yield in culture.Aim of the work: Was isolation of the rat bone marrow MSCs (BM-MSCs) and adipose tissue MSCs (AD-MSCs) and assessing their growth kinetics.Material and Methods: The rat bone marrow and adipose tissue were isolated from 10 male adult albino rats and cultured and expanded through 6 passages. BM-MSCs and AD-MSCs biological characteristics evaluated for cell therapy (morphology, flow cytometric analysis, colony-forming unit-fibroblast assay, proliferation capacity at passages 2, 4 and 6, population doubling time (PDT) and cell growth curves). Results: BM-MSCs and AD-MSCs attached to the culture flask and displayed spindle-shaped morphology, more evident in AD-MSCs. Proliferation rate of AD-MSCs in the analyzed passages was more than BM-MSCs. The increase in the PDT of both types of MSCs occurred with the increase in the number of passages.Conclusion: The rat AD- MSCs have growth kinetic advantages in the proliferative capacity, colony-forming unite fibroblast and population doubling time more than that of BM-MSCs. these advantages should be considered when choosing a stem cell source for specific clinical application.
Pharmacotherapeutic management of paediatric heart failure and ACE-I use patterns: a European survey

Objective To characterise heart failure (HF) maintenance pharmacotherapy for children across Europe and investigate how angiotensin-converting enzyme inhibitors (ACE-I) are used in this setting. Methods A Europe-wide web-based survey was conducted between January and May 2015 among European paediatricians dedicated to cardiology. Results Out of 200-eligible, 100 physicians representing 100 hospitals in 27 European countries participated. All participants reported prescribing ACE-I to treat dilated cardiomyopathy-related HF and 97% in the context of congenital heart defects; 87% for single ventricle physiology. Twenty-six per cent avoid ACE-I in newborns. Captopril was most frequently selected as first-choice for newborns (73%) and infants and toddlers (66%) and enalapril for children (56%) and adolescents (58%). Reported starting and maintenance doses varied widely. Up to 72% of participants follow formal creatinine increase limits for decision-making when up-titrating; however, heterogeneity in the cut-off points selected existed. ACE-I formulations prescribed by 47% of participants are obtained from more than a single source. Regarding symptomatic HF maintenance therapy, 25 different initial drug combinations were reported, although 79% select a regimen that includes ACE-I and diuretic (thiazide and/or loop), 61% ACE-I and aldosterone antagonist; 44% start with beta-blocker, 52% use beta-blockers as an add-on drug. Of the 89 participants that prescribe pharmacotherapy to asymptomatic patients, 40% do not use ACE-I monotherapy or ACE-I-beta-blocker two-drug only combination. Conclusions Despite some reluctance to use them in newborns, ACE-I seem key in paediatric HF treatment strategies. Use in single ventricle patients seems frequent, in apparent contradiction with current paediatric evidence. Disparate dosage criteria and potential formulation-induced variability suggest significant differences may exist in the risk-benefit profile children are exposed to. No uniformity seems to exist in the drug regimens in use. The information collected provides relevant insight into real-life clinical practice and may facilitate research to identify the best therapeutic options for HF children.
Consensus on the management of astigmatism in cataract surgery

This project was aimed at achieving consensus on the management of astigmatism during cataract surgery by ophthalmologists from Latin America using modified Delphi technique. Relevant peer-reviewed literature was identified, and 21 clinical research questions associated with the definition, classification, measurement, and treatment of astigmatism during cataract surgery were formulated. Twenty participants were divided into seven groups, and each group was assigned three questions to which they had to respond in written form, after thoroughly reviewing the literature. The assigned questions with corresponding responses by each group were discussed with other participants in round 4 – presentation of findings. The consensus was achieved if approval was obtained from at least 80% of participants. The present paper provides several agreements and recommendations for management of astigmatism during cataract surgery, which could potentially minimize the variability in practice patterns and help ophthalmologists adopt optimal practices for cataract patients with astigmatism and improve patient satisfaction.
Distinct Gut Virome Profile of Pregnant Women With Type 1 Diabetes in the ENDIA Study

Abstract Background The importance of gut bacteria in human physiology, immune regulation, and disease pathogenesis is well established. In contrast, the composition and dynamics of the gut virome are largely unknown; particularly lacking are studies in pregnancy. We used comprehensive virome capture sequencing to characterize the gut virome of pregnant women with and without type 1 diabetes (T1D), longitudinally followed in the Environmental Determinants of Islet Autoimmunity study. Methods In total, 61 pregnant women (35 with T1D and 26 without) from Australia were examined. Nucleic acid was extracted from serial fecal specimens obtained at prenatal visits, and viral genomes were sequenced by virome capture enrichment. The frequency, richness, and abundance of viruses were compared between women with and without T1D. Results Two viruses were more prevalent in pregnant women with T1D: picobirnaviruses (odds ratio [OR], 4.2; 95% confidence interval [CI], 1.0–17.1; P = .046) and tobamoviruses (OR, 3.2; 95% CI, 1.1–9.3; P = .037). The abundance of 77 viruses significantly differed between the 2 maternal groups (≥2-fold difference; P < .02), including 8 Enterovirus B types present at a higher abundance in women with T1D. Conclusions These findings provide novel insight into the composition of the gut virome during pregnancy and demonstrate a distinct profile of viruses in women with T1D.