Miracle-dz/UniFAR-FTUs huggingface dataset:
Oxidative Damage in an Experimentally Induced Gastric and Gastroduodenal Reflux Model

The exact pathophysiologic mechanisms of esophageal cell damage and carcinogenesis by gastroesophageal reflux are not clearly understood. The aim of this study was to evaluate the damage to the esophageal epithelium that occurs after acid reflex and mixed acid and bile reflux by assessing histopathology, reactive oxygen species, and DNA damage. Eighty 10-week-old male Sprague-Dawley rats were divided into two groups, an acid reflux group and a mixed (acid/bile) reflux group. Acid reflux was achieved by esophagogastroplasty in which mixed reflux was encouraged via esophagoduodenal anastomosis. Each group contained a control subgroup that underwent sham laparotomy alone. The rats were killed 3, 6, 9, and 12 months after surgery. Malondialdehyde, protein carbonyl content, and DNA damage were determined in lymphocytes. Histopathologic analysis was performed according to the histologic activity index. Inflammation, ulcer, and regeneration in both reflux groups were significantly increased in the esophagus at 3, 6, 9, and 12 months compared with the control group. Mucosal damage was greater in the mixed reflux group compared with the gastric reflux group. Malondialdehyde and carbonyl content in the serum, and DNA damage in lymphocytes, were significantly increased in both reflux groups. At 9 and 12 months, oxidative damage was increased in the mixed reflux group compared with the acid reflux group. Oxygen-derived free radicals seem to be one of the important mediators in the evaluation and generation of reflux esophagitis. The impact of oxygen free radicals, as demonstrated in this study, can be evaluated by assessing the damage that they incur to lipid membranes, serum proteins, and circulating lymphocyte DNA. Serum malondialdehyde and carbonyl content as well as lymphocyte DNA damage were significantly increased in the setting of acid and mixed acid/bile reflux in these rodent models. Further, these serum and lymphocytic changes were associated with esophageal ulceration, inflammation, and regeneration. Evaluation of such markers as serum malondialdehyde and carbonyl content as well as evaluation of lymphocyte DNA might prove to be useful investigations in patients with precancerous and cancerous conditions in addition to conventional methods of diagnosis. Further studies, both animal and human are warranted.
Evaluation of variation in the palatal gingival biotypes using an ultrasound device.

BACKGROUND The dimensions of gingiva and different parts of the masticatory mucosa have become a subject of considerable interest in Periodontics. Studies assessing the thickness of the facial gingiva are often seen in the literature. The thickness of the palatal gingiva is a subject still less researched in periodontal therapy and implantology. OBJECTIVES To measure the thickness of the palatal gingiva using an ultrasound device 'Biometric A- Scan' and to evaluate the variation in the thickness of the palatal gingiva at the sites examined. MATERIALS AND METHODS In the 50 subjects examined, the thickness of the palatal gingiva was assessed at the maxillary anteriors, premolars and molars by an ultrasound device 'Biometric A-Scan'. The results were subjected to statistical analysis using one-way ANOVA test and Newman-Keuls multiple post hoc procedure. RESULTS Statistically significant variations existed in the palatal gingival thickness. The thickness was highest at the lateral incisor region, followed by canine, premolars, molars and central incisor. INTERPRETATION AND CONCLUSION In the subjects assessed, the thickness of the palatal gingiva at the lateral-canine area was the highest followed by the premolar area. In periodontal root coverage procedures and during implant therapy, we suggest the inclusion of the lateral incisor area, apart from the canine and premolar area, as a potential donor site for harvesting soft tissue grafts from the palatal area. However, the effect of several factors like age and sex of the patient, the anatomy of the palatal area, the influence of rugae patterns and racial and geographical differences should be taken into consideration prior to harvesting a graft from these sites. Apart from this, the study suggests that, the ultrasonographic measurements provide an elegant means of obtaining the measurements of gingival and mucosal tissues rapidly, accurately and non-invasively. Our endeavour in this research project attempts to open more avenues for studies in the field of advanced periodontal diagnosis, with the use of ultrasound, and expand the horizons of periodontal plastic surgery and implant therapy as well.
Determination of very low levels of 5-(hydroxymethyl)-2-furaldehyde (HMF) in natural honey: comparison between the HPLC technique and the spectrophotometric white method.

UNLABELLED In this work we compared 2 official methods for the determination of HMF in honey, the spectrophotometric White method and the HPLC method (International Honey Commission) for the determination of HMF in unifloral honey and honeydew samples with a very low HMF content (<4 mg/kg), which is the most critical determination in terms of accuracy and precision of methods. In honey solutions, the limits of quantification for HPLC and White methods are 0.83 mg/L and 0.67 mg/L, respectively, and the linearity range is confirmed up to 20 mg/L for the HPLC method and up to 5 mg/L for the White method. In honeys with HMF >5 mg/kg, the molar extinction coefficient is 15369, lower than the literature value of 16830, and should be used for HMF determination. For samples with HMF content in the range 1-4 mg/kg the accuracy of the 2 methods is comparable both for unifloral and honeydew samples, whereas as regards precision, the HPLC method gives better results (3.5% compared with 6.4% for the White method). So, in general, the HPLC method seems to be more appropriate for the determination of HMF in honey in the range 1-4 mg/kg thanks to its greater precision, but for samples with a HMF content of less than 1 mg/kg the analyses are inaccurate for both methods. PRACTICAL APPLICATION This work can help governmental and private laboratories that perform food analyses to choose the best method for the determination of HMF at very low levels in unifloral honey and honeydew samples.
A clustering phenomenon among HCV‐1a strains among patients coinfected with HIV from Buenos Aires, Argentina

The human immunodeficiency virus (HIV) and hepatitis C virus (HCV) share the same transmission routes which lead to high coinfection rates. Among HIV‐infected individuals such rates reached 21% in Argentina, being HCV‐1a the most predominant subtype. In this work, 25 HCV subtype 1a (HCV‐1a) strains from Argentinean patients coinfected with HIV were studied based on E2 and NS5A sequences. Phylogenetic analyses indicated that 12 strains were highly related to each other, constituting a highly supported (posterior probability = 0.95) monophyletic group that we called “M. ” The remaining HCV strains (group dispersed or “D”) were interspersed along the phylogenetic trees. When comparing both groups of HCV‐1a, 10 amino acid differences were located in functional domains of E2 and NS5A proteins that appeared to affect eventually the peptides binding to MHC‐I molecules thus favoring immune escape and contributing to the divergence of HCV genotypes. Bayesian coalescent analyses for HCV‐1a cluster M isolates indicated that the time to the most recent common ancestor (tMRCA) overlaps with the age estimated recently for the HIV‐BF epidemic in Argentina. Furthermore, the genomic characterization based on pol gene analysis from HIV viremic patients showed that most HIV isolates from patients coinfected with HCV‐1a cluster M were BF recombinants with identical recombination patterns. In conclusion, these results suggest the presence of an HCV‐1a monophyletic cluster with a potential HIV co‐transmission by phylogenetic analyses. J. Med. Virol. 84:570–581, 2012. © 2011 Wiley Periodicals, Inc.
Membrane‐type 1 matrix metalloproteinase cytoplasmic tail binding protein‐1 (MTCBP‐1) acts as an eukaryotic aci‐reductone dioxygenase (ARD) in the methionine salvage pathway

MTCBP‐1 was identified as a protein that binds the cytoplasmic tail of membrane‐type 1 matrix metalloproteinase (MT1‐MMP/MMP‐14). Since MTCBP‐1 has a putative β‐barrel structure, it is presumably a member of the recently proposed cupin superfamily that contains tremendously diverged functions of proteins in spite of their well‐conserved β‐barrel structure. MTCBP‐1 shows significant homology to the bacterial aci‐reductone dioxygenase (ARD) in the cupin family, which is an enzyme in the methionine salvage pathway (MTA cycle). Since it is difficult to speculate the functions of cupin proteins simply based on their sequence homology, we examined whether the eukaryotic ARD homologs surely function in the methionine metabolism. Under sulfur‐depleted conditions, yeast could grow when substrate of MTA cycle was provided. Disruption of the yeast ARD homolog, YMR009w gene, abolished ability of the cells to grow in this culture condition. Re‐expression of either the YMR009w or MTCBP‐1 gene restored the cell growth. Mutation analysis revealed that the glutamic acid residue in the β‐barrel fold and the N‐terminal extension from the β‐barrel fold were found to be important for the activity to restore the growth. Thus, MTCBP‐1 isolated as a binding protein for MT1‐MMP was demonstrated to function as an ARD‐like enzyme in the MTA cycle in yeast.
Influence of cue word perceptual information on metamemory accuracy in judgement of learning

Previous studies have suggested that perceptual information regarding to-be-remembered words in the study phase affects the accuracy of judgement of learning (JOL). However, few have investigated whether the perceptual information in the JOL phase influences JOL accuracy. This study examined the influence of cue word perceptual information in the JOL phase on immediate and delayed JOL accuracy through changes in cue word font size. In Experiment 1, large-cue word pairs had significantly higher mean JOL magnitude than small-cue word pairs in immediate JOLs and higher relative accuracy than small-cue pairs in delayed JOLs, but font size had no influence on recall performance. Experiment 2 increased the JOL time, and mean JOL magnitude did not reliably differ for large-cue compared with small-cue pairs in immediate JOLs. However, the influence on relative accuracy still existed in delayed JOLs. Experiment 3 increased the familiarity of small-cue words in the delayed JOL phase by adding a lexical decision task. The results indicated that cue word font size no longer affected relative accuracy in delayed JOLs. The three experiments in our study indicated that the perceptual information regarding cue words in the JOL phase affects immediate and delayed JOLs in different ways.
Who Scared the Cat? A Molecular Crime Scene Investigation Laboratory Exercise†

This introductory laboratory exercise gives first-year life science majors or nonmajors an opportunity to gain knowledge and experience in basic bioinformatics and molecular biology laboratory techniques and analysis in the context of a mock crime scene investigation. In this laboratory, students determine if a human (Lady) or dog (Kona) committed the fictional crime of scaring a cat. Students begin by performing in silico PCR using provided dog- and human-specific PCR primers to determine the sequences to be amplified and predict PCR amplicon sizes. They then BLAST (Basic Local Alignment Search Tool) the in silico PCR results to confirm that the PCR primers are designed to amplify genomic fragments of the cardiac actin gene in both dogs and humans. Finally, they use DNA quantification techniques, PCR, and agarose gel electrophoresis to identify the culprit and they confirm results by analyzing Sanger sequencing. Student learning gains were demonstrated by successful execution of the lab and by analysis and interpretation of data in the completion of laboratory reports. The student learning gains were also demonstrated by increased performance on a post-laboratory assessment compared to the pre-assessment. A post-activity assessment also revealed that students perceived gains in the skills and conceptual knowledge associated with the student learning outcomes. Finally, assessment of this introductory molecular biology and bio-informatics activity reveals that it allows first-year students to develop higher-order data analysis and interpretation skills.
Inducible overexpression and secretion of int-1 protein

The int-1 proto-oncogene is a target for insertional activation of transcription by mouse mammary tumor virus in many murine mammary tumors. Whereas no expression of int-1 is seen in normal mammary tissue, int-1 RNA can be detected in normal mice in the neural tubes of midgestation embryos and in postmeiotic spermatocytes from adult testes. I report here the results of a study in which several different antibodies against synthetic peptides were produced and used to characterize the processing and secretion of int-1 protein. CHO cells were transfected with an inducible int-1 expression vector that was subsequently amplified to generate cell lines expressing very high levels of int-1 protein. Immunoprecipitation of [35S]cysteine-labeled cell lysates from these CHO cells yielded large amounts of four immature forms of int-1 glycoprotein (molecular weights of 36,000, 38,000, 40,000, and 42,000). A significant fraction of these int-1 species formed disulfide-linked multimers. Pulse-chase and glycosidase digestion studies demonstrated that some of the immature species of int-1 protein move through the secretory pathway and are processed to a mature heterogeneous glycoprotein with a molecular weight of about 44,000. Suramin treatment of the CHO cells during pulse-chase experiments increased the amount of 44,000-molecular-weight int-1 protein in the culture medium.
Niosomal methotrexate gel in the treatment of localized psoriasis: phase I and phase II studies.

BACKGROUND Efficacy of topical methotrexate in psoriasis is limited by its penetration. AIMS The study involved the preparation of niosomal methotrexate in chitosan gel and to test the same for irritation and sensitization on healthy human volunteers followed by assessing the efficacy of the gel through double-blind placebo-controlled study on psoriasis patients and also comparing its efficacy with a marketed methotrexate gel. METHODS The methotrexate niosomes were prepared by lipid layer hydration method. The characterized niosomes were incorporated in chitosan gel. The gels were tested on 10 human volunteers to check for irritation and skin sensitivity by human repeated insult patch test (HRIPT). The formulations were assessed for efficacy by double-blind placebo-controlled study in 10 psoriasis patients for each formulation. The efficacy was calculated by psoriasis area and severity index scoring method. The global score was used to assess the progress of the disease. RESULTS The HRIPT test did not produce any significant irritation or sensitization on healthy human volunteers. The placebo and marketed gels were compared with niosomal methotrexate gel. At Week 12, with niosomal methotrexate gel, there was reduction in total score from 6.2378+/-1.4857 to 2.0023+/-0.1371. CONCLUSION These results suggest that niosomal methotrexate gel is more efficacious than placebo and marketed methotrexate gel.
ATP inhibits the hydrosmotic effect of AVP in rabbit CCT: evidence for a nucleotide P2u receptor.

In rabbit renal cortical collecting tubule (CCT), perfused in vitro at 38 degrees C, ATP in concentrations of 10(-7) M and greater inhibits arginine vasopressin (AVP)-stimulated osmotic water permeability (Pf). The P1-purinergic receptor antagonist 8-phenyltheophylline did not attenuate the inhibitory action of ATP, and the poorly hydrolyzable ATP analogue, 5'-adenylylimidodiphosphate (AMP-PNP), mimicked the effect of ATP, arguing against an effect of ATP on a P1 receptor or the "P site. " Purinergic receptor agonists inhibited AVP-stimulated Pf with the following rank order efficacy: ATP = ADP = UTP = AMP-PNP = alpha, beta-methylene-ATP > 2-methylthio-ATP >> AMP > adenosine, consistent with the pharmacology of a "nucleotide" receptor subtype. Pertussis toxin pretreatment attenuated the action of 10(-5) and 10(-6) MATP; however, 10(-4) MATP failed to inhibit the hydrosmotic action of forskolin or 8-bromoadenosine 3',5'-cyclic monophosphate. Pretreatment with the phosphodiesterase inhibitor RO20-1724 or indomethacin did not inhibit the action of ATP. Staurosporin and 3,4,5-trimethoxybenzoic acid 8-(diethylamino)octyl ester significantly attenuated the inhibition of Pf by lower concentrations of ATP. These data suggest that ATP activates nucleotide receptors on the CCT, mobilizing intracellular Ca2+, which inhibits the hydrosmotic action of AVP.
Molecular diagnosis of parasitic nematodes

There is an essential requirement for highly sensitive tools that will differentiate nematode parasites of animals and plants to the species level. For studying host range, genetic variation, virulence and resistance, the availability of well defined populations is vital. Many nematode species cannot be identified with certainty using traditional morphological or morphometric techniques. This is particularly the case for the more accessible developmental stages that, depending on the particular group concerned, live as eggs and larvae in the environment or as micro-filariae that circulate in the blood or inhabit the skin. Morphological identification of these stages requires specialized expertise and is extremely time consuming. Immunological assays have their place in nematode identification but they do not discriminate between current and previous infections, an essential requirement in many epidemiological and prevalence studies. In addition to being highly sensitive, DNA-based methods of detection define present over past infection and are not dependent on the parasite stage. Many types of methodology are available for the detection and definition of nematode DNA. This paper reviews these methods citing examples that have been used with success in the laboratory as well as the field.
Analysis of a Switched-Capacitor Converter Above its Resonant Frequency to Overcome Voltage Regulation Issue of Resonant SCCs

A resonant switched-capacitor converter (SCC) has been analyzed above its resonant frequency to realize zero-voltage switching (ZVS) and to overcome voltage regulation issue of SCCs even when wide input voltage and output power variations are applied. ZVS operation under the continuous conduction mode (CCM) conditions improves efficiency due to lower conduction and switching losses. It is more efficient than the widely used zero-current switching (ZCS) approach in recent years under the discontinuous conduction mode (DCM) condition. Because, switching losses dominant components are reduced in MOSFET-based converters under the ZVS not ZCS conditions. Also, it has been demonstrated that output voltage can be well regulated under the CCM operation when wide input voltage and load variations are used. When output voltage regulation is not the major issue, operating at fixed switching frequency higher than, but near to, the resonant frequency results smaller components, higher power density, and lower electromagnetic interference level, as compared to the constant voltage ratio DCM operation mode, widely used in recent years. Also, output voltage ripple has been calculated, in details, by considering parasitic components of the output capacitor. A 110-165 to 200 V SCC has been implemented in 206.6-402.5 kHz frequency range to deliver 100-500 W. Maximum and average efficiency values equal to 96.8% and 94% are achieved, respectively.
Habitual control of goal selection in humans

Significance Human cognition makes widespread use of goal-directed planning. However, exhaustive forward planning for tasks of real-world complexity is prohibitively computationally demanding. Much research aims to find efficient mechanisms for approximate planning. We describe an approach to this problem that exploits the computational efficiency of habit learning to select goal states that are subsequently used in planning. We also provide experimental evidence that humans implement this approach. Our findings illuminate the basis of learning and choice in humans, demonstrate an integration between mechanisms of habitual and planned control, and contribute to the development of computationally tractable planning algorithms. Humans choose actions based on both habit and planning. Habitual control is computationally frugal but adapts slowly to novel circumstances, whereas planning is computationally expensive but can adapt swiftly. Current research emphasizes the competition between habits and plans for behavioral control, yet many complex tasks instead favor their integration. We consider a hierarchical architecture that exploits the computational efficiency of habitual control to select goals while preserving the flexibility of planning to achieve those goals. We formalize this mechanism in a reinforcement learning setting, illustrate its costs and benefits, and experimentally demonstrate its spontaneous application in a sequential decision-making task.
Topical Allopurinol or Corticosteroids and Acetylcysteine in the Early Treatment of Experimental Corneal Alkali Burns: A Pilot Study

Purpose To investigate the effect of topical allopurinol on experimental corneal burns and to compare this to established treatment modalities such as topical prednisolone and acetylcysteine. Methods Twenty Wistar rats were randomly assigned to four groups (n=5 each). The groups were controls (normal saline), allopurinol 0.4% eye drops, prednisolone acetate 1% eye drops and acetylcysteine 8% eyedrops. Corneal burn was induced using a 3 mm paper disc soaked in 1N NaOH for 60 seconds. Drops were instilled 6 times per day. In addition, one drop/day ofloxacine was given to prevent secondary infections. Eyes were enucleated 50 hours later and fixed in 4.5% formaldehyde. Three histological levels of each globe were stained with hematoxylin-eosin and examined by two independent masked investigators using a 0 to 4+ inflammatory score. All pair-wise multiple comparison procedures (Student-Newman-Keuls method) were applied for statistical work-up. Results All three substances significantly reduced the number of histologically visible inflammatory cells compared to the control group (p<0,05). Conclusions In the present study, topical allopurinol was as effective as established drugs, namely steroids and acetylcysteine, in the early treatment of experimental alkali corneal burns.
Extracellular Calcium Is a Potent Inducer of Cyclo‐oxygenase‐2 in Murine Osteoblasts Through an ERK Signaling Pathway

[Ca2+]e may be important in bone turnover. We found [Ca2+]e induces COX‐2 transcription and PGE2 production in primary calvarial osteoblasts through an ERK signaling pathway. Inhibition of PGE2 production inhibited the [Ca2+]e stimulation of osteoblastic differentiation but not the increase in cell number. Hence, some effects of [Ca2+]e on bone may be mediated by COX‐2.