Miracle-dz/UniFAR-FTUs huggingface dataset:
Nitrification and Autotrophic Nitrifying Bacteria in a Hydrocarbon-Polluted Soil

ABSTRACT In vitro ammonia-oxidizing bacteria are capable of oxidizing hydrocarbons incompletely. This transformation is accompanied by competitive inhibition of ammonia monooxygenase, the first key enzyme in nitrification. The effect of hydrocarbon pollution on soil nitrification was examined in situ. In a microcosm study, adding diesel fuel hydrocarbon to an uncontaminated soil (agricultural unfertilized soil) treated with ammonium sulfate dramatically reduced the amount of KCl-extractable nitrate but stimulated ammonium consumption. In a soil with long history of pollution that was treated with ammonium sulfate, 90% of the ammonium was transformed into nitrate after 3 weeks of incubation. Nitrate production was twofold higher in the contaminated soil than in the agricultural soil to which hydrocarbon was not added. To assess if ammonia-oxidizing bacteria acquired resistance to inhibition by hydrocarbon, the contaminated soil was reexposed to diesel fuel. Ammonium consumption was not affected, but nitrate production was 30% lower than nitrate production in the absence of hydrocarbon. The apparent reduction in nitrification resulted from immobilization of ammonium by hydrocarbon-stimulated microbial activity. These results indicated that the hydrocarbon inhibited nitrification in the noncontaminated soil (agricultural soil) and that ammonia-oxidizing bacteria in the polluted soil acquired resistance to inhibition by the hydrocarbon, possibly by increasing the affinity of nitrifying bacteria for ammonium in the soil.
Cognitive factors that lead people to comply with spam email

ABSTRACT Because of the annoyance and productivity loss associated with spam email, significant resources are devoted to detect and block it. Despite these deterrents, people receive and respond to spam email in sufficient numbers to support the continuing efforts of spammers. It is surprising given this situation that little is known about the cognitive processes that message receivers apply to evaluate spam email, although such knowledge could be useful in mitigating some of its worst aspects. We address this research gap by investigating three cognitive factors that are hypothesized to motivate individuals to comply with message requests. We find receivers’ perceptions of social presence and trust regarding the message sender and, to a lesser extent, receivers’ benefit goals explain over half of the variance in their intention to comply with a message request. In addition, receivers’ identification of the message sender as having strong interpersonal ties predicts their perception of trust and benefit goals related to the message, and we find that effects of strong interpersonal ties on receivers’ intention to comply with the message request are entirely mediated by the three cognitive factors we studied. Overall, the findings indicate that receivers who read spam email evaluate messages based on diverse criteria that vary substantially based on strength of their perceived interpersonal ties with the message sender.
Internet Auction Fraud Detection Using Social Network Analysis and Classification Tree Approaches

Effective Internet auction fraud detection has become an emergent issue in real-world scenarios in conjunction with the rapid development and prevalence of Internet auctions. Accurate detection of fraudsters can assist law enforcement agencies in preventing potential fraud cases that could result in large monetary losses. This paper proposes a hybrid approach utilizing network metrics and data-mining techniques to discover fraudsters based on Internet auction transaction records. Using experimental data gathered from the Yahoo! Auctions Web site, extensive experiments demonstrate that the proposed approach is capable of detecting Internet auction fraudsters both effectively and almost instantaneously with an acceptable classification accuracy rate. The research findings will assist in probing the implications regarding different transaction account types, and they also reveal the specific transactions within various transaction patterns.
Outcomes of Vascular Resection in Pancreaticoduodenectomy: Single-surgeon Experience

Extension of pancreatic adenocarcinoma into adjacent vasculature often necessitates resection of the portal vein (PV) and/or superior mesenteric vein (SMV) during pancreaticoduodenectomy (PD). The vein is reconstructed primarily by end-to-end anastomosis of vein remnants or venoplasty or by use of autologous or synthetic vein grafts. The objective of this study was to review outcomes in patients undergoing PD for pancreatic adenocarcinoma, specifically comparing the short- and long-term outcomes between the patients undergoing vascular resection and those undergoing standard PD. All patients undergoing PD for pancreatic adenocarcinoma by a single surgeon between 2007 and 2012 were reviewed. Of the 61 patients identified, 18 patients underwent vascular resection of the PV (four patients), SMV (10 patients), or both (four patients). The remaining 43 patients had standard PD. Demographic, perioperative, pathological, and long-term outcomes data were collected and both vascular and standard groups were compared. Both groups had similar demographics. The vascular group had significantly longer operative times (529 vs 406 minutes; P < 0.01) with a trend to greater estimated blood loss (0.64 vs 0.53 L; P = 0.06). Pathological analysis showed no difference between the two groups with regard to lymph node status/ratio and rate of R0 resection (94 vs 91%; P = 0.57); however, the size of the tumor was significantly greater in the vascular group (4.2 vs 3 cm; P < 0.01). Short-term outcomes were similar in the vascular group and standard group, respectively, with no difference in pancreatic fistula rate (6 vs 7%; P = 1.0), transfusion rate (44 vs 35%; P = 0.57), and median length of stay (8 vs 7 days; P = 0.10), and there was no 30-day mortality in either group. Based on Kaplan-Meier methods, the median recurrence-free survival was 18 versus 23 months (P = 0.37) in the vascular and standard groups, respectively, and the overall survival was almost identical in both groups, each with a median of 31 months (P = 0.91). In our experience, mesenteric and PV resection during PD was performed safely and without compromise of short- or longer-term outcomes. It can be performed safely and patients have no significant difference in perioperative outcomes or overall survival.
Correlation of the expression of miR-146a in peripheral blood mononuclear cells of patients with ankylosing spondylitis and inflammatory factors

We investigated the expression of miR-146a in peripheral blood mononuclear cell (PBMC) of patients with ankylosing spondylitis (AS) and its correlation with inflammatory factors to explore the clinical significance. In total 45 patients with AS were selected at the Weifang People's Hospital from June, 2014 to January, 2016. At the same time, 30 healthy volunteers were also selected to serve as control group. Expression level of miR-146a in PBMC cells of patients in each group was detected by quantitative real-time-polymerase chain reaction (qRT-PCR). Levels of tumor necrosis factor-α (TNF-α), interleukin-1β (IL-1β) and IL-6 in serum and the supernatant of culture medium of PBMC derived from each group were detected by enzyme-linked immunosorbent assay (ELISA). Correlations between expression level of miR-146a and serum inflammatory factors, and clinical indicators were analyzed. Clinical indicators included bath ankylosing spondylitis disease activity index (BASDAI), C-reactive protein (CRP), erythrocyte sedimentation rate (ESR) and duration of morning stiffness. Expression level of miR-146a in PBMC of AS patients was significantly higher than that of healthy control (P<0.01); levels of TNF-α, IL-1β and IL-6 in serum and the supernatant of culture medium of PBMC derived from AS patients were significant compared to those of control group (P<0.01); expression of miR-146a in PBMC of patients with AS was positively correlated with the levels of TNF-α, IL-1β and IL-6 in serum (r=0.632, P<0.01; r=0.574, P<0.01; r=0.483, P<0.01). In addition, expression level of miR-146a in PBMC of patients with AS was positively correlated with BASDAI, ESR, CRP and duration of morning stiffness (r=0.551, P<0.01; r=0.738, P<0.01; r=0.685, P<0.01; r=0.497, P<0.01). Expression level of miR-146a in PBMC of AS patients was significantly increased and the expression level was positively correlated with the levels of TNF-α, IL-1β and IL-6 in serum (P<0.05). In addition, expression level of miR-146a in PBMC of AS patients was also positively correlated with BASDAI, ESR, CRP and duration of morning stiffness. Those results suggest that miR-146a may be involved in the pathogenesis of AS, and the expression level of miR-146a in PBMC cells may be helpful for diagnosis of AS and judgment of disease activity.
Gendered Violence, HIV Acquisition, and Clinical/Behavioral Research

HIV incidence and prevalence rates for US women continue to increase, especially among Black and Latina women. In addition, the link between violence and HIV acquisition has been well documented. However, the interaction between violence, HIV risk, and HIV acquisition remains an under-addressed issue in current clinical and behavioral HIV research designs. Because violence against women plays an important role in HIV acquisition and transmission, it is imperative for clinical research to address violence in trial design and implementation. In this article, we discuss the prevalence of violence in women’s lives; the role violence plays in HIV acquisition; and the absence of violence in clinical research designs. We conclude with recommendations for integrating concerns about HIV and violence against women into sponsor- and investigator-driven HIV research priorities and clinical trial design.
Viral etiology of aseptic meningitis among children in Southern Iran

Aseptic meningitis refers to a clinical syndrome of meningeal inflammation in which bacteria cannot be identified in the cerebrospinal fluid (CSF). The viral etiology and the epidemiological, clinical, and laboratory characteristics of aseptic meningitis among children aged 2 months to 15 years in Shiraz, southern Iran were determined. From May 2007 to April 2008, 65 patients were admitted to the hospital with aseptic meningitis. Seven viruses, non‐polio human enteroviruses, mumps virus, herpes simplex virus (HSV), varicella‐zoster virus (VZV), human cytomegalovirus (HCMV), human herpes virus type 6 (HHV‐6), and Epstein–Barr virus (EBV) were investigated by polymerase chain reaction (PCR) method. Viruses were detected in 30 (46.2%) patients in whom non‐polio human enterovirus and mumps virus were detected in 13 (43.3%) and 11 (36.7%), respectively. The remaining 6 (20%) of the cases were caused by HSV, VZV, HCMV, and HHV‐6. Haemophilus influenzae and non‐polio human enterovirus were detected in one patient simultaneously. Viral meningitis was found to be more frequent during spring and summer. The majority (66.6%) of the patients were treated in the hospital for 10 days and had received antibiotics in the case of bacterial meningitis. Rapid diagnosis of viral meningitis using PCR testing of CSF can help shorten hospitalization, and avoid the unnecessary use of antibiotics. J. Med. Virol. 83:884–888, 2011. © 2011 Wiley‐Liss, Inc.
Rapid Emergence of Echinocandin Resistance in Candida glabrata Resulting in Clinical and Microbiologic Failure

ABSTRACT We report a case of Candida glabrata candidemia that developed resistance to micafungin within 8 days of initiation of therapy in a patient without previous echinocandin exposure or other known risk factors for clinical or microbiological failure. Pre- and postresistant isolates were confirmed to be isogenic, and sequencing of hot spots known to confer echinocandin resistance revealed a phenylalanine deletion at codon 659 within FKS2.
Outage probability for MIMO MAC channels

In this paper, we investigate the outage probability for the mutual information of the sum rate for the MIMO (multiple input multiple output) MAC (multiple access channel) channel. We derive exact results for the “two users” case with two antennas and a general result for K users with an arbitrary number of antennas and different signal-to-noise ratios. As a secondary result, we derive an exact expression for the single user outage probability for the MIMO channel with two antennas.
Aryl hydrocarbon receptor mediates both proinflammatory and anti‐inflammatory effects in lipopolysaccharide‐activated microglia

The aryl hydrocarbon receptor (AhR) regulates peripheral immunity; but its role in microglia‐mediated neuroinflammation in the brain remains unknown. Here, we demonstrate that AhR mediates both anti‐inflammatory and proinflammatory effects in lipopolysaccharide (LPS)‐activated microglia. Activation of AhR by its ligands, formylindolo[3,2‐b]carbazole (FICZ) or 3‐methylcholanthrene (3MC), attenuated LPS‐induced microglial immune responses. AhR also showed proinflammatory effects, as evidenced by the findings that genetic silence of AhR ameliorated the LPS‐induced microglial immune responses and LPS‐activated microglia‐mediated neurotoxicity. Similarly, LPS‐induced expressions of tumor necrosis factor α (TNFα) and inducible nitric oxide synthase (iNOS) were reduced in the cerebral cortex of AhR‐deficient mice. Intriguingly, LPS upregulated and activated AhR in the absence of AhR ligands via the MEK1/2 signaling pathway, which effects were associated with a transient inhibition of cytochrome P450 1A1 (CYP1A1). Although AhR ligands synergistically enhance LPS‐induced AhR activation, leading to suppression of LPS‐induced microglial immune responses, they cannot do so on their own in microglia. Chromatin immunoprecipitation results further revealed that LPS‐FICZ co‐treatment, but not LPS alone, not only resulted in co‐recruitment of both AhR and NFκB onto the κB site of TNFα gene promoter but also reduced LPS‐induced AhR binding to the DRE site of iNOS gene promoter. Together, we provide evidence showing that microglial AhR, which can be activated by LPS, exerts bi‐directional effects on the regulation of LPS‐induced neuroinflammation, depending on the availability of external AhR ligands. These findings confer further insights into the potential link between environmental factors and the inflammatory brain disorders. GLIA 2015;63:1138–1154
An Enzymatic Fluorometric Assay for Pyridoxal with High Specificity and Sensitivity

An enzymatic fluorometric assay for pyridoxal with pyridoxal dehydrogenase was developed. The detection limit was about 10 pmol: the calibration curve of pyridoxal showed high linearity (r=0.993). The values obtained by this method correlated well with those by the HPLC method. The enzyme had a high specificity for pyridoxal, and thus animal samples could be directly analyzed without separation of pyridoxal 5′-phosphate by column chromatography.
All-trans retinoic acid and rapamycin normalize Hutchinson Gilford progeria fibroblast phenotype

Hutchinson Gilford progeria syndrome is a fatal disorder characterized by accelerated aging, bone resorption and atherosclerosis, caused by a LMNA mutation which produces progerin, a mutant lamin A precursor. Progeria cells display progerin and prelamin A nuclear accumulation, altered histone methylation pattern, heterochromatin loss, increased DNA damage and cell cycle alterations. Since the LMNA promoter contains a retinoic acid responsive element, we investigated if all-trans retinoic acid administration could lower progerin levels in cultured fibroblasts. We also evaluated the effect of associating rapamycin, which induces autophagic degradation of progerin and prelamin A. We demonstrate that all-trans retinoic acid acts synergistically with low-dosage rapamycin reducing progerin and prelamin A, via transcriptional downregulation associated with protein degradation, and increasing the lamin A to progerin ratio. These effects rescue cell dynamics and cellular proliferation through recovery of DNA damage response factor PARP1 and chromatin-associated nuclear envelope proteins LAP2α and BAF. The combined all-trans retinoic acid-rapamycin treatment is dramatically efficient, highly reproducible, represents a promising new approach in Hutchinson-Gilford Progeria therapy and deserves investigation in ageing-associated disorders.
Co‐evolution with chicken class I genes

The concept of co‐evolution (or co‐adaptation) has a long history, but application at molecular levels (e.g., ‘supergenes’ in genetics) is more recent, with a consensus definition still developing. One interesting example is the chicken major histocompatibility complex (MHC). In contrast to typical mammals that have many class I and class I‐like genes, only two classical class I genes, two CD1 genes and some non‐classical Rfp‐Y genes are known in chicken, and all are found on the microchromosome that bears the MHC. Rarity of recombination between the closely linked and polymorphic genes encoding classical class I and TAPs allows co‐evolution, leading to a single dominantly expressed class I molecule in each MHC haplotype, with strong functional consequences in terms of resistance to infectious pathogens. Chicken tapasin is highly polymorphic, but co‐evolution with TAP and class I genes remains unclear. T‐cell receptors, natural killer (NK) cell receptors, and CD8 co‐receptor genes are found on non‐MHC chromosomes, with some evidence for co‐evolution of surface residues and number of genes along the avian and mammalian lineages. Over even longer periods, co‐evolution has been invoked to explain how the adaptive immune system of jawed vertebrates arose from closely linked receptor, ligand, and antigen‐processing genes in the primordial MHC.
Regulation of protein metabolism in middle-aged, premenopausal women: roles of adiposity and estradiol.

The age-related loss of fat-free mass (FFM) is accelerated in women during the middle-age years and continues at an increased rate throughout the postmenopausal period. Because protein is the primary structural component of fat-free tissue, changes in FFM are largely due to alterations in protein metabolism. Knowledge of the hormonal and physiological correlates of protein metabolism in middle-aged women, therefore, has important implications for understanding the mechanisms underlying changes in FFM. We measured leucine kinetics (expressed relative to FFM: micromol/kg FFM/h) in 46 middle-aged, premenopausal women (mean +/- SD, 47 +/- 3 yr) after an overnight fast (i.e. basal) and during euglycemic hyperinsulinemia (40 mU/m2/min) using a 5.5-h infusion of [1-13C]leucine. Additionally, we measured insulin-stimulated glucose disposal by euglycemic hyperinsulinemic clamp, body composition by dual energy x-ray absorptiometry, abdominal fat distribution by computed tomography, and hormone levels by RIA as possible correlates of protein metabolism. Under basal conditions, stepwise regression analysis showed that leucine appearance (i.e. protein breakdown) was related to percent body fat and serum estradiol (r2 = 40%; P < 0.01), and leucine oxidation was related to serum estradiol and percent body fat (r2 = 26%; P < 0.05). Under euglycemic hyperinsulinemic conditions, no variables correlated with the percent change in leucine appearance. The percent change in leucine oxidation was related to intraabdominal adipose tissue area and glucose disposal rate (r2 = 48%; P < 0.01). Correlates and r2 values for nonoxidative leucine disposal (i.e. protein synthesis) under basal and euglycemic hyperinsulinemic conditions were similar to those observed for leucine appearance. From these results, we conclude that adiposity and/or serum estradiol may contribute to the regulation of protein metabolism and FFM in middle-aged, premenopausal women.
Artículos originales IL-10 Expression is Associated with Lack of HPV-16 E 7 Specific Th 1 Response in Cervical Cancer Patients

Objective: To examine the association between the presence of HPV specific T cell response in relation to HLA class I, HLA-G and IL-10 expression in the tumor cells of cervical cancer patients. Materials and methods: Lymphocytes were isolated from 18 cervical cancer patients and stimulated with autologous HPV16 E7-pulsed monocyte-derived dendritic cells or directly with synthetic peptides: E751-70, E765-84, and E779-98. The cells were stained for CD4, CD69, intracellular IFN-g and IL-4 cytokines and analyzed by flow cytometry. HLA-I, HLA-G and IL-10 expression on tumor cells was analyzed by immunohistochemistry. Results: HLA class I expression was completely lost in 11/18 and downregulated in 4/18 of patients. HLA G expression was observed in 4/18 of patients and IL-10 expression was observed in 6/17 of patients. An inverse association between IL-10 expression and a lack of HPV-specific immune response was observed (P = 0.041). No clear associations between HLA class I or HLA-G expression and specific immune response were observed. Conclusions: Our results underline the importance of other immune factors, like IL-10 expression, that could influence the antitumoral response. These results could have important implications during development of new therapeutic strategies like immunotherapy.
Googling Trends in Conservation Biology

Web‐crawling approaches, that is, automated programs data mining the internet to obtain information about a particular process, have recently been proposed for monitoring early signs of ecosystem degradation or for establishing crop calendars. However, lack of a clear conceptual and methodological framework has prevented the development of such approaches within the field of conservation biology. Our objective was to illustrate how Google Trends, a freely accessible web‐crawling engine, can be used to track changes in timing of biological processes, spatial distribution of invasive species, and level of public awareness about key conservation issues. Google Trends returns the number of internet searches that were made for a keyword in a given region of the world over a defined period. Using data retrieved online for 13 countries, we exemplify how Google Trends can be used to study the timing of biological processes, such as the seasonal recurrence of pollen release or mosquito outbreaks across a latitudinal gradient. We mapped the spatial extent of results from Google Trends for 5 invasive species in the United States and found geographic patterns in invasions that are consistent with their coarse‐grained distribution at state levels. From 2004 through 2012, Google Trends showed that the level of public interest and awareness about conservation issues related to ecosystem services, biodiversity, and climate change increased, decreased, and followed both trends, respectively. Finally, to further the development of research approaches at the interface of conservation biology, collective knowledge, and environmental management, we developed an algorithm that allows the rapid retrieval of Google Trends data.
Performance Analysis of Caching and Forwarding Strategies in Content Centric Networking

Content-Centric Networking (CCN) is a promising implementation of the Information-Centric Networking architecture that was introduced to address recent needs related to the proliferation of multimedia traffic in the Internet. One of the fundamental features of CCN is in-network caching that aims to reduce delays, optimize bandwidth, and resource usage. Designing better in-network caching strategies along with optimal replacement policies is a challenging research issue in CCN. Moreover, the lack of a common comparison framework has obfuscated the real performance of these strategies when compared with each other. Based on realistic assumptions and a common environment, this paper gives a comprehensive view on performance comparison of popular caching strategies and replacement policies employed in CCN, while considering different forwarding strategies and multiple network topologies.