Miracle-dz/UniFAR-FTUs huggingface dataset:
DNA Methyltransferase and Alcohol Dehydrogenase: Gene-Nutrient Interactions in Relation to Risk of Colorectal Polyps

Disturbances in DNA methylation are a characteristic of colorectal carcinogenesis. Folate-mediated one-carbon metabolism is essential for providing one-carbon groups for DNA methylation via DNA methyltransferases (DNMTs). Alcohol, a folate antagonist, could adversely affect one-carbon metabolism. In a case-control study of colorectal polyps, we evaluated three single nucleotide polymorphisms (−149C>T, −283T>C, −579G>T) in the promoter region of the DNMT3b gene, and a functional polymorphism in the coding region of the alcohol dehydrogenase ADH1C gene, ADH1C *2. Cases had a first diagnosis of colorectal adenomatous (n = 530) or hyperplastic (n = 202) polyps at the time of colonoscopy, whereas controls were polyp-free (n = 649). Multivariate logistic regression analysis was used to estimate odds ratios (OR) and corresponding 95% confidence intervals (CI). There were no significant main associations between the DNMT3b or ADH1C polymorphisms and polyp risk. However, DNMT3b −149TT was associated with an increase in adenoma risk among individuals with low folate and methionine intake (OR, 2.00; 95% CI, 1.06-3.78, P interaction = 0.10). The ADH1C *2/*2 genotype was associated with a possibly elevated risk for adenomatous polyps among individuals who consumed >26 g of alcohol/d (OR, 1.95; 95% CI, 0.60-6.30), whereas individuals who were wild-type for ADH1C were not at increased risk of adenoma (P interaction = 0.01). These gene-diet interactions suggest that polymorphisms relevant to DNA methylation or alcohol metabolism may play a role in colorectal carcinogenesis in conjunction with a high-risk diet. (Cancer Epidemiol Biomarkers Prev 2008;17(2):330–8)
Causes of mortality among tuberculosis and HIV co-infected patients in Chiang Rai, Northern Thailand

Background The case fatality rate in patients with tuberculosis (TB) associated with human immunodeficiency virus (HIV) has been particularly high in Chiang Rai, Northern Thailand. It was almost 50% before the introduction of antiretroviral therapy in the last decade, and was still at 28% in 2008, despite expanding access to antiretroviral therapy. Reviewing the causes of death may lead to further understanding of the timeline and natural history of TB-HIV coinfection, and in so doing help to devise an effective prevention strategy in Chiang Rai. In this study, we aimed to investigate the distribution of confirmed causes of death in patients coinfected with TB and HIV in Chiang Rai, describe the causes of such deaths along the timeline of TB treatment, and identify predictors of each cause of death. Methods In this retrospective study, we reviewed the causes of death for 331 patients who died of TB-HIV coinfection at Chiang Rai Prachanukroh Hospital from 2005 to 2008. Causes of death were confirmed by reviewing medical records, vital registration, and the TB register in the province, as well as obtaining reconfirmation by two experienced HIV physicians. Results The confirmed causes of death were TB (39%), acquired immune deficiency syndrome (AIDS)-related opportunistic infections other than TB (AOI) (29%), and other systemic diseases which were neither TB nor AIDS-related opportunistic infections (nonTB-nonAOI) (16%). The definitive cause could not be confirmed in the remaining 16% of deaths. After starting the TB treatment, deaths caused by TB occurred earlier compared with deaths caused by AOI, which occurred steadily throughout the course of TB treatment, whilst deaths caused by non-TB-nonAOI increased gradually in later months. Further analysis by multivariate multinomial regression analysis showed that deaths in the first month (adjusted odds ratio [aOR] 4.64, 95% confidence interval [CI] 2.49–8.63), CD4 count ≥ 200 cells/mm3 (aOR 5.33, CI 1.05–26.10), non-category 1 TB treatment regimens (aOR 5.23, CI 1.04–9.77), and TB meningitis (aOR 3.27, CI 1.37–7.82) were significant predictors of confirmed TB deaths. Moreover, age over 45 years (aOR 3, CI 1.32–6.84) and admission as an inpatient were predictors of death caused by neither TB nor AIDS-related opportunistic infections (aOR 3.08, CI 1.39–6.80). Additional analysis showed that non-Thai patients (aOR 0.35, CI 0.12–0.99), those with an unknown CD4 count at TB diagnosis (aOR 0.16, CI 0.08–0.33), and those without an HIV diagnosis before TB treatment (aOR 0.32, CI 0.18–0.59) were less able to access antiretroviral therapy. Conclusion The timeline and predictors of causes of death may assist in devising an intervention strategy for further reduction of the TB-HIV case fatality rate.
The effects of Aspergillus fumigatus challenge on exhaled and nasal NO levels

Several studies have previously shown that exposure to indoor air microbes from moisture-damaged buildings can cause adverse health effects. Aspergillus fumigatus is one of the best-documented moulds causing health problems to those exposed. In this study, inhalation of a commercial A. fumigatus solution was assessed, to establish if it would have effects on fractional exhaled (FeNO) and nasal (FnNO) nitric oxide levels and on lung function. The results were compared with placebo challenge. A total of 28 subjects were divided into three study groups: group 1 had been exposed to occupational mould; group 2 consisted of atopic subjects; and group 3 was a control group. Some 3 h after A. fumigatus challenge, there was a considerable increase in FeNO, and a significant difference was observed between the A. fumigatus and placebo inhalations. The difference was seen in all study groups. No such differences were found in the levels of FnNO or nitrite in nasal lavage fluid. Subjects reported significantly more frequent respiratory tract symptoms after the A. fumigatus inhalation compared with placebo challenge. In conclusion, it was shown here that inhalation challenge of Aspergillus fumigatus elevated fractional exhaled nitric oxide levels. An increase in fractional exhaled nitric oxide may serve as an indicator of respiratory inflammation of acute mould exposure.
The Mode of Activation of a Barrel Column: Response Properties of Single Units in the Somatosensory Cortex of the Mouse upon Whisker Deflection

Response properties of single units in the mouse barrel cortex were studied to determine the sequence in which the neurons that form a cortical column become activated by a single‘natural’stimulus. Mice (n= 11) were anaesthetized with urethane. For a total of 153 cells, grouped by cortical layer, responses to a standardized deflection of a single whisker were characterized using poststimulus time and latency histograms. Usually, for each unit, data were collected for stimulation of its principal whisker (PW; the whiskers corresponding to the barrel column in which the cell was located) and of the four whiskers surrounding the PW. In all layers, PW stimulation evoked responses at shorter latency than surround whisker stimulation. In layers II – III and IV a bimodal distribution of cells according to latency to PW stimulation was found. Statistical analysis indicated the presence of two classes of cells in each of these layers:‘fast’units (latency < 15 ms) and 'slow’units (latency >15 ms). The great majority of cells in layers I, V and VI fired at latencies of >20 ms to PW stimulation. In general, stimulation of surround whiskers evoked a smaller response than PW stimulation. The fast cells of layer IV showed the greatest response to PW stimulation (mean = 1.78 spikes/100 ms poststimulus). Their firing was maximal during the 10–20 ms poststimulus epoch, while the slow layer IV cells fired maximally during the 20 – 30 ms poststimulus epoch. Surround inhibition occurred in all layers within the first 10 ms after stimulus onset, during which period the fast cells are the most active ones, and are thus likely to be responsible for the surround inhibition. This notion is supported by an analysis of spike duration that showed that eight of the ten cells with a thin spike (supposed to be GABAergic; McCormick et al., J. Neurophysiol., 54, 782 – 806, 1985), had PW latencies of <15 ms. We conclude that the activation of a barrel column is initially inhibitory in nature.
Rethinking dynamic capabilities from a creative action perspective

Dynamic capabilities research aims to explain how firms manage to change in order to sustain their competitive advantage. Yet, despite considerable progress, dynamic capabilities theorizing struggles to capture novelty, which lies at the heart of change. We argue that this is caused by inherent limitations of the ways in which human action has been conceptualized: dynamic capabilities theorizing to date is based on rational or normative notions of actions, neither of which account for novelty in action. Hence, we propose that to overcome this impasse dynamic capabilities research needs to incorporate a concept of creative action into its theoretical apparatus. We elaborate on the positioning of creative action relative to existing dynamic capabilities theorizing and outline its implications for future dynamic capabilities research.
Variation in leukocyte subset concentrations affects calcineurin activity measurement: implications for pharmacodynamic monitoring strategies.

BACKGROUND In renal transplantation patients, therapeutic drug monitoring of the calcineurin (CN) inhibitor cyclosporin A (CsA) is mandatory because of the drug's narrow therapeutic index. Pharmacodynamic monitoring of CN inhibition therapy could provide a tool to define and maintain the therapeutic efficacy of CsA therapy. We investigated the effect of variation in cell counts of leukocyte subsets on leukocyte CN activity measurement in renal transplant recipients. METHODS We measured leukocyte CN activity, whole blood CsA concentrations, and leukocyte subset cell counts in 25 renal transplant recipients. Blood was collected before graft implantation and CsA therapy, 1 day before transplantation when CsA therapy was already started, and 5 days after transplantation. Monocyte, granulocyte, CD4+ T-cell, CD8+ T-cell, B-cell, and natural killer-cell CN activities and CsA inhibition sensitivities were determined in vitro by a spectrophotometric CN assay. RESULTS Leukocyte CN activity was inhibited after drug intake. Inter- and intrapatient variation in leukocyte subset cell counts resulted in variation of sample composition. The mean (SD) CN activity varied among leukocyte cell subsets, ranging from 650 (230) to 166 (26) pmol/min/10(6) cells for monocytes and CD4+ T cells, respectively. CsA half maximal inhibitory concentration (IC(50)) values ranged from 15 to 78 microg/L for monocytes and B cells, respectively. CONCLUSION Inter- and intraindividual leukocyte subset cell count variation can affect measured CN activity independent of CsA concentration. Cell-specific activity and drug sensitivity should be considered for sample validation to optimize method specificity when pharmacodynamic monitoring strategies are applied in a clinical setting.
A two-stage constraint based dependency parser for free word order languages

The paper proposes a broad coverage twostage constraint based dependency parser for free word order languages. For evaluating the parser and to ascertain its coverage we show its performance on Hindi which is a free word order language. We compare our results with that of two data-driven parsers which were trained on a subpart of a Hindi Treebank. The final results are good with a maximum attachment and labeled attachment accuracy of 90.1% and 75% respectively. The results point towards the phenomena which the data driven parsers find easier to learn vs. those for which the grammar driven approach can prove more effective.
Best Practices in Perovskite Solar Cell Efficiency Measurements. Avoiding the Error of Making Bad Cells Look Good.

Avoiding the Error of Making Bad Cells Look Good P solar cells employing hybrid organic−inorganic halide perovskites (e.g., CH3NH3PbI3) have taken the photovoltaic community by storm. In the short time since being deemed its own class of emerging photovoltaic technologies by the National Renewable Energy Laboratory (October, 2013), the certified record efficiency of perovskite solar cells has increased nearly 50%, from 14.1 to 20.1% (http://www.nrel.gov/ncpv/). In addition, several groups have reported reproducible efficiencies in excess of 16%. These devices show great promise for commercial applications as they combine low-cost fabrication techniques with earthabundant materials yet still deliver efficiencies rivaling traditional photovoltaic technologies. The possibility of using them in building facades or as a top cell in a tandem perovskite−Si architecture only increases their desirability. However, there is currently a dire need in the field for increased care on the part of authors in reporting their photovoltaic performance and on the side of reviewers and the scientific community at large in discriminating and evaluating reported results. Our hope is that this Viewpoint brings to light some of the issues pertaining to perovskite solar cells and provides the field with best practices for measuring and reporting perovskite solar cell performance.
P2X Receptors Inhibit NaCl Absorption in mTAL Independently of Nitric Oxide

Activation of basolateral P2X receptors markedly reduces NaCl absorption in mouse medullary thick ascending limb (mTAL). Here we tested the role of nitric oxide (NO) in the ATP-mediated (P2X) transport inhibition. We used isolated, perfused mTALs from mice to electrically measure NaCl absorption. By microelectrodes we determined the transepithelial voltage (Vte) and transepithelial resistance (Rte). Via these two parameters, we calculated the equivalent short circuit current, I'sc as a measure of the transepithelial Na+ absorption. Basolateral ATP (100 μM) acutely induced reversible inhibition of Na+ absorption (24 ± 4%, n = 10). Addition of L-arginine (100 μM) had no apparent effect on the ATP-induced transport inhibition. Acute reduction of extracellular [Ca2+] to either 100 nM or 0 nM by addition of EGTA had no effect on the ATP-induced transport inhibition. In the presence of the NO synthase (NOS) inhibitor L-NAME (100 μM) and/or ODQ to inhibit the guanylyl cyclase, the ATP effect remained unaffected. Increasing the concentration and incubation time for L-NAME (1 mM) still did not reveal any effect on the ATP-mediated transport inhibition. Acute addition of the NO donors SNAP (100 μM) and Spermine NONOate (10 μM) did not alter tubular transport. High concentrations of L-NAME (1 mM) in itself, however, reduced the transepithelial transport significantly. Thus, we find no evidence for nitric oxide (NO) as second messenger for P2X receptor-dependent transport inhibition in mTAL. Moreover, Ca2+ signaling appears not involved in the ATP-mediated effect. It remains undefined how P2X receptors trigger the marked reduction of transport in the TAL.
Personality and Aggression Compared between Sportsman and Non-Sportsmen in Erzurum Province

This study has been carried out in Erzurum with the aim of comparing the personalities and levels of aggressiveness of individuals who are interested in different branches of sport and of those who are not doing any sports. A sample survey was applied to 242 people, all men: 180 sportsman (volleyball, football, karate, box, tennis, basketball, curling, ice-hockey and wrestler) and 62 people who do not do any sports. In the age group 16 to 28 years, 74 percent of participants were sportsman and 26 percent were non-sportsmen. Participants completed the NEO Personality Inventory-Revised (NEO-FFI) and the Aggression Scale (BPAQ). The results indicated that the individuals who do sports scored significantly higher on extraversion than non- athletes. The non- athletes scored significantly higher on hostility and aggression than did the individuals who do sports. There is no significant difference was found between the two groups on openness to experience, physical aggression and verbal aggression. It can be concluded that the individuals who do sports are more extroverted and have fewer aggressive attitudes compared with non- athletes.
Modeling network intrusion detection alerts for correlation

Signature-based network intrusion-detection systems (NIDSs) often report a massive number of simple alerts of low-level security-related events. Many of these alerts are logically involved in a single multi-stage intrusion incident and a security officer often wants to analyze the complete incident instead of each individual simple alert. This paper proposes a well-structured model that abstracts the logical relation between the alerts in order to support automatic correlation of those alerts involved in the same intrusion. The basic building block of the model is a logical formula called a capability. We use capability to abstract consistently and precisely all levels of accesses obtained by the attacker in each step of a multistage intrusion. We then derive inference rules to define logical relations between different capabilities. Based on the model and the inference rules, we have developed several novel alert correlation algorithms and implemented a prototype alert correlator. The experimental results of the correlator using several intrusion datasets demonstrate that the approach is effective in both alert fusion and alert correlation and has the ability to correlate alerts of complex multistage intrusions. In several instances, the alert correlator successfully correlated more than two thousand Snort alerts involved in massive scanning incidents. It also helped us find two multistage intrusions that were missed in auditing by the security officers.
The Profitable Arc Tour Problem: Solution with a Branch-and-Price Algorithm

In this article, we introduce a new arc routing problem that we call the profitable arc tour problem. This problem is defined on a graph in which profits and travel costs are associated with the arcs. The objective is to find a set of cycles in the graph that maximizes the collection of profit minus travel costs, subject to constraints limiting the number of times that profit is available on arcs and the maximal length of cycles. The problem is related both to constrained flow problems and to vehicle-routing problems. We tackle it from this standpoint and propose a branch-and-price algorithm for its solution. In the column-generation phase, the issue of the collection decisions while traveling through the arcs is addressed. In the branching phase, the fact that viewing solutions in terms of flow variables regularly induces an integer flow matrix leads us to introduce a branching method called the flow-splitting method. Finally, the relationships of this problem with constrained flow optimization are taken into account in an initial phase of the algorithm.
Alpha2-macroglobulin levels in disease in man

Serum α2-macroglobulin levels were measured in normal subjects and in patients with various diseases by an immunochemical method. The values for normal men were 284 mg. /100 ml. (±89·6 mg./100 ml.) and for normal women 350 mg. /100 ml. (±94·5 mg./100 ml.). Men with rheumatoid arthritis had normal levels, but the levels in women were depressed. There was no relationship to the concentrations of the acute phase reactive proteins, haptoglobin, and C-reactive protein. In chronic liver disease, the levels in men were significantly higher than normal and were slightly higher than normal in women. A small group of patients with nephrotic syndrome had very high levels. No significant variations from the normal were found in sera from a group of patients with miscellaneous diseases.
‘‘Time after time’’: A Quali-T method for assessing music's impact on well-being

This article considers the question of how to produce ecologically valid assessments of music's role as a health technology. To address this question, I consider critically some of the standard quantitative instruments used to assess well-being and quality of life. I suggest that these instruments do not lend themselves well to the production of ecologically valid assessments and understandings for two reasons: (1) the process of data elicitation is removed from everyday meanings and practices and therefore risks producing data that is an artifact of the situation in which it is elicited (2) standard, quantitative instruments are not neutral but are rather discursive texts that are inevitably imbued with a politics of expertise and an image of the health care client. For these reasons, I suggest that we consider the question of how to develop ecologically valid, client-centered assessment measures. To that end, I introduce a third critique of the standard quantitative instruments, namely that they are associated with, and promote, an ontology of wellness/illness that downplays the temporally variable and situationally emergent nature of both wellness/illness and musical interventions themselves. As an alternative mode of assessment, I suggest that we reconsider the value of singular case studies and I describe a set of principles that can assist researchers to produce ecologically valid assessments. To this end I introduce the concept of the musical event as a more ecologically valid means for illuminating the specific mechanisms by which music aids well-being. I suggest that the case study approach is temporally sensitive, that it lends itself to an emergent ontology of wellness/illness, and that it is client-centered (and can also be user-led).
The Historical Nature of Cities

Endemic uncertainties surrounding urban industrial waste raise important theoretical and methodological challenges for understanding the historical nature of cities. Our study advances a synthetic framework for engaging these challenges by extending theories of modern risk society and classic urban ecology to investigate the accumulation of industrial hazards over time and space. Data for our study come from a unique longitudinal dataset containing geospatial and organizational information on more than 2,800 hazardous manufacturing sites operating between 1956 and 2006 in Portland, Oregon. We pair these site data with historical data from the U.S. population census and the Oregon Department of Environmental Quality (DEQ) to examine the historical accumulation of hazardous parcels in relation to changing patterns of industrial land use, neighborhood composition, new residential development, and environmental regulation. Results indicate that historical accumulation of hazardous sites is scaling up in ways that exhibit little regard for shifting neighborhood demographics or existing regulatory policies as sites merge into larger, more contiguous industrialized areas of historically generated hazards, creating the environmental conditions of urban risk society.