Miracle-dz/UniFAR-FTUs huggingface dataset:
Photodynamic therapy as an alternative treatment for disinfection of bacteria in oral biofilms

Biofilm‐related diseases such as caries and periodontal disease are prevalent chronic oral infections which pose significant oral and general health risks. Biofilms are sessile communities attached to surfaces. Photodynamic therapy (PDT) has been demonstrated to have a significant anti‐microbial effect and presents as an alternative to treating biofilm‐related disease. The aim of this study was to determine the ability of porfimer sodium induced PDT to treat localized infections of Streptococcus mutans in biofilm communities.
Dissolved Organic Nitrogen Production and Export by Meridional Overturning in the Eastern Subpolar North Atlantic

Dissolved organic matter (DOM) is produced in the surface and exported towards the deep ocean, adding ∼2 PgC/year to the global carbon export. Due to its central role in the Meridional Overturning Circulation, the eastern subpolar North Atlantic (eSPNA) contributes largely to this export. Here we quantify the transport and budget of dissolved organic nitrogen (DON) in the eSPNA, in a box delimited by the OVIDE 2002 section and the Greenland‐Iceland‐Scotland sills. The Meridional Overturning Circulation exports >15.9 TgN/year of DON downward and, contrary to the extended view that these are materials of subtropical origin, up to 33% of the vertical flux derives from a net local DON production of 7.1 ± 2.6 TgN/year. The low C:N molar ratio of DOM production (7.4 ± 4.1) and the relatively short transit times in the eSPNA (3 ± 1 year) suggest that local biogeochemical transformations result in the injection of fresh bioavailable DOM to the deep ocean.
The effect of moderate acute psychological stress on working memory-related neural activity is modulated by a genetic variation in catecholaminergic function in humans

Acute stress has an important impact on higher-order cognitive functions supported by the prefrontal cortex (PFC) such as working memory (WM). In rodents, such effects are mediated by stress-induced alterations in catecholaminergic signaling, but human data in support of this notion is lacking. A common variation in the gene encoding Catechol-O-methyltransferase (COMT) is known to affect basal catecholaminergic availability and PFC functions. Here, we investigated whether this genetic variation (Val158Met) modulates effects of stress on WM-related neural activity in humans. In a counterbalanced crossover design, 41 healthy young men underwent functional magnetic resonance imaging (fMRI) while performing a numerical N-back WM task embedded in a stressful or neutral context. Moderate psychological stress was induced by a well-controlled procedure involving viewing strongly aversive (versus emotionally neutral) movie material in combination with a self-referencing instruction. Acute stress resulted in genotype-dependent effects on WM performance and WM-related activation in the dorsolateral PFC, with a relatively negative impact of stress in COMT Met-homozygotes as opposed to a relatively positive effect in Val-carriers. A parallel interaction was found for WM-related deactivation in the anterior medial temporal lobe (MTL). Our findings suggest that individuals with higher baseline catecholaminergic availability (COMT Met-homozygotes) appear to reach a supraoptimal state under moderate levels of stress. In contrast, individuals with lower baselines (Val-carriers) may reach an optimal state. Thus, our data show that effects of acute stress on higher-order cognitive functions vary depending on catecholaminergic availability at baseline, and thereby corroborate animal models of catecholaminergic signaling that propose a non-linear relationship between catecholaminergic activity and prefrontal functions.
GSTT1 Null Genotype Contributes to Lung Cancer Risk in Asian Populations: A Meta-Analysis of 23 Studies

Background Genetic variation in glutathione S-transferases (GSTs) may contribute to lung cancer risk. Many studies have investigated the correlation between the Glutathione S-transferase T1 (GSTT1) null genotype and lung cancer risk in Asian population but yielded inconclusive results. Methodology/Principal Findings We performed a meta-analysis of 23 studies including 4065 cases and 5390 controls. We assessed the strength of the association of GSTT1 with lung cancer risk and performed sub-group analyses by source of controls, smoking status, histological types, and sample size. A statistically significant correlation between GSTT1 null genotype and lung cancer in Asian population was observed (OR = 1.28, 95% CI = 1.10, 1.49; Pheterogeneity<0.001 and I2 = 62.0%). Sub-group analysis revealed there was a statistically increased lung cancer risk in ever-smokers who carried the GSTT1 null genotype (OR = 1.94, 95% CI = 1.27, 2.96; P heterogeneity = 0.02 and I2 = 58.1%). It was also indicated that GSTT1 null genotype could increase lung cancer risk among population-based studies (OR = 1.25, 95% CI = 1.04, 1.50; Pheterogeneity = 0.003 and I2 = 56.8%). The positive association was also found in studies of sample size (≤500 participants) (OR = 1.34, 95% CI = 1.10, 1.62; Pheterogeneity<0.001 and I2 = 65.4%). Conclusions These meta-analysis results suggest that GSTT1 null genotype is associated with a significantly increased risk of lung cancer in Asian population.
Exciton-phonon scattering effects on photoluminescence of hybrid lead halide perovskite

Organometal halide perovskite materials have gained tremendous attention in the field of photovoltaic, light emitting and lasing devices. Perovskite materials offer some promising optical properties like tunable direct band gap, large light absorption coefficient, high quantum efficiency and long-range balanced electron-hole transport length. The mobility and the photoluminescence line width broadening in hybrid lead halide perovskite are affected by phonon scattering. For the development of efficient perovskite devices it is thus crucially important to establish how excitons interact with phonons in this material. Here we investigate the temperature dependence of the photoluminescence full width at half maximum (FWHM) for CH3NH3PM3 perovskite in the temperature regime of 10–300 K. We developed a quantitative model to calculate the photoluminescence (PL) peak energy variation as well as FWHM broadening adoptiong the Monte-Carlo simulation. Miller-Abrahams expression is used to incorporate the exciton hopping between the localized states assuming the Gaussian distribution of the excitons. Our computation elucidates that the FWHM broadens with increasing temperature due to scattering with exciton-optical phonons.
Mitochondrial C-tract alteration in premalignant lesions of the head and neck: a marker for progression and clonal proliferation.

PURPOSE Although mitochondrial DNA mutations have been described recently in many different tumor types, the nature and timing of such alterations remain unclear. In an effort to further examine the role of mitochondrial DNA mutations in carcinogenesis, we examined 137 premalignant lesions of the head and neck from 93 patients for DNA alterations in the poly-cytosine tract (C-tract) of the displacement loop, discovered recently to be a hot spot of mitochondrial DNA alteration. EXPERIMENTAL DESING: All premalignant lesions were tested using a length-based PCR assay, which amplified the C-tract region of mitochondrial DNA. Somatic microsatellites at six loci were also tested on a subset of patients with metachronous or synchronous lesions found to possess a mitochondrial C-tract alteration. RESULTS Thirty-four of 93 (37%) patients harbored lesions that displayed a C-tract alteration. There was a clear increase in incidence from histologically benign hyperplasia (22%) to squamous carcinoma in situ (62%: P < 0.01). We also tested synchronous dysplastic lesions, metachronous dysplastic lesions, and normal epithelium adjacent to dysplastic epithelium with this assay. In most cases, the mitochondrial C-tract status identified a clonal relationship between these lesions. Genomic microsatellites also confirmed that a clonal relationship was present in many of these cases. CONCLUSIONS Mitochondrial DNA alterations in the head and neck occur in the earliest premalignant lesions and demonstrate a rising incidence that parallels histological severity. These alterations are valuable as additional markers of histopathological progression.
Restoration of telomeres in human papillomavirus-immortalized human anogenital epithelial cells

Loss of telomeres has been hypothesized to be important in cellular senescence and may play a role in carcinogenesis. In this study, we have measured telomere length in association with the immortalization and transformation of human cervical and foreskin epithelial cells by the human papillomavirus type 16 or 18 E6 and E7 open reading frames. By using a telomeric TTAGGG repeat probe, it was shown that the telomeres of precrisis normal and E6-, E7-, and E6/E7-expressing cells gradually shortened with passaging (30 to 100 bp per population doubling). Cells that expressed both E6 and E7 went through a crisis period and gave rise to immortalized lines. In contrast to precrisis cells, E6/E7-immortalized cells generally showed an increase in telomere length as they were passaged in culture, with some later passage lines having telomeres that were similar to or longer than the earliest-passage precrisis cells examined. No consistent association could be made between telomere length and tumorigenicity of cells in nude mice. However, of the three cell lines that grew in vivo, two had long telomeres, thus arguing against the hypothesis that cancer cells favor shortened telomeres. Our results indicate that arrest of telomere shortening may be important in human papillomavirus-associated immortalization and that restoration of telomere length may be advantageous to cells with regard to their ability to proliferate.
Inhibitory Potential of Prodomain of Plasmodium falciparum Protease Serine Repeat Antigen 5 for Asexual Blood Stages of Parasite

Plasmodium falciparum serine repeat antigen 5 (SERA5) is a target for both drug and vaccine intervention against malaria. SERA5 is secreted in the parasitophorous vacuole where it is proteolytically processed before schizont rupture. Among the processed products is a 50.8-kDa central domain of the protease, which possesses chymotrypsin-like activity and consists of a 28.9-kDa catalytic domain with a 21.9-kDa N-terminal prodomain, which remain attached together. Because SERA5 has been implicated in merozoite egress from host erythrocytes, the effect of the prodomain and a heptapeptide derived from its C-terminus spanning from D560 to F566 (DNSDNMF) on parasite growth was studied. When E. coli-expressed prodomain was incubated with parasite culture, a significant delay in transition from schizont to ring stages was observed up to nanomolar concentrations. The peptide, DNSDNMF also showed similar effects but at nearly 1000-fold higher concentrations. The peptide was also found to interact with the catalytic domain. These data demonstrate the crucial role of SERA5 prodomain for the egress process. Given the inhibitory potential of the prodomain for the parasite, we suggest that peptidomimetic inhibitors based on SERA5 prodomain sequences can be developed as future therapeutics against malaria.
Pan1p, Yeast eps15, Functions as a Multivalent Adaptor That Coordinates Protein–Protein Interactions Essential for Endocytosis

A genetic screen for factors required for endocytosis in the budding yeast Saccharomyces cerevisiae previously identified PAN1. Pan1p is a homologue of the mammalian protein eps15, which has been implicated in endocytosis by virtue of its association with the plasma membrane clathrin adaptor complex AP-2. Pan1p contains two eps15 homology (EH) domains, a protein–protein interaction motif also present in other proteins that function in membrane trafficking. To address the role of Pan1p and EH domains in endocytosis, a yeast two-hybrid screen was performed using the EH domain–containing region of Pan1p. This screen identified yAP180A, one of two yeast homologues of a class of clathrin assembly proteins (AP180) that exhibit in vitro clathrin cage assembly activity. In vitro binding studies using GST fusion proteins and yeast extracts defined distinct binding sites on yAP180A for Pan1p and clathrin. yAP180 proteins and Pan1p, like actin, localize to peripheral patches along the plasma membrane. Mammalian synaptojanin, a phosphatidylinositol polyphosphate-5-phosphatase, also has been implicated in endocytosis recently, and three synaptojanin-like genes have been identified in yeast. We observed genetic interactions between the yeast SJL1 gene and PAN1, which suggest a role for phosphoinositide metabolites in Pan1p function. Together with other studies, these findings suggest that Pan1p coordinates regulatory interactions between proteins required for both endocytosis and actin-cytoskeleton organization; these proteins include the yAP180 proteins, clathrin, the ubiquitin–protein ligase Rsp5p, End3p, and synaptojanin. We suggest that Pan1p (and by extension eps15) serves as a multivalent adaptor around which dynamic interactions between structural and regulatory components of the endocytic pathway converge.
On the minimality and global consistency of row-convex constraint networks

Constraint networks have been shown to be useful in formulating such diverse problems as scene labeling, natural language parsing, and temporal reasoning. Given a constraint network, we often wish to (i) find a solution that satisfies the constraints and (ii) find the corresponding minimal network where the constraints are as explicit as possible. Both tasks are known to be NP-complete in the general case. Task (1) is usually solved using a backtracking algorithm, and task (ii) is often solved only approximately by enforcing various levels of local consistency. In this paper, we identify a property of binary constraint called row convexity and show its usefulness in deciding when a form of local consistency called path consistency is sufficient to guarantee that a network is both minimal and globally consistent. Globally consistent networks have the property that a solution can be found without backtracking. We show that one can test for the row convexity property efficiently and we show, by examining applications of constraint networks discussed in the literature, that our results are useful in practice. Thus, we identify a class of binary constraint networks for which we can solve both tasks (i) and (ii) efficiently. Finally, we generalize the results for binary constraint networks to networks with nonbinary constraints.
Ray Tracing with the Single Slab Hierarchy

Bounding volume hierarchies have become a very popular way to speed up ray tracing. In this paper we present a novel traversal and approximation scheme for bounding volume hierarchies, which is comparable in speed, has a very compact traversal algorithm and uses only 25% of the memory, compared to a standard bounding volume hierarchy.
B Vitamins, Homocysteine and Bone Health

Nutrition is one of the most important modifiable factors involved in the development and maintenance of good bone health. Calcium and Vitamin D have confirmed and established roles in the maintenance of proper bone health. However, other nutritional factors could also be implicated. This review will explore the emerging evidence of the supporting role of certain B Vitamins as modifiable factors associated with bone health. Individuals with high levels of homocysteine (hcy) exhibit reduced bone mineral density (BMD), alteration in microarchitecture and increased bone fragility. The pathophysiology caused by high serum homocysteine is not completely clear regarding fractures, but it may involve factors, such as bone mineral density, bone turnover, bone blood flow and collagen cross-linking. It is uncertain whether supplementation with B Vitamins, such as folate, Vitamin B1, and Vitamin B6, could decrease hip fracture incidence, but the results of further clinical trials should be awaited before a conclusion is drawn.
Seasonal Elevated and Variable Groundwater Iron in Chandrapur District, Central India

Groundwater iron concentrations were monitored from rural area of the Chandrapur district, Central India during winter, summer and post-monsoon at 36 sampling locations so as to map and quantify its levels. Grab sampling was carried out for groundwater sampling from dug wells (DW) (n=2, 5.55%) and hand pumps (HP) (n=34, 94.44%). Iron concentration was determined by acid digestion method and further analysis by using ICP-OES. Maximum iron concentration in winter was 47.100 mg/L (Ballarpur, HP), 3.825 mg/L (Ballarpur, HP) in summer and 3.714 mg/L (Visapur, HP) in post-monsoon. Average iron concentration in winter, summer, and post-monsoon was 3.522 mg/L, 0.730 mg/L and 0.582 mg/L respectively, which were above the acceptable limit of the Indian Standard (IS) and WHO aesthetic limit for iron (0.3 mg/L). Seasonal variation in groundwater iron concentration was observed in the order of winter>post-monsoon>summer. Distribution of iron with IS revealed a number of samples above the permissible limit and in the order of summer>winter>post-monsoon. In case of a distribution on WHO, JECFA and IOM recommendations, number of samples in high to very high category was in the order of winter>summer>post-monsoon. It can be concluded that seasonal elevated and variable groundwater iron concentration was observed from the study area. A number of samples had the concentration several times above the IS acceptable limit and WHO aesthetic cut-off. The plausible reasons for these observations can be assigned to geology, water source type (HP/DW), space and time, the proximity of water source to minerals and ores present in the earth crust, physicochemical characteristics of water and dissolution and leaching of metal in groundwater
RISK FACTORS AND OUTCOME OF PRIMARY INTRACEREBRAL HEMORRHAGE WITH SPECIAL REFERENCE TO ASPIRIN PERTTI SALOHEIMO

Primary intracerebral hemorrhage (ICH) comprises 10–15% of all strokes. Arterial hypertension and warfarin use are well documented risk factors for ICH, but aspirin use also seems to predispose to ICH. The annual incidence of primary ICH in western populations is 12–31 / 100,000. Mortality is high: 14–52% during the first month and 14–80% during the first year after ICH. The size and location of the hemorrhage, a midline shift in head computed tomography, intraventricular spread of the hemorrhage, level of consciousness on admission, and high blood glucose independently predict mortality. For a risk factor study, 98 consecutive patients admitted into the Department of Neurology, Oulu University Hospital, because of ICH between January 1993 and September 1995 were compared with 206 control subjects drawn from a population register. Thromboxane and prostacyclin biosynthesis were measured from serial urine samples of 43 patients. For outcome studies, all subjects (n = 208) with incident ICH during the study period in the population of Northern Ostrobothnia, Finland, were identified. Untreated hypertension was the main modifiable risk factor for ICH. Use of aspirin appeared to be a significant risk factor for ICH in the subjects with a history of epistaxis. Enhanced thromboxane and prostacyclin biosynthesis were observed in the acute phase and 3 months after ICH. Regular use of aspirin preceding ICH doubled the 3-month mortality rate compared with nonusers of aspirin/ warfarin. Aspirin use also associated with early hematoma growth. Patients with ICH showed increased long-term mortality up to 7 years after ICH compared to controls. No excess mortality was observed among those with good recovery at 3 months, but those who were severely disabled at 3 months after ICH showed marked excess mortality.
Endothelial nitric oxide synthase Glu298Asp gene polymorphism in periodontal diseases.

BACKGROUND Endothelial nitric oxide synthase (eNOS) is involved in key steps of immune response. The aim of the present study was to evaluate genotype distribution and genotype-phenotype association in periodontal disease regarding Glu298Asp polymorphism of the eNOS gene. METHODS A total of 272 subjects were included into the study. Genomic DNA was obtained from the peripheral blood of 51 chronic periodontitis (CP) patients, 48 generalized aggressive periodontitis (GAgP), and 173 reference controls. Polymerase chain reaction (PCR) amplification and subsequent BanII restriction fragment length polymorphism (RFLP) analysis were used to detect eNOS Glu298Asp polymorphism. Probing depth, clinical attachment loss, plaque accumulation, and bleeding on probing (BOP) were recorded. The data were analyzed by the chi2 test, logistic regression, and Mann-Whitney U test. RESULTS The distributions of eNOS Glu298Asp genotypes and alleles were similar among study groups. Subjects with the Asp allele (Asp+) were statistically higher in the CP group compared to the control group (odds ratio [OR] = 1.957; 95% confidence interval [95% CI] = 1.038 to 3.689). In the GAgP group, BOP (%) was significantly higher in patients with the 298Asp allele (Asp+) compared to patients without the Asp allele (Asp-) (P = 0.015). CONCLUSIONS The present study showed that eNOS Glu298Asp polymorphism is associated with BOP in GAgP patients. Moreover, the 298Asp allele of the eNOS gene might be related to CP in the Turkish population.
Intestinal dipeptidases. Dipeptidase activities in small intestinal biopsy specimens from a clinical material.

Quantitative assay of dipeptidase activity in small intestinal biopsies now can be made as routine analysis. Nine different dipeptidase activities have been studied in biopsies from 22 patients with gastrointestinal disorders. According to the histology of the mucosa and the fecal fat excretion the patients were divided into three groups. No significant difference in the dipeptidase activities was found between nine patients with normal mucosa and normal fecal fat excretion (Group I) and ten patients with normal mucosa and steatorrhea of unknown origin (Group II). Three patients (Group III) with gluten-induced enteropathy (abnormal mucosa and steatorrhea) showed, in contrast, significantly lower dipeptidase activities. A general increase in the activities was observed after treatment with gluten-free diet. It is suggested that the low activities obtained in these patients should be ascribed to the ‘atrophy’ of villi rather than to a primary lack of dipeptidases.
Does morbid obesity influence the success and complication rates of extracorporeal shockwave lithotripsy for upper ureteral stones?

OBJECTIVE The aim of the current study was to investigate whether obesity influences the outcome of extra-corporeal shockwave lithotripsy (ESWL) treatment for upper ureteral stones. MATERIAL AND METHODS This is a retrospective study of 134 patients who underwent ESWL between June 2011 and May 2014. Patients were divided into 2 groups. Group 1 comprised 94 patients of normal weight, and group 2 comprised 40 morbidly obese patients. Patients in both groups had upper ureteral stones. RESULTS The mean age of groups 1 and 2 was 45.6±12.1 and 45.3±15.5 years, respectively (p=0.98). There was no significant difference in demographic variables between the groups. The mean stone size in groups 1 and 2 was 81.7±25.7 mm(2) and 86.3±22.4 mm(2), respectively (p=0.51), the mean body mass index (BMI) was 27.4±2.9 and 42.9±2.1, respectively (p<0.01), the mean number of ESWL sessions was 2.4±0.6 and 2.4±0.7, respectively (p=0.97), and the mean follow-up time was 7.1±3.4 and 6.6±2.8 weeks, respectively (p=0.67). The overall stone-free rate was 82% in group 1 and 67% in group 2 (p=0.01). CONCLUSION It is well-known that morbidly obese patients have higher rates of anesthesia-related problems due to the comorbidities commonly observed in this population. In the current study, we found that ESWL is a safe and acceptable treatment option for morbidly obese patients with upper ureteral stones.