Miracle-dz/UniFAR-FTUs huggingface dataset:
Microbial Communities Associated with Anaerobic Benzene Degradation in a Petroleum-Contaminated Aquifer

ABSTRACT Microbial community composition associated with benzene oxidation under in situ Fe(III)-reducing conditions in a petroleum-contaminated aquifer located in Bemidji, Minn. , was investigated. Community structure associated with benzene degradation was compared to sediment communities that did not anaerobically oxidize benzene which were obtained from two adjacent Fe(III)-reducing sites and from methanogenic and uncontaminated zones. Denaturing gradient gel electrophoresis of 16S rDNA sequences amplified with bacterial orGeobacteraceae-specific primers indicated significant differences in the composition of the microbial communities at the different sites. Most notable was a selective enrichment of microorganisms in the Geobacter cluster seen in the benzene-degrading sediments. This finding was in accordance with phospholipid fatty acid analysis and most-probable-number–PCR enumeration, which indicated that members of the familyGeobacteraceae were more numerous in these sediments. A benzene-oxidizing Fe(III)-reducing enrichment culture was established from benzene-degrading sediments and contained an organism closely related to the uncultivated Geobacter spp. This genus contains the only known organisms that can oxidize aromatic compounds with the reduction of Fe(III). Sequences closely related to the Fe(III) reducer Geothrix fermentans and the aerobe Variovorax paradoxus were also amplified from the benzene-degrading enrichment and were present in the benzene-degrading sediments. However, neither G. fermentans nor V. paradoxusis known to oxidize aromatic compounds with the reduction of Fe(III), and there was no apparent enrichment of these organisms in the benzene-degrading sediments. These results suggest thatGeobacter spp. play an important role in the anaerobic oxidation of benzene in the Bemidji aquifer and that molecular community analysis may be a powerful tool for predicting a site’s capacity for anaerobic benzene degradation.
Genome-Wide Synthetic Lethal Screens Identify an Interaction Between the Nuclear Envelope Protein, Apq12p, and the Kinetochore in Saccharomyces cerevisiae

The maintenance of genome stability is a fundamental requirement for normal cell cycle progression. The budding yeast Saccharomyces cerevisiae is an excellent model to study chromosome maintenance due to its well-defined centromere and kinetochore, the region of the chromosome and associated protein complex, respectively, that link chromosomes to microtubules. To identify genes that are linked to chromosome stability, we performed genome-wide synthetic lethal screens using a series of novel temperature-sensitive mutations in genes encoding a central and outer kinetochore protein. By performing the screens using different mutant alleles of each gene, we aimed to identify genetic interactions that revealed diverse pathways affecting chromosome stability. Our study, which is the first example of genome-wide synthetic lethal screening with multiple alleles of a single gene, demonstrates that functionally distinct mutants uncover different cellular processes required for chromosome maintenance. Two of our screens identified APQ12, which encodes a nuclear envelope protein that is required for proper nucleocytoplasmic transport of mRNA. We find that apq12 mutants are delayed in anaphase, rereplicate their DNA, and rebud prior to completion of cytokinesis, suggesting a defect in controlling mitotic progression. Our analysis reveals a novel relationship between nucleocytoplasmic transport and chromosome stability.
Efficient Volumetric PolyCube‐Map Construction

PolyCubes provide compact representations for closed complex shapes and are essential to many computer graphics applications. Existing automatic PolyCube construction methods usually suffer from poor quality or time‐consuming computation. In this paper, we provide a highly efficient method to compute volumetric PolyCube‐maps. Given an input tetrahedral mesh, we utilize two novel normal‐driven volumetric deformation schemes and a polycube‐allowable mesh segmentation to drive the input to a volumetric PolyCube structure. Our method can robustly generate foldover‐free and low‐distortion PolyCube‐maps in practice, and provide a flexible control on the number of corners of Polycubes. Compared with state‐of‐the‐art methods, our method is at least one order of magnitude faster and has better mapping qualities. We demonstrate the efficiency and efficacy of our method in PolyCube construction and all‐hexahedral meshing on various complex models.
Posterior circulation flow diversion: a single-center experience and literature review

Background Flow diverters have been used predominantly for large anterior circulation aneurysms. Data on the safety and efficacy of this treatment for posterior circulation aneurysms are limited. Objective To present our posterior circulation flow diverter experience, outcomes and morbidity in comparison with recent studies. Methods A retrospective chart and imaging review of six patients with seven aneurysms in posterior circulation vessels, treated with flow diverter technology was carried out. A literature review was performed using standard online search tools. Results We included five saccular and two fusiform posterior circulation aneurysms. An average of two flow diverters was placed for each patient. Adjunctive coiling was used in three cases. Follow-up at an average of 14.5 months showed complete angiographic occlusion in 4 (57.1%) cases, including one patient with in-stent thrombosis and major brainstem stroke at 4.5 months, a week after self-discontinuing dual antiplatelet therapy. Two other patients developed small periprocedural strokes but had excellent recovery. One death occurred 18 months after the initial procedure. No aneurysm rupture or parenchymal hemorrhage was seen. Overall, 5 (71%) cases, all with saccular aneurysms, had good clinical outcome (modified Rankin score (mRS) 0–1). Fusiform basilar aneurysms had markedly worse outcomes (mRS 5 and 6). Our literature review yielded six other studies with 100 additional patients. Overall, good outcome was seen in 74.3%, with a 12.3% average mortality and 11% permanent neurologic deficit rate. Complete occlusion varied from 43% to 100%. Conclusions Flow diversion may be a possible treatment in carefully selected patients with high-risk atypical posterior circulation aneurysms, with poor natural history and no optimal treatment strategy. Symptomatic and fusiform large aneurysms appear to carry the highest risk. Further studies are necessary to assess the role of flow diversion in the posterior circulation.
Mitral Annuloplasty Device Implantation for Non-Surgical Treatment of Mitral Regurgitation: Clinical Experience After the Approval Studies.

BACKGROUND AND AIMS One option for interventional treatment of secondary mitral regurgitation is the placement of an indirect mitral annuloplasty device (Carillon Mitral Contour System) cinching the mitral annulus to facilitate coaptation of the mitral leaflets. The aim of this study is to evaluate the implantation success and hemodynamic results. METHODS AND RESULTS Seventeen consecutive patients (11 females, 6 males) suffering from moderate to severe secondary mitral regurgitation (40% ischemic, 59% non-ischemic) received a Carillon Mitral Contour System device, which was evaluated prospectively in a single-center setting. The mean procedure time was 95.5 ± 2.1 minutes, fluoroscopy time was 13.1 ± 6.1 minutes, and the amount of contrast dye was 120.6 ± 39.3 mL. The mitral regurgitation grade was reduced from 2.8 ± 2.4 to 1.9 ± 0.8 acutely (P<.01), with an additional improvement seen after 3 months to 1.5 ± 0.75 (P<.01 to baseline). In 41.2% of patients, acute reduction of coronary artery flow was seen and managed with a stepwise approach: (1) intracoronary nitroglycerin was administered; (2) release of device tension; (3) a new device was changed and placed at a different location; and (4) the device was left in place and a stent was implanted in the coronary artery. Only 1 patient (5.8%) could not receive the device due to coronary compression. No periprocedural myocardial infarction occurred. CONCLUSION Indirect mitral annuloplasty is feasible outside of controlled trials, and is associated with successful improvement of mitral regurgitation. Although coronary compromise needs to be addressed as part of the implantation procedure, this issue limits implantation of the device in only a small percentage of cases.
Use of HOG descriptors in phishing detection

Phishing is a scamming activity which deals with making a visual illusion on computer users by providing fake web pages which mimic their legitimate targets in order to steal valuable digital data such as credit card information or e-mail passwords. In contrast to other anti-phishing attempts this paper proposes to evaluate and solve this problem by leveraging a pure computer vision based method in the concept of web page layout similarity. Proposed approach employs Histogram of Oriented Gradients (HOG) descriptor in order to capture cues of page layout without the need of time consuming intermediate stage of segmentation. Moreover, histogram intersection kernel has been used as a similarity metric for computing similarity. Thus, an efficient and fast phishing page detection scheme has been developed in order to combat with zero-day phishing page attacks. To verify the efficiency of our phishing page detection mechanism, 50 unique phishing pages and their legitimate targets have been collected. Furthermore, 100 pairs of legitimate pages have been gathered. As the next stage, the similarity scores in these two groups were computed and compared. According to promising results, similarity degree around 75% and above can be adequate for alarming.
Dimethylarginine levels and nutritional status in hemodialysis patients.

BACKGROUND Asymmetric dimethylarginine (ADMA)and symmetric dimethylarginine (SDMA) originate from hydrolysis of methylated proteins, including dietary proteins, and are retained in end-stage renal disease(ESRD). This study aimed to detect the correlation of ADMA and SDMA to nutritional parameters in dialysis patients. METHODS Before and after a single dialysis session, larginine, ADMA and SDMA plasma levels were measured in 38 hemodialysis patients by HPLC-tandem mass spectrometry. Biochemistry, protein intake, anthropometry and bioelectric impedance analysis were evaluated. RESULTS Predialysis plasma levels of ADMA were higher than in normal controls (n=20) (1.14 +/- 0.27 mumol/Lvs. 0.56 +/- 0.09 mumol/L, p<0.001), as were SDMA levels(3.49 +/- 1.00 mumol/L vs. 0.44 +/- 0.13 mumol/L, p<0.001). On univariate analysis, predialysis ADMA levels were inversely related to BMI and albumin levels, whereas SDMA was directly related to nPNA, phase angle, prealbumin and creatinine serum levels. ADMA/SDMA ratio was inversely related to prealbumin and albumin, creatinine, urea and phosphorus serum levels, as wellas nPNA, but positively to C-reactive protein. On multiple regression analysis, serum albumin and BMI were the stronger predictors of ADMA, whereas prealbumin serum levels followed by dietary protein intake were the stronger predictors of SDMA. Prealbumin followed by C-reactive protein was predictive of the ADMA/SDMA molar ratio. CONCLUSIONS Our results confirm that ADMA and SDMA levels are increased in ESRD patients and suggest that a link may exist with inflammation and nutritional status. High ADMA levels associated with reduced SDMA may be a predictive marker of malnutrition-inflammation-atherosclerosis syndrome.
Carbon taxation in Malaysia: insights from the enhanced PAGE09 integrated assessment model

ABSTRACT If an emerging economy were to adopt climate policy as part of a larger tax reform, what is the ideal initial carbon tax (CT), and its trajectory over time, that internalizes the mean social cost of carbon dioxide (SCCO2)? Here we use the PAGE09 model to show that in Malaysia, a rapidly developing economy, this would be an initial CT in the year 2020 of about US$68.40. 7/tCO2 in constant 2005 US$ prices under the A1B Business-as-Usual (BAU) scenario, rising steadily to around US$225.13. 8/tCO2 in 2050. Under a low-emissions scenario, it would be a lower CT at around US$33.30. 5/tCO2 in 2020 rising to US$100.93. 2/tCO2 in 2050.
Which Sentiment Indicators Matter? An Analysis of the European Commercial Real Estate Market

Property markets exhibit several classic market inefficiencies, which can lead to irrational behaviour and a better understanding of connections between yield modeling and the role of sentiment is of immense interest to property funds, pension funds, banks, insurance companies and other participants. While past studies have examined the role of sentiment in market performance, the conclusions have remained mixed. This paper compares established models against two new innovative methods, paying more attention towards the expectations of market participants to explain yield adjustments and swings in property values. Forecast evaluations reveal that models incorporating property-specific and google trend sentiment outperform the base model. The European market offers an interesting testing ground for our research questions as the interest of investors and banks in abrupt movements in yields and pricing and the role of market sentiment has grown in Europe post global financial crisis due to high level of nonperforming loans.
Twenty years of cell-penetrating peptides: from molecular mechanisms to therapeutics

The recent discovery of new potent therapeutic molecules that do not reach the clinic due to poor delivery and low bioavailability have made of delivery a key stone in therapeutic development. Several technologies have been designed to improve cellular uptake of therapeutic molecules, including cell‐penetrating peptides (CPPs). CPPs were first discovered based on the potency of several proteins to enter cells. Numerous CPPs have been described so far, which can be grouped into two major classes, the first requiring chemical linkage with the drug for cellular internalization and the second involving formation of stable, non‐covalent complexes with drugs. Nowadays, CPPs constitute very promising tools for non‐invasive cellular import of cargo and have been successfully applied for in vitro and in vivo delivery of therapeutic molecules varying from small chemical molecule, nucleic acids, proteins, peptides, liposomes and particles. This review will focus on the structure/function and cellular uptake mechanism of CPPs in the general context of drug delivery. We will also highlight the application of peptide carriers for the delivery of therapeutic molecules and provide an update of their clinical evaluation.
Tapered Edge Readout Wiring for Transition Edge Sensor Calorimeter Arrays Using Ion Milling

We are developing transition edge sensor (TES) arrays using multilayer superconducting readout wiring for future X-ray astronomical missions. The TES pixels are formed on the multilayer readout wiring composed of hot and return wires sandwiching an insulation layer. The interface between the wiring and the TES is formed by patterning the topmost wiring layer followed by deposition of the TES layer. To mitigate problems found in a past device, edges of the upper readout wiring are tapered with an ion milling method to enhance an electrical contact between the TES film and the upper readout wiring. To verify this design, we fabricated a 400-pixel test array with the TES pixels on the tapered upper readout wiring. Good physical contact between the TES film and the readout wiring was confirmed with scanning electron microscope. Furthermore, a low transition temperature (~160 mK), a sharp transition edge and a low residual resistance (~1 mΩ) were observed in RT measurements of representative pixels. The critical current was small 10 ~ 30 μA, although it is still larger than the previous device (<; 10 μA). These results suggest that this method will enable a multilayer wiring TES array with good electrical properties.
Beyond office sphygmomanometry: Ways to better assess blood pressure

To diagnose and manage hypertension optimally, we may need to do more than measure the patient’s blood pressure in the office using traditional sphygmomanometry. A variety of devices—some already available, validated, and reimbursable, some still in development—provide more information and give us a better picture of the patient’s true hypertensive status, degree of blood pressure control, and risk of end-organ damage. Several new devices provide more information than does traditional sphygmomanometry about the patient’s true hypertensive status, blood pressure control, and risk of end-organ damage.
Effectiveness of electronic media in project communication

Electronic media was assessed to identify the most effective means to communicate project information during the Transnet (South African parastatal responsible for rail, port and pipelines) Capital Projects lifecycle. A quantitative study, in the form of a survey questionnaire targeting Transnet Executives, Senior Managers, Specialists and Operational staff based in 4 different locations (Johannesburg, Vryhurd, Ermelo and Richards Bay) was applied as a data collection instrument. The stratified random sampling technique was used to ensure that respondents were fairly selected across positions and geographical locations. Old ways of communication that included email and telephone facilities were perceived to be highly effective in communicating project information to management at Transnet Capital Projects. On the other hand, intranet, videoconferencing, online notice board and facsimile were perceived to be poor in communicating project information to management. Similarly, the email and telephone electronic channels of communication were perceived to be highly effective in sharing project information among project teams. Likewise, the email and telephone electronic modes of communication were also perceived to be highly effective in communicating project information with clients and suppliers. Facsimile was ranked third after the email and telephone when communicating project information with clients and suppliers, though its effectiveness was still perceived to be low. Therefore, in order to effectively communicate Transnet Capital Project information with stakeholders, Transnet leadership should ensure that all its sites (both remote and accessible) have adequate infrastructure to support email and telephone facilities, which are perceived to be relevant and cost effective.
Terror Per Capita

Usually, studies analyzing terrorism focus on the total number of casualties or attacks in a given county. However, per capita rates of terrorism are more likely to matter for individual welfare. Analyzing 214 countries from 1970-2014, we show that three stylized findings are overturned in terms of sign, magnitude, and statistical significance when investigating terror per capita. Democracy, previously associated with more casualties, emerges as a marginally negative predictor of terror per capita. A larger share of Muslims in society is, if anything, associated with less terrorism. Similar conclusions apply to language fractionalization.
Psychopharmacology of compulsive buying.

No standard treatment exists for the DSM-IV Impulse Control Disorders, Not Elsewhere Classified, including Compulsive Buying Disorder. This paper reviews the suggested pharmacotherapies for this disorder and their theoretical basis. McElroy et al. first reported benefit from antidepressant therapy in three cases of Compulsive Buying Disorder with comorbid depression and anxiety. In a retrospective chart review, McElroy's group reported on 20 patients that benefited from antidepressants, often in combination with mood stabilizers. Lejoyeux reported on two patients in whom treatment of a comorbid mood disorder led to remission of compulsive buying behavior. Black reported fluvoxamine to be effective in patients without comorbid major depression, suggesting that improvement was independent of the treatment of mood symptoms. Kim reported improvement with naltrexone, an opioid antagonist, in a case series. Two double-blind placebo-controlled trials found fluvoxamine no better than placebo; however, in both studies patients kept shopping logs, which may have confounded the results. An open-label trial of citalopram and a double-blind crossover trial which excluded shopping logs both reported positive results. Twelve-month follow-up data for the open-label group found that remission rates at quarterly time points were independent of continuing drug therapy. The data reviewed above suggest that pharmacologic interventions may be effective for compulsive buying disorder. Whether pharmacological treatment is superior to placebo and whether it is more, less or equally effective compared to psychotherapeutic interventions remains to be established.
Strategic Grouping and Search for Quality Journalism, Online versus Offline

This paper investigates how supply-side factors influence the search for quality content in online and offline environments. We show that lower fixed costs of online publishing reduce the incentives to bundle content, as compared to offline journalism. In the presence of asymmetric information over journalistic quality, bundling of content by journalists who publish as a group generates positive informational externalities for users. Journalists group assortatively, better journalists having better partners. Then a consumer who discovers one quality journalist, has found several. The online environment, by reducing the pressure to group up, can lower welfare in our baseline model. We establish conditions for this result and investigate a number of countervailing forces.
Teaching Social Studies/History to Elementary School Students through a Discipline-Specific Approach

This mixed methods study explored students’ learning following an intervention unit, which focused on discipline-specific practices in elementary social studies/history. The following questions guided the research: To what extent does students’ learning in social studies/history change following their participation in a unit emphasizing disciplinary-specific practices? and How does their learning compare to students who learn the same content without this approach? Two fifth-grade teachers in a low socioeconomic district taught a disciplinary unit to their students, and a third fifth-grade teacher in the same district taught the same content to her students using a transmission approach. All students performed similarly on the pre-assessment; following the intervention students in the experimental classrooms made greater gains and demonstrated disciplinary-specific practices. This study has implications for elementary school instruction in social studies/history and literacy.