Miracle-dz/UniFAR-FTUs huggingface dataset:
Soft tissue thickness for placement of an orthodontic miniscrew using an ultrasonic device.

OBJECTIVES To evaluate area- and gender-related differences in the soft tissue thickness of potential areas for installing miniscrews in the buccal-attached gingiva and the palatal masticatory mucosa. MATERIALS AND METHODS The sample consisted of 61 Korean young adults. An ultrasonic gingival-thickness meter was used to measure the soft-tissue thickness in the buccal-attached gingiva just adjacent to the mucogingival junction of the upper and lower arches and 4 mm and 8 mm below the gingival crest in the palatal masticatory mucosa. Independent t-test, paired t-test, and one-way analysis of variance were used for statistical analysis. RESULTS Buccal-attached gingiva thickness in the upper arch was significantly greater in men than in women, but buccal-attached gingiva thickness in the lower arch and palatal masticatory mucosa thickness 4 and 8 mm below the gingival crest did not show gender differences. Significantly thicker soft tissue occurred in the anterior areas in the upper arch and in the posterior areas in the lower arch. In the palatal masticatory mucosa, significantly thicker soft tissue was found 4 mm below the gingival crest in the anterior areas and 8 mm below the gingival crest in the posterior areas. The areas between the canines and the premolars showed higher values than other areas 4 mm below the gingival crest. However, the soft-tissue thickness 8 mm below the gingival crest showed a progressive increase from the anterior to the posterior areas. CONCLUSION Measurements of the soft-tissue thickness using an ultrasonic device could help practitioners select the proper orthodontic miniscrew in daily clinical practice.
Comparison of Preprocessing Procedures for Oligo-nucleotide Micro-arrays by Parametric Bootstrap Simulation of Spike-in Experiments

Summary Objective: Due to scarcity of calibration data for micro-array experiments, simulation methods are employed to assess preprocessing procedures. Here we analyze several procedures’ robustness against increasing numbers of differentially expressed genes and varying proportions of up-regulation. Methods: Raw probe data from oligo-nucleotide micro-arrays are assumed to be approximately multivariate normally distributed on the log scale. Chips can be simulated from a multivariate normal distribution with mean and variance-covariance matrix estimated from a real raw data set. A chip effect induces strong positive correlations. In reverse, sampling from a normal distribution with strong correlation variance-covariance matrix generates data exhibiting a chip effect. No explicit model of chip-effect is needed. Differences can be artificially spiked-in according to a given distribution of effect sizes. Thirty preprocessing procedures combining background correction, normalization, perfect match correction and summarization methods available from the BioConductor project were compared. Results: In the symmetrical setting “50% differentially expressed genes, 50% of which up-regulated” background correction reduces bias, but inflates low intensity probe variance as well as the mean squared error of the estimates. Any normalization reduces variance and increases sensitivity with no clear winner. Asymmetry between up and down regulation causes bias in the effect-size estimate of non-differentially expressed genes. This markedly inflates the false positive discovery rates. Variance stabilizing normalization (VSN) behaved best. Conclusion: A simple parametric bootstrap was used to simulate oligo-nucleotide micro-array raw data. Current normalization methods inflate the false positive rate when many genes show an effect in the same direction.
A COMMON PROTEIN EXTRACTION PROTOCOL FOR PROTEOMIC ANALYSIS: HORSE GRAM A CASE STUDY

Three protocols viz. Trichloroacetic Acid (TCA)-acetone, phenol and multi-detergent were compared for the extraction of proteins from horsegram (Macrotyloma uniflorum) which is less studied yet nutritionally and economically very important pulse crop. Almost equal quantity of proteins was extracted by all the three protocols. However, quality of protein from phenol method was superior to that from other protocols. Bands in One-Dimensional (1-D) and Two-Dimensional Electrophoresis (2-DE) of phenol protocol were reproducible and better. We report here a modified and common protocol for the extraction of proteins for proteomic analysis. The developed protocol is applicable not only to other economically important leguminous but also non-leguminous crops.
Culture if spikes? Indications and yield of blood cultures in hospitalized medical patients.

BACKGROUND Although optimal utilization of blood cultures has been studied in populations, including emergency room and intensive care patients, less is known about the use of blood cultures in populations consisting exclusively of patients on a medical service. OBJECTIVE To identify the physician-selected indication and yield of blood cultures ordered after hospitalization to an acute medical service and to identify populations in which blood cultures may not be necessary. DESIGN, SETTING, AND PATIENTS A prospective cohort study was performed at a single Veterans Affairs Medical Center from October 1, 2014 through April 15, 2015. Participants included all hospitalized patients on a medical service for whom a blood culture was ordered. MEASUREMENTS The main outcomes were the rate of true positive blood cultures and the predictors of true positive cultures. RESULTS The true positive rate was 3.6% per order. The most common physician-selected indications were fever and leukocytosis, neither of which alone was highly predictive of true positive blood cultures. The only indication significantly associated with a true positive blood culture was "follow-up previous positive" (likelihood ratio [LR]+ 3.4, 95% confidence interval [CI]: 1.8-6.5). The only clinical predictors were a working diagnosis of bacteremia/endocarditis (LR+ 3.7, 95% CI: 2.5-5.7) and absence of antibiotic exposure within 72 hours of the culture (LR+ 2.4, 95% CI: 1.2-4.9). CONCLUSIONS The rate of true positive blood cultures among patients on a medical service was lower than previously studied. Using objective and easily obtainable clinical characteristics, including antibiotic exposure and working diagnosis, may improve the likelihood of true positive blood cultures. Journal of Hospital Medicine 2016;11:336-340. © 2016 Society of Hospital Medicine.
Rapid shoreward encroachment of salt marsh cordgrass in response to accelerated sea-level rise

The distribution of New England salt marsh communities is intrinsically linked to the magnitude, frequency, and duration of tidal inundation. Cordgrass (Spartina alterniflora) exclusively inhabits the frequently flooded lower elevations, whereas a mosaic of marsh hay (Spartina patens), spike grass (Distichlis spicata), and black rush (Juncus gerardi) typically dominate higher elevations. Monitoring plant zonal boundaries in two New England salt marshes revealed that low-marsh cordgrass rapidly moved landward at the expense of higher-marsh species between 1995 and 1998. Plant macrofossils from sediment cores across modern plant community boundaries provided a 2,500-year record of marsh community composition and documented the migration of cordgrass into the high marsh. Isotopic dating revealed that the initiation of cordgrass migration occurred in the late 19th century and continued through the 20th century. The timing of the initiation of cordgrass migration is coincident with an acceleration in the rate of sea-level rise recorded by the New York tide gauge. These results suggest that increased flooding associated with accelerating rates of sea-level rise has stressed high-marsh communities and promoted landward migration of cordgrass. If current rates of sea-level rise continue or increase slightly over the next century, New England salt marshes will be dominated by cordgrass. If climate warming causes sea-level rise rates to increase significantly over the next century, these cordgrass-dominated marshes will likely drown, resulting in extensive losses of coastal wetlands.
Heat capacities and inversions in tridymite, cristobalite, and tridymite-cristobalite mixed phases

Samples of synthetic tridymite, cristobalite and tridymite-cristobalite mixed phases, examined by differential scanning calorimetry (DSC) from 360 to 770 or 840K, showed distinct peaks in heat capacity (Cp). For "pure" tridymite the lambda transition at 390K and two peaks near 436K and 470K, which may also be lambda transitions, appear to correlate respectively with the structural changes from (MC) monoclinic (Cc) to (OP) orthorhombic P2t2t2t, (oP) to (oS) orthorhombic with a non-integral superstructure, and (oS) to (oc) orthorhombic c222' descibed by Nukui et at. (1978) as occurring at 3g3K, 423K, and 463K respectively. It may also be possible to correlate a weak cp effect near 653K with the (oc) to (HP) hexagonal P6/mmc inversion of Nukui et al. The DSC measurements agree with the heat-content measurements by Mosesman and Pitzer (1941) and the dynamic calorimeter data of Shahid and Glasser (1970) for tridymite, although the feature observed in both these studies at 498K was absent in our tridymite sample. This 498K discontinuity probably reflects inversion in cristobalite portions of the "tridymite" samples used in the previous studies, as suggested by our DSC examination of tridymite-cristobalite mixed phases. The present Cp data for tridymite above 500K and for cristobalite above 560K agree reasonably well with thi polynomial flts presented by Robie et at. (1978, p.2l7, Zl8).
Impact of curve sawing on kiln-drying and MSR grading

This research evaluated how curve sawing affects drying degrade and machine stress rating (MSR) of lumber. The study was based on comparative mill tests involving a sample of 204 black spruce 16-foot logs. From this sample, a first lot was processed by conventional straight sawing, the second lot by optimized curve sawing (arc sawing), and the third according to the natural curve sawing. The results demonstrated that, as expected, the two curve sawing techniques allowed for improved volume recovery and a higher proportion of 16-foot lumber than straight line sawing. Yield was increased by 2.4 percent with optimized curve sawing, and 2.2 percent with natural curve sawing. From the drying process, the sawing technique was found to have little effect on warp. Curve sawing was observed to cause a slight increase in face warp (bow), but this did not affect grade recovery under National Lumber Grade Authority (NLGA) rules. For the three sawing techniques under study, overall drying degrade was mostly due to twist. Drying degrade was slightly lower in lumber produced by natural curve sawing. Curve sawing led to enhanced mechanical properties. The average MOE for curve-sawn lumber was approximately 4 percent higher than for straight sawing, and the premium achieved through improved MSR yield was about $4 per thousand board feet (MBF) to $5/MBF. Finally, an economic analysis comparing net finished product values from 1 m 3 of logs showed that optimized curve sawing could increase value recovery by 3.5 percent over straight sawing, and by 5.7 percent over natural curve sawing.
Immunoexpression of BAP1, ROS1, and ALK in Spitzoid Melanocytic Tumors

Background. Spitzoid tumors are a heterogeneous group of melanocytic neoplasms that frequently imposes diagnostic difficulties. Lately, several advances in molecular biology afforded significant discoveries on the pathogenesis of these tumors. BAP1 (BRCA-1 associated protein-1) inactivation and anomalous expression of kinase translocation-related proteins are among the main criteria launched by new classification proposals. Our aim was to systematically assess the immunoexpression of BAP1, ROS1 (receptor tyrosine kinase c-Ros oncogene 1), and ALK (anaplastic lymphoma receptor tyrosine kinase) proteins in an unpublished series of spitzoid tumors. Methods. Retrospective study based on 47 formalin-fixed paraffin-embedded tissue samples from 3 different institutions. BAP1, ROS1, and ALK immunostains were performed in all cases. We included 27 Spitz tumors without significant abnormality, 15 atypical spitzoid tumors, and 5 spitzoid melanomas. Results. We observed loss of BAP1 nuclear immunolabeling in 4.3% of evaluable cases (2/46), both of them atypical spitzoid tumors. The proportional frequency of BAP1-inactivated cases among atypical spitzoid tumors was 14.2% (2/14). No immunoexpression of ROS1 or ALK was found. Conclusions. Our study revealed 2 additional BAP1-inactived cases and described its respective frequency. The absence of anomalous expression of translocation-related proteins ALK and ROS1 in this series, composed predominantly of low-grade/low-risk tumors, indicates that translocated spitzoid lesions may not be as prevalent as initially suggested, at least in some populations. Furthermore, our findings encourage additional investigation on unequal occurrence of such immunomarkers among different diagnostic categories of spitzoid neoplasms.
PREDICTIVE VALUE OF VARIOUS RISK FACTORS FOR PRETERM LABOR

Objective: The objectives of this study were to study the various etiological factors responsible for onset of preterm labor and to evaluate the predictive value of these risk factors for spontaneous preterm labor. Methods: This prospective comparative study was conducted over a period of 1 year and included 240 women; of which 120 in preterm labor were enrolled in the study group and 120 with term pregnancy in labor were enrolled in the control group. History, clinical examination and investigations were carried out and risk factors for preterm labor were noted and analyzed to find out the predictive value of the risk factors for preterm labor. Results: Maximum numbers of patients (31.6%) were in the 35-36 weeks gestational age group. When both the groups were compared as regards risk factors, the cases showed a high incidence of infections; 21.7% incidence of chorioamnionitis, 32.5% incidence of bacterial vaginosis and a 12.5% incidence of urinary tract infections. Prior second trimester abortion was found in 13.3% cases and a history of prior preterm birth was found in 15% cases. Uterine over distension was observed in 20.83% cases. Maternal medical disorders were present in 60% cases. Conclusions: Multiple pregnancy, Prior preterm birth, Infections, Prior second trimester abortions and medical disorders in mother are strongly associated with an increased risk of preterm labor.
Protein CoAlation and antioxidant function of coenzyme A in prokaryotic cells

In all living organisms, coenzyme A (CoA) is an essential cofactor with a unique design allowing it to function as an acyl group carrier and a carbonyl-activating group in diverse biochemical reactions. It is synthesized in a highly conserved process in prokaryotes and eukaryotes that requires pantothenic acid (vitamin B5), cysteine and ATP. CoA and its thioester derivatives are involved in major metabolic pathways, allosteric interactions and the regulation of gene expression. A novel unconventional function of CoA in redox regulation has been recently discovered in mammalian cells and termed protein CoAlation. Here, we report for the first time that protein CoAlation occurs at a background level in exponentially growing bacteria and is strongly induced in response to oxidizing agents and metabolic stress. Over 12% of Staphylococcus aureus gene products were shown to be CoAlated in response to diamide-induced stress. In vitro CoAlation of S. aureus glyceraldehyde-3-phosphate dehydrogenase was found to inhibit its enzymatic activity and to protect the catalytic cysteine 151 from overoxidation by hydrogen peroxide. These findings suggest that in exponentially growing bacteria, CoA functions to generate metabolically active thioesters, while it also has the potential to act as a low-molecular-weight antioxidant in response to oxidative and metabolic stress.
Precipitation Effects on Microbial Pollution in a River: Lag Structures and Seasonal Effect Modification

Background The river Göta Älv is a source of freshwater for 0.7 million swedes. The river is subject to contamination from sewer systems discharge and runoff from agricultural lands. Climate models projects an increase in precipitation and heavy rainfall in this region. This study aimed to determine how daily rainfall causes variation in indicators of pathogen loads, to increase knowledge of variations in river water quality and discuss implications for risk management. Methods Data covering 7 years of daily monitoring of river water turbidity and concentrations of E. coli, Clostridium and coliforms were obtained, and their short-term variations in relation with precipitation were analyzed with time series regression and non-linear distributed lag models. We studied how precipitation effects varied with season and compared different weather stations for predictive ability. Results Generally, the lowest raw water quality occurs 2 days after rainfall, with poor raw water quality continuing for several more days. A rainfall event of >15 mm/24-h (local 95 percentile) was associated with a three-fold higher concentration of E. coli and 30% higher turbidity levels (lag 2). Rainfall was associated with exponential increases in concentrations of indicator bacteria while the effect on turbidity attenuated with very heavy rainfall. Clear associations were also observed between consecutive days of wet weather and decreased water quality. The precipitation effect on increased levels of indicator bacteria was significant in all seasons. Conclusions Rainfall elevates microbial risks year-round in this river and freshwater source and acts as the main driver of varying water quality. Heavy rainfall appears to be a better predictor of fecal pollution than water turbidity. An increase of wet weather and extreme events with climate change will lower river water quality even more, indicating greater challenges for drinking water producers, and suggesting better control of sources of pollution.
Understanding Well-Being and Optimal Functioning: Applying the Multilevel Personality in Context (MPIC) Model

In this article we first describe a broad multilevel framework representing the determinants of human behavior and consider its advantages. Expanding on the upper part of this framework, we then propose the Multilevel Personality in Context (MPIC) model, showing how it integrates and extends past theorizing on the hierarchical organization of personality. The model builds upon McAdams's three-tier (traits, goals, and selves) conception of personality, adding a foundational level (psychological needs) beneath individual differences and incorporating social relations and cultural factors as higher level influences upon behavior and individual differences. New data (N= 3,665 in 21 cultures) are briefly presented showing that culture, self, motive, and trait variables each have independent effects upon subjective well-being (SWB) and showing that psychological need satisfaction (at the foundational level) mediates these effects as predicted. Consistent with McAdams and Pals's (2006) “fifth principle” of personality, culture had top-down effects upon self-level variables and moderated several of the relations to SWB. We conclude by suggesting some general heuristics for designing studies using the MPIC approach.
Protective role of melatonin on skeletal muscle injury in rats

Background: The functional restoration of skeletal muscle after injury is highly affected by its regenerative response that requires the coordinated regulation of inflammation, energy metabolism, and growth. Aim: The aim of the present study was to investigate the possible protective role of melatonin on cellular functions and tissue homeostasis during muscular regeneration after skeletal muscle injury in rats. Materials and Methods: The study was conducted on 80 male Wister rats with an open blunt injury of the left soleus muscle. Rats were divided into 2 groups; Group I (melatonin treated group), 40 rats with left soleus muscle injury and received intra peritoneal (i.p) injection of 10 mg/kg body weight/ day of melatonin. Group II (untreated group) 40 rats with soleus muscle injury and received equivalent volumes of 4.5% ethanol i.p. 3.3 mL/kg/day. Subsequent observations were performed at day 1, 4, 7, and 14 after injury, including muscle strength assessment, melatonin receptor Ia expression, bcl2-associated-X protein (Bax) level and histological imaging. Results: Melatonin treatment significantly increased the twitch force of the injured muscle at day 1, 4, 7, and 14. MT1a receptor mRNA in the injured muscle showed a significant up-regulation in the melatonin treated group at day 4, 7 and 14. Intra peritoneal daily injection of melatonin for 4, 7, and 14 days resulted in significant decrease in Bax level in the injured soleus muscle in comparison to the corresponding injured muscles of untreated group. Histological examination further elucidated the anti-apoptotic and the anti-inflammatory action of melatonin. Conclusions: These data supported the hypothesis that melatonin supports muscle restoration after muscle injury, via its anti-inflammatory and anti apoptotic effects and thus might represent an attractive adjuvant therapy to optimize muscle healing after injury.
Evaluation of Some Physical, Chemical and Sensory Properties of Kasar Cheese and Its Processed and Analogue Types

The objective of this study was to evaluate the changes in physical, chemical and sensory properties of the kasar cheese and its processed and analogue types during 90-day storage. Aroma-active compounds in the cheeses were identified by gas chromatography-olfactometry. Sensory properties of the cheeses were determined by descriptive sensory analysis. Differences in basic composition of the cheeses were found. There were also significant differences among the cheeses in terms of meltability, oil separation index, L* and a* values. Whey, cooked, creamy and fermented were the most intense sensory descriptors in the cheeses analyzed on days 1 and 30. However, waxy and animal intensities were much higher in analogue cheese than others. 18 aroma-active compounds were determined in the cheeses during 90 day storage. Diacetyl, acetic acid, butyric acid, 2-/3-methyl butyric acid, 2-acetyl-2-thiazoline, b-ionene, 2-phenylethyl alcohol, maltol, p-cresol, sotolon, d-decalactone and g-dodecalactone were some of the characteristic aroma-active compounds. Kasar cheese was the most liked cheese while analogue cheese was the least liked cheese by consumers.