Miracle-dz/UniFAR-FTUs huggingface dataset:
Outcome variables in periodontal research: means and threshold-based site changes.

BACKGROUND The exclusive use of mean measurements in periodontal research might at times be misleading, as changes in different sites in the same individual might nullify each other. The purpose of the present study was to compare disease progression and response to periodontal therapy using both individual site activity with thresholds and mean patient changes. METHODS Seventy-nine (79) subjects with established periodontitis were monitored for 1 year (no treatment [NTx] group); 108 subjects who received scaling, root planing, and quarterly prophylaxis were observed in a similar time interval (treatment [Tx] group). Probing depth (PD), attachment level (AL) and alveolar crestal height (ACH) were measured at baseline and 1 year using pressure-sensitive probes and computer-assisted image analysis of radiographs. RESULTS Mean reduction in PD (0.50 mm) was observed in the Tx group compared to a small increase (-0.04 mm) in the NTx group (P= 0.0001). Treatment resulted in mean AL gain (0.44 mm) compared to net AL loss (-0.21 mm) in the NTx group (P= 0.0001). Subjects in the Tx group had twice as many sites with AL gain (beyond the threshold) compared to NTx subjects (16.64+/-1.07% versus 8.11+/-0.68%) which was highly significant (P = 0.0001, Student t test). Similarly, although in the opposite direction, percentage of sites with AL loss beyond threshold was 6.21+/-0.47% (Tx group) and 14.02+/-1.15% (NTx group) which was also highly significant (P = 0.0001, Student t test). Change in ACH was minimal for the Tx group (-0.07+/-0.03 mm) while NTx subjects experienced greater bone loss throughout the year (-0.16+/-0.02 mm); percentage of sites with ACH loss was similar for both groups, while the Tx group had 3 times the number of sites with ACH gain (11.76% versus 3.42%), suggesting that the reduction in mean bone loss in the Tx group did not result from a reduction in losing sites, but rather from an increase in gaining sites. The use of both means and binary data seems to supplement the information regarding the nature and mechanism of disease progression and arrest. CONCLUSIONS The characteristics of periodontal disease with its multifactorial patient, local, and site-related etiology support the use of both mean and site-based changes in clinical studies of periodontal disease and treatment.
Transulnar versus transradial access for coronary angiography or percutaneous coronary intervention: A meta‐analysis of randomized controlled trials

Although transfemoral access (TFA) remains the standard of care for patients undergoing coronary angiography (CA) or percutaneous coronary intervention (PCI) in the USA, TRA is being increasingly used over TFA due to lower bleeding and mortality rates on the basis of meta‐analyses and recently published MATRIX trial. In patients with unsuccessful ipsilateral radial access, TUA has been used as an alternative approach. The randomized controlled trials (RCTs) comparing TUA and TRA have reached mixed conclusions regarding the use of transulnar approach for coronary procedures.
Effects of bottom trawling on the benthic assemblages in the south Adriatic Sea (Montenegro)

Trawling remains a controversial method of fishing due to the perceived lack of selectivity of the trawl net, which can result in the capture of a huge quantity and diversity of non-target species, including endangered species, and have a significant effect on the marine ecosystem (KUMAR & DEEPTHI, 2006). Trawl fishing has both direct and indirect impacts on the marine ecosystem as well as on biodiversity, as it collects and kills a huge amount of non-target species and young individuals of commercially valuable species, mechanically disturbs the sea bottom, and injures a wide variety of marine benthic organisms (KNIEB, 1991). The environmental damage caused by bottom trawling can be substantial and irreversible (WATLING & NORSE, 1998). Trawling does not cause damage just to the physical attributes of the habitats, therefore implying a reduction in biodiversity, but can also cause changes to the benthic assemblage structure, species abundance, and their size structure (GARCÍA-RODRÍGUES et al., 2011). However, most of the disturbances at the sea bottom remain unrecorded as they are hidden from direct human The purpose of this study is to show the effects of bottom trawling on the benthic assemblages in the south Adriatic Sea as well as to report detailed quantitative and qualitative data on some invertebrate groups of no commercial value that are affected by trawling. Short-term effects of bottom trawling on the soft bottom seafloor were studied on the continental shelf and upper slope in the southeastern Adriatic Sea. Ten sites were trawled in July 2011. A total of 14,069 invertebrate organisms belonging to 44 taxa were collected within the study period. Of these, 93 were Sponges (4 species), 509 Cnidarians (7 species), 3,670 Molluscs (5 species), 48 Bryozoa (1 species), 3,154 Echinoderms (14 species), and 7,054 Tunicates (13 species). Cluster analysis performed with the data from different depth layers showed two clearly separated main groups that corresponded to shelf and slope zone. The shelf zone samples were characterized by higher species richness, while samples taken from the slope contained one species, Pteroeides spinosums. The obtained results showed that the most common species during the survey were Pteria hirundo, Ascidia virginea, Phallusia mammillata, Botryllus schlosseri, and Centrostephanus longispinus. Species P. mammillata, B. schlosseri, and P. regalis presented the highest value of biomass index (kg/km2). Our results showed that ascidians, cnidarians, and echinoderms are the most vulnerable taxa to trawling.
Beneficial metabolic effects of prompt surgical treatment in patients with an adrenal incidentaloma causing biochemical hypercortisolism.

CONTEXT In patients with adrenal incidentalomas, subclinical hypercortisolism (SH) is associated with an increased prevalence of the metabolic syndrome. The effect of surgical/conservative approach is debated. OBJECTIVE The objective of the study was to determine the effect of the surgical and conservative approaches on the metabolic syndrome in patients with adrenal incidentalomas. DESIGN This was a retrospective longitudinal study (18-48 months follow-up). SETTING The study was conducted on an in- and outpatient basis. PATIENTS One hundred eight patients with adrenal incidentalomas were studied for the presence of SH, which was diagnosed in the presence of more than two of the following: urinary free cortisol greater than 70 microg per 24 h (193 nmol per 24 h), cortisol after 1 mg dexamethasone suppression test greater than 3.0 microg/dl (83 nmol/liter), ACTH less than 10 pg/ml (2.2 pmol/liter). INTERVENTIONS Surgery was performed in 25 patients with SH (group TrSH+) and 30 without SH (group TrSH-), whereas the conservative approach was chosen by 16 patients with SH (group UntrSH+) and 37 without SH (group UntrSH-). MAIN OUTCOME MEASURES During the follow-up, the improvement/worsening of body weight, blood pressure, or glucose and cholesterol levels was defined in the presence of a greater than 5% weight decrease/increase and following the European Society of Cardiology or the Adult Treatment Panel III criteria, respectively. RESULTS In group TrSH+, weight, blood pressure, and glucose levels improved (32, 56, and 48%, respectively) more frequently than in group UntrSH+ (12.5%, P = 0.05; 0.0%, P < 0.0001; 0.0%, P = 0.001; and 0.0%, P = 0.0014, respectively). In group UntrSH+, blood pressure, glucose, and low-density lipoprotein levels worsened more frequently (50.0, 37.5, and 50.0%, respectively) than in group TrSH+ (0.0%, P < 0.0001; 0.0%, P = 0.001; and 20.0%, P = 0.05, respectively). CONCLUSIONS Regarding the various components of the metabolic syndrome, in patients with adrenal incidentalomas and SH, surgery is beneficial.
Molecular Typing of Pneumococci for Investigation of Linked Cases of Invasive Pneumococcal Disease

ABSTRACT In winter 2007-2008, an outbreak of pediatric pneumonia caused by serotype 5 pneumococci was identified in a northeast London suburb. Variable number of tandem repeat analyses clustered these pneumococci from the other serotype 5 pneumococci in the United Kingdom, highlighting the importance of this discriminative typing method in supporting epidemiological investigations.
Projections of the nucleus of the optic tract to the nucleus reticularis tegmenti pontis and prepositus hypoglossi nucleus in the pigmented rat as demonstrated by anterograde and retrograde transport methods

Abstract The visual pathways from the nucleus of the optic tract (NOT) to the nucleus reticularis tegmenti pontis (NRTP) and prepositus hypoglossi nucleus (ph) were studied following injections of tritiated leucine into the NOT of pigmented rats. The cell bodies of origin of the pretectal-NRTP, NRTP-ph, and pretectal-ph projections were determined using retrograde horseradish peroxidase (HRP) technique. The pretectum projects strongly to the rostral two-thirds of the central and pericentral subdivisions of the NRTP and sends a remarkably smaller projection to the ph. Both are entirely ipsilateral. The fibers destined for the ph travel with the NOT-NRTP bundle, pass through the NRTP, traverse the medial longitudinal fasciculus, and are distributed to the rostral one-half of the ph. The retrograde HRP studies confirm these pathways. The pretectal projections to the NRTP arise from neurons in the rostromedial NOT; those to the ph are located primarily in the rostral NOT although small numbers are found within the anterior, posterior, and olivary pretectal nuclei. Of major importance is the fact that the ph injections retrogradely label neurons within the NRTP and the adjacent paramedian pontine reticular formation. This NRTP-ph projection is entirely bilateral and arises from parts of both subdivisions of the nucleus targeted by NOT afferents. Both the direct NOT-ph and indirect NOT-NRTP-ph connections provide the anatomical basis for the relay of visual (optokinetic) information to the perihypoglossal complex and, presumably, by virtue of reciprocal ph-vestibular nuclear connections, to the vestibular nuclei itself. Such pathways confirm previous physiological studies in rat and, in particular, clarify the contrasting effects of electrolytic lesions of NRTP in rat which completely abolishes optokinetic nystagmus (OKN) (Cazin et al., 1980a) vs kainic acid lesions which produce only minor effects on OKN slow velocity (Hess et al., 1988). Given these differential effects, one concludes that the critical pathway for OKN passes in relation to, but is not significantly relayed by, the neurons of the NRTP or adjacent pontine tegmentum. The present studies suggest that one such fiber system is the NOT-ph bundle. How this relatively small projection compares to other possible fiber of passage systems remains to be determined electrophysiologically.
The effects of intrinsic vasopressin on urinary aquaporin-2 excretion and urine osmolality during surgery under general anesthesia.

UNLABELLED A radioimmunoassay has been established to measure urinary aquaporin-2 excretion (u-AQP2). To elucidate how u-AQP2 changes when endogenous vasopressin is increased independently of plasma osmolality, we estimated u-AQP2 during general anesthesia for surgery. We collected urine and blood samples from 50 patients before and 90 and 180 min after anesthetic induction. Plasma (29.1+/-12.6 pg/mL) and urinary (565.1+/-207.0 ng/gCr) vasopressin levels were markedly increased after anesthetic induction. Although no significant alteration of plasma osmolality or serum sodium concentration was observed during 180 min, u-AQP2 was significantly increased (preinduction 224.5+/-24.2 fmol/ mgCr; 90 min 243.3+/-31.8; 180 min 331.4+/-45.9), paralleling an increase of plasma and urinary vasopressin. The plasma vasopressin concentration after anesthetic induction was far in excess of that expected based on plasma osmolality. Individual plasma and urinary vasopressin concentrations correlated significantly with u-AQP2. At 180 min after anesthesia, plasma osmolality did not change, but urine osmolality decreased despite increased u-AQP2, and a preanesthetic positive correlation between urine osmolality and u-AQP2 disappeared. Thus, although u-AQP2 correlates with increased intrinsic vasopressin levels, the increase in u-AQP2 did not directly contribute to urine concentration. Apparently, an escape from the physiologic effects of high vasopressin level occurs during anesthesia via a mechanism independent of aquaporin-2. We conclude that the anesthetic would interfere with the urinary concentrating capacity at the level of AQP2-action. IMPLICATIONS The excessive increase of intrinsic vasopressin exactly augmented urinary aquaporin-2 excretion, resulting in urine concentration; however, anesthesia seemed to modify this process possibly by interfering with the aquaporin-2 action.
Overcoming fixed mindsets: The role of affect

When there is an established strategy to solve a problem, we often approach the problem with a mindset that makes us blind for more efficient solutions. We examined the role of affect in overcoming such blinding effects of mindsets. As positive affect is known to broaden and negative affect to narrow thought–action repertoires, we speculated that positive affect facilitates and negative affect impedes the overcoming of a current mindset. To induce a mindset, participants initially solved 60 similar problems which were only solvable using the same complex strategy. After a short break in which positive or negative affect was induced, participants continued to work on the problems. Critically, there now was an additional simple way to solve the problems. Participants experiencing positive affect were more likely to detect the simple solution than participants experiencing negative affect. These findings reveal that affect modulates how much we are constrained by current mindsets.
First-Cousin Matings and Congenital Heart Disease in Saudi Arabia

Background: Consanguinity may be a risk factor that contributes to congenital heart disease in an inbred population, particularly among first cousins; with high rates of intermarriage between relatives, consanguinity is associated with congenital heart disease particularly among first cousins. Patients and Methods: This study examines a group of 1,028 consecutive congenital heart disease (CHD) patients identified through the Congenital Heart Disease Registry at King Faisal Specialist Hospital in Riyadh, Saudi Arabia. Families were interviewed by an Arabic-speaking data collector for information on consanguinity and demographic data. After exclusions for nonavailability, data were collected on 949 cases and the proportions of first-cousin consanguinity in the study sample were compared to national population data. A z test of proportions was utilized to test the hypothesis that there are higher proportions of first-cousin consanguinity in the study sample of congenital heart patients than in the general population. Findings: Data indicate that the proportion of first-cousin matings among CHD patients is significantly higher than that of first-cousin intermarriages reported in the general population (p < 0.001). Regional breakdowns of the data substantiate significant differences (p < 0.001) in the proportions of first-cousin consanguinity in the study sample compared to the general population. Interpretation: In a population with a high degree of inbreeding, consanguinity may exacerbate underlying genetic risk factors, particularly for offspring of first-cousin matings. This finding has public health implications for genetic counseling and prevention of some cardiac malformations.
Statistical analysis regarding: statins alleviate experimental nerve injury-induced neuropathic pain.

Letter To Editor: We read with great interest the article by Shi et al. The article indicated that rosuvastatin and simvastatin could attenuate neuropathic pain, respectively, by mediating nerve injury– associated inflammatory responses. We agree with their conclusion that statins may have benefits in alleviating the neuropathic pain, and this viewpoint has been confirmed by other studies. However, we found some flaws in the statistical analysis in this article. The authors stated that they obtained the following effects of rosuvastatin on reversing mechanical and thermal hyperalgesia: (1) the 2 mg/kg dose of rosuvastatin was less effective than the 5, 10, and 20 mg/kg doses when administered daily, beginning on the day of partially ligated sciatic nerve, (2) the 10 mg/kg dose of rosuvastatin was more effective than the 2 and 5 mg/kg doses, but the 20 mg/kg dose was not as effective as the 10mg/kg dose when administered 8 to 14 days after nerve injury, and (3) the 20 mg/kg dose of simvastatin was more effective than the 10 mg/kg dose when administered 8 to 14 days after nerve injury. In other preclinical studies, different doses of statins have been reported to reverse neuropathic pain. Nevertheless, in the article by Shi et al., comparisons of the effects of rosuvastatin were made among different dose groups on mechanical and thermal sensitivity when administered 8 to 14 days after nerve injury. The samemethod was performed to examine the effects of different doses of simvastatin. However, according to the statistical analysis they provided (from the figures), we found that the authors only performed an unpaired t test. An unpaired t test was used to compare the effects of different doses of rosuvastatin and simvastatin groups, respectively, with the vehicle group at their corresponding time points on mechanical and thermal sensitivity. In other words, the authors’ assertions regarding group comparisons were not directly supported by any specific statistical test or P value. Although the authors talked about comparisons between groups, there was no proper statistical test overall. All comparisons were made with the vehicle group or baseline. In research reports, one should only report comparisons that were supported by a statistical test. However to our knowledge, under the assumption of the data having a normal distribution and when there are 3 or more groups for multiple comparisons, it is better either to use 1-way analysis of variance followed by post hoc multiple tests directly or to use unpaired t tests corrected by Bonferroni corrections or other correcting methods. This approach is more appropriate than using unpaired t tests only. Therefore, this article would be much stronger and useful to readers if the authors’ assertions regarding dose effects were supported with such statistical tests.
Secondary metabolites from endophytic Streptomyces aureofaciens CMUAc130 and their antifungal activity.

RETRACTION The results and conclusions reported in this paper, which was accepted for publication on 11 February 2005, are substantively the same as those reported in a paper by the same authors published in Annals of Microbiology (Taechowisan et al., 2005), accepted for publication on 14 January 2005. The authors agree that the slight differences do not justify the publication of this second paper, and they acknowledge that this paper would not have been accepted for publication in Microbiology if the Editors had been aware of this earlier submission; this paper is therefore retracted.
Folding, interaction with GRP78-BiP, assembly, and transport of the human immunodeficiency virus type 1 envelope protein

A detailed kinetic and quantitative analysis of the early and late biosynthetic events undergone by the human immunodeficiency virus type 1 envelope protein expressed by a recombinant vaccinia virus was performed. Early folding events that occurred in the endoplasmic reticulum included disulfide bond formation (t1/2 approximately 10 min), folding of envelope protein into a form competent to bind CD4 (t1/2 approximately 15 min), and specific and transient association and dissociation with GRP78-BiP (t1/2 approximately 25 min). After initial folding, envelope protein monomers formed noncovalently associated dimers with high efficiency (t1/2 approximately 30 min). Studies with brefeldin A, a compound that inhibits endoplasmic reticulum-to-Golgi transport, suggested that assembly occurred in the endoplasmic reticulum while cleavage of gp160 into gp120/gp41 subunits occurred in a post-endoplasmic reticulum compartment. Transport to the Golgi was monitored by modification of N-linked sugars to forms partially resistant to endoglycosidase H. The kinetics of endoglycosidase H resistance were nearly identical to the kinetics of gp160 cleavage (t1/2 approximately 80 min). Cleavage efficiency was strongly cell type dependent, ranging from 13 to 70%. By contrast, approximately 50% of the gp120 generated by the cleavage event was shed (t1/2 approximately 120 min) regardless of the cell type used. The results are discussed in terms of the overall biosynthetic pathway of the envelope protein and provide a framework with which to assess the effects of mutations on structure and function.
Using semidiscrete decomposition and vector space models to identify users of social networks

Users of social media interact with the network and its users. Each interaction creates network‐specific data between the engaged users and the chosen social avenue. Over time, these engagements accumulate to describe the user's social fingerprint, a data trail that encapsulates the user's identity on the network. The agglomeration of this information showcases the user's activity on the social network and establishes a traceable social fingerprint. The focus of this study is to examine the accuracy of user identification via semidiscrete decomposition of social network adjacency matrices. The use of semidiscrete decomposition in this application creates separability amongst observed data trails as a means to establish uniqueness amongst the users of the social network. The results presented herein illustrate to what extent a user's social fingerprint can be both quantified and identified on a social network through time. Copyright © 2015 John Wiley & Sons, Ltd.
Theoretical study of the Si(100) surface reconstruction.

We present the results of a systematic study of the reconstruction of the Si(100) surface based upon total energies calculated within the framework of the local-density approximation. We focus on the extent to which total energy differences may be calculated reliably by examining these differences for the ideal surface and four proposed reconstructions: p(2\ifmmode\times\else\texttimes\fi{}1) symmetric, p(2\ifmmode\times\else\texttimes\fi{}1) asymmetric, p(2\ifmmode\times\else\texttimes\fi{}2), and c(4\ifmmode\times\else\texttimes\fi{}2). The calculations were performed using norm-conserving pseudopotentials and a plane-wave basis. The convergence of the total energy differences was assessed by varying the energy cutoff used to truncate the plane-wave basis and the number of sampling points used to perform Brillouin zone (BZ) integrals over a large range. The effect of optimizing atomic geometries as a function of the energy cutoff and density of BZ sampling points was determined. With the exception of the p(2\ifmmode\times\else\texttimes\fi{}2) and c(4\ifmmode\times\else\texttimes\fi{}2) reconstructions, whose energies only differ by 3 meV per dimer, we are able to unambiguously determine the energy ordering of the five systems studied. Disagreements between previous calculations can be largely understood in terms of the different energy cutoffs and BZ samplings used. The electronic structures of the different reconstructions are calculated and compared.