Miracle-dz/UniFAR-FTUs huggingface dataset:
S-Adenosylmethionine-Binding Properties of a Bacterial Phospholipid N-Methyltransferase

ABSTRACT The presence of the membrane lipid phosphatidylcholine (PC) in the bacterial membrane is critically important for many host-microbe interactions. The phospholipid N-methyltransferase PmtA from the plant pathogen Agrobacterium tumefaciens catalyzes the formation of PC by a three-step methylation of phosphatidylethanolamine via monomethylphosphatidylethanolamine and dimethylphosphatidylethanolamine. The methyl group is provided by S-adenosylmethionine (SAM), which is converted to S-adenosylhomocysteine (SAH) during transmethylation. Despite the biological importance of bacterial phospholipid N-methyltransferases, little is known about amino acids critical for binding to SAM or phospholipids and catalysis. Alanine substitutions in the predicted SAM-binding residues E58, G60, G62, and E84 in A. tumefaciens PmtA dramatically reduced SAM-binding and enzyme activity. Homology modeling of PmtA satisfactorily explained the mutational results. The enzyme is predicted to exhibit a consensus topology of the SAM-binding fold consistent with cofactor interaction as seen with most structurally characterized SAM-methyltransferases. Nuclear magnetic resonance (NMR) titration experiments and 14C-SAM-binding studies revealed binding constants for SAM and SAH in the low micromolar range. Our study provides first insights into structural features and SAM binding of a bacterial phospholipid N-methyltransferase.
A high performance liquid chromatography-tandem mass spectrometric method for the determination of mefenamic acid in human plasma: application to pharmacokinetic study.

In the present study, the development and validation of an LC-MS/MS method for quantifying mefenamic acid in human plasma is described. The method involves liquid-liquid extraction using diclofenac as an internal standard (IS). Chromatographic separation was achieved on a Thermo Hypurity C(18) , 50 × 4.6 mm, 5 µm column with a mobile phase consisting of 2 m m ammonium acetate buffer and methanol (pH 4.5 adjusted with glacial acetic acid; 15:85, v/v) at a flow-rate of 0.75 mL/min and the total run time was 1.75 min. Analyte was introduced to the LC-MS/MS using an atmospheric pressure ionization source. Both the drug and IS were detected in negative-ion mode using multiple reaction monitoring m/z 240.0 → 196.3 and m/z 294.0 → 250.2, respectively, with a dwell time of 200 ms for each of the transitions. The standard curve was linear from 20 to 6000 ng/mL. This assay allows quantification of mefenamic acid at a concentration as low as 20 ng/mL in human plasma. The observed mean recovery was 73% for the drug. The applicability of this method for pharmacokinetic studies has been established after successful application during a 12-subject bioavailabity study.
AN ENHANCED ALGORITHM FOR AUTOMATIC RADIOMETRIC HARMONIZATION OF HIGH-RESOLUTION OPTICAL SATELLITE IMAGERY USING PSEUDOINVARIANT FEATURES AND LINEAR REGRESSION

Abstract. The growing number of available optical remote sensing data providing large spatial and temporal coverage enables the coherent and gapless observation of the earth’s surface on the scale of whole countries or continents. To produce datasets of that size, individual satellite scenes have to be stitched together forming so-called mosaics. Here the problem arises that the different images feature varying radiometric properties depending on the momentary acquisition conditions. The interpretation of optical remote sensing data is to a great extent based on the analysis of the spectral composition of an observed surface reflection. Therefore the normalization of all images included in a large image mosaic is necessary to ensure consistent results concerning the application of procedures to the whole dataset. In this work an algorithm is described which enables the automated spectral harmonization of satellite images to a reference scene. As the stable and satisfying functionality of the proposed algorithm was already put to operational use to process a high number of SPOT-4/-5, IRS LISS-III and Landsat-5 scenes in the frame of the European Environment Agency's Copernicus/GMES Initial Operations (GIO) High-Resolution Layer (HRL) mapping of the HRL Forest for 20 Western, Central and (South)Eastern European countries, it is further evaluated on its reliability concerning the application to newer Sentinel-2 multispectral imaging products. The results show that the algorithm is comparably efficient for the processing of satellite image data from sources other than the sensor configurations it was originally designed for.
The effects of a system echo in a restricted natural language database interface for novice users

A system echo is a structured restatement of the user's query and informs the user what the system intends to do for the query. This provides backtracking of the user's query so that the user knows how the system has interpreted the query. This study scrutinizes whether the system echo, as currently available in the Intellect commercial system, can improve the performance of a novice using a restricted natural language database interface. The results indicate that the system echo of Intellect does not improve the performance of novice users in terms of error recovery rate and confidence. <<ETX>>
Tweeting about Sustainability: Can Emotional Nowcasting Discourage Greenwashing?

Less than 100 firms worldwide are recognised by Bloomberg to report accurate greenhouse gas emissions. Yet, tens of thousands of people are talking and tweeting about climate change every day. How can this attention be converted into accurate action? We propose that sustainable data science might help, specifically that ‘emotional nowcasting’ of societal responses to sustainability related statements as expressed on Twitter. First, we differentiate between various types of corporate sustainability performance data and highlight the challenge that corporate greenwashing and a potential lack of financial independence of the assessor from the assessed poses for these data sets. Second, we adopt Lampos and Christianini’s (2012) emotional nowcasting with two case studies of an emotionally non-ambivalent context, the football matches England vs. Germany and England vs. USA at the 2010 world cup. These case studies serve as a proof of concept for emotional nowcasting. Finally, we discuss the potential for emotional nowcasting to mitigate the pandemic of greenwashing currently experienced in sustainability communication. We conclude that emotional nowcasting can serve as one test of greenwashing which is on its own though not necessarily sufficient.
Version Vector Weighted Voting protocol: efficient and fault‐tolerant commitment for weakly connected replicas

Mobile and other loosely coupled environments call for decentralized optimistic replication protocols that provide highly available access to shared objects, while ensuring eventual consistency. We propose a protocol based on epidemic weighted voting for achieving such a goal with better availability than traditional primary commit approaches. We improve previous epidemic weighted voting solutions by allowing commitment of multiple, happened‐before related updates at a single distributed election round. We demonstrate that our protocol, in contrast to basic weighted voting solutions, achieves similar update commitment ratios to the primary commit alternative. The improvement over basic weighted voting is especially amplified with weaker replica connectivity, as in mobile and other loosely coupled environments. We support such claims by presenting comparison performance results obtained from side‐by‐side execution of reference protocols in a simulated environment. Copyright © 2007 John Wiley & Sons, Ltd.
A Randomized, Placebo-Controlled, Multicenter, Biomarker-Selected, Phase 2 Study of Apricoxib in Combination with Erlotinib in Patients with Advanced Non–Small-Cell Lung Cancer

Cyclooxygenase-2 (COX-2) overexpression is associated with a poor prognosis in non–small-cell lung cancer (NSCLC) and may promote resistance to epidermal growth factor receptor inhibitors. This randomized phase 2 trial evaluated apricoxib, a novel COX-2 inhibitor, in combination with erlotinib in biomarker-selected patients. Patients with stage IIIB/IV NSCLC previously treated with platinum-based chemotherapy were randomized (2:1) to 400 mg/day apricoxib plus 150 mg/day erlotinib (AP/E) or placebo plus erlotinib (P/E) in 21-day cycles until disease progression or unacceptable toxicity. The primary endpoint was time to progression (TTP). A decrease of 50% or more from baseline urinary prostaglandin E2 metabolite after a 5-day, open-label, run-in period was used to select eligible patients. One hundred twenty patients (median age 64 years) were randomized (78 to AP/E and 42 to P/E). Overall median TTP was 1.8 months in the AP/E group and 2.1 months in the P/E group, with a 12% objective response rate in both groups (intent-to-treat analysis). A subgroup analysis in patients aged 65 years or younger demonstrated a statistically significant TTP benefit for AP/E (hazard ratio 0.5 [95% confidence interval: not applicable–0.9]; p=0.018) and overall survival advantage at minimum 1-year follow-up (median 12.2 versus 4.0 months; hazard ratio=0.5; p=0.021). The most common adverse events were rash, diarrhea, fatigue, and nausea. Toxicity contributed to early discontinuations in patients aged more than 65 years treated with AP/E. This is the first randomized placebo-controlled study of a COX-2 inhibitor in NSCLC to use a prospective patient-selection strategy. Although AP/E seemed to improve TTP and overall survival in a subset of patients aged 65 years or younger, the primary endpoint of the trial was not met.
Photochromism of dithienylethene single crystals having anthracene substituents

Three dithienylethene derivatives having anthracene substituents (connected at 1-, 2- and 9-positions) were prepared. Although these three derivatives exhibit photochromic reactivity in solution, only one of the derivatives (connected at 2-position) undergoes the photochromic reaction in the crystalline phase. X-Ray crystallographic analysis and DFT calculation revealed that conformation of the anthracene substituents plays an important role in the crystalline photochromism.
Novel frameshift mutations in CRX associated with Leber congenital amaurosis

Mutations in CRX, a photoreceptor‐specific transcription factor, can cause Leber congenital amaurosis (LCA), cone‐rod dystrophy (CORD), and retinitis pigmentosa (RP), all of which feature severe visual impairment. Upon screening 55 patients with Leber congenital amaurosis, 75 patients with cone‐rod dystrophy, 13 with cone dystrophy, and 36 with recessive or isolate RP for changes in the CRX sequence, we found two patients with Leber congenital amaurosis who carried heterozygously one of two novel frameshift mutations. The first mutation, Tyr191(1‐bp del), was a de novo change and the second change, Pro263(1‐bp del) was inherited from the proband’s affected father. Both mutations are predicted to encode mutant versions of CRX with altered carboxy termini. We also found a previously reported missense mutation, Arg41Gln, heterozygously in a 47‐year‐old patient with a form of RP. The missense change Val242Met was found in an isolate case of CORD and no controls; however, its pathogenicity remains uncertain because only limited segregation analysis was possible. A nonpathogenic missense change, Ala158Thr, was found to be a variant present at relatively high frequency among African‐Americans. © 2001 Wiley‐Liss, Inc.
The Rox1 repressor of the Saccharomyces cerevisiae hypoxic genes is a specific DNA-binding protein with a high-mobility-group motif

The ROX1 gene encodes a repressor of the hypoxic functions of the yeast Saccharomyces cerevisiae. The DNA sequence of the gene was determined and found to encode a protein of 368 amino acids. The amino-terminal third of the protein contains a high-mobility-group motif characteristic of DNA-binding proteins. To determine whether the Rox1 repressor bound DNA, the gene was expressed in Escherichia coli cells as a fusion to the maltose-binding protein and this fusion was partially purified by amylose affinity chromatography. By using a gel retardation assay, both the fusion protein and Rox1 itself were found to bind specifically to a synthetic 32-bp DNA containing the hypoxic consensus sequence. We assessed the role of the general repressor Ssn6 in ANB1 repression. An ANB1-lacZ fusion was expressed constitutively in an ssn6 deletion strain, and deletion of the Rox1 binding sites in the ANB1 upstream region did not increase the level of derepression, suggesting that Ssn6 exerts its effect through Rox1. Finally, ROX1 was mapped to yeast chromosome XVI, near the ARO7-OSM2 locus.
A scheme for copy-move forgery detection in digital images based on 2D-DWT

In this paper, a copy-move image forgery detection scheme is developed based on a block matching algorithm. Instead of considering spatial blocks, 2D-DWT is performed on the forged image and then DWT domain blocks are considered, where only approximate DWT coefficients are utilized. In order to reduce the computational burden, unlike conventional approaches, instead of performing block matching operation among all blocks, some candidate blocks are first selected from the non-overlapping blocks based on a similarity measure. In the next stage, all overlapping blocks are compared with the candidate blocks. A similarity criterion is introduced to finally detect the forged blocks. Extensive simulation is carried out on several forged images and it is found that proposed algorithm can efficiently detect copy-move forgery.
Análisis Numerico De Las Tensiones Producidas Por El Secado Del Hormigon.

En este trabajo se realiza un estudio numerico del estado de tensiones asociado al proceso de secado del hormigon. La motivacion del mismo es el de prever la fisuracion temprana observada en piezas premoldeadas de hormigon de pequeno espesor. Para ello se realiza un estudio sistematico de los fenomenos que producen este problema. En primer lugar se realiza el planteo teorico del problema de difusion del agua entre los poros del hormigon que se produce durante el secado. Este estudio conduce a un problema en derivadas parciales transitorio no lineal, el cual se resuelve discretizando espacialmente por elementos finitos y temporalmente con un esquema implicito, con un software propio especialmente desarrollado para tal proposito. La informacion obtenida del problema de difusion se traduce a una retraccion volumetrica para cada instante considerado, a partir de relaciones empiricas entre humedad y deformacion. Una ultima etapa del procedimiento corresponde al analisis estatico lineal del cual se obtiene el estado tensional correspondiente. En funcion de ello se dispone de un criterio para evaluar la posibilidad de fisuracion en piezas de hormigon para edades tempranas. Se muestran ejemplos de aplicacion.
Quality of Ambulatory Care for Diabetes and Lower-Extremity Amputation

Lower extremity amputation (LEA) is a serious complication of diabetes. We sought to determine whether quality of ambulatory care affects risk of LEA. We conducted a claims-based case-control study of 409 Medicare beneficiaries younger than age 75 with diabetes and LEA between January 1, 2003, and December 31, 2005. They were matched with controls with diabetes without LEA, on age, gender, number of diabetes outpatient visits, and (for those with hospital admissions between January 1, 2000, and December 31, 2002) number of comorbid conditions, diabetes complications, and peripheral vascular disease. Quality-of-care measures for cases and controls covered the period April 1, 1999, through March 31, 2001. LEA patients were less likely to have had lipid screening than controls (odds ratio = 0.73; 95% confidence interval = 0.53-0.99), and controls were more likely to use physicians with high performance in lipid screening (χ 2 = 6.631, P = .012) and hemoglobin A1c testing (χ 2 = 6.079, P = .014). (Am J Med Qual 2007;22:410-417)
PTA1, an essential gene of Saccharomyces cerevisiae affecting pre-tRNA processing

We have identified an essential Saccharomyces cerevisiae gene, PTA1, that affects pre-tRNA processing. PTA1 was initially defined by a UV-induced mutation, pta1-1, that causes the accumulation of all 10 end-trimmed, intron-containing pre-tRNAs and temperature-sensitive but osmotic-remedial growth. pta1-1 does not appear to be an allele of any other known gene affecting pre-tRNA processing. Extracts prepared from pta1-1 strains had normal pre-tRNA splicing endonuclease activity. pta1-1 was suppressed by the ochre suppressor tRNA gene SUP11, indicating that the pta1-1 mutation creates a termination codon within a protein reading frame. The PTA1 gene was isolated from a genomic library by complementation of the pta1-1 growth defect. Episome-borne PTA1 directs recombination to the pta1-1 locus. PTA1 has been mapped to the left arm of chromosome I near CDC24; the gene was sequenced and could encode a protein of 785 amino acids with a molecular weight of 88,417. No other protein sequences similar to that of the predicted PTA1 gene product have been identified within the EMBL or GenBank data base. Disruption of PTA1 near the carboxy terminus of the putative open reading frame was lethal. Possible functions of the PTA1 gene product are discussed.
Targeting and processing of site‐specific DNA interstrand crosslinks

DNA interstrand crosslinks (ICLs) are among the most cytotoxic types of DNA damage, and thus ICL‐inducing agents such as cyclophosphamide, melphalan, cisplatin, psoralen, and mitomycin C have been used clinically as anticancer drugs for decades. ICLs can also be formed endogenously as a consequence of cellular metabolic processes. ICL‐inducing agents continue to be among the most effective chemotherapeutic treatments for many cancers; however, treatment with these agents can lead to secondary malignancies, in part due to mutagenic processing of the DNA lesions. The mechanisms of ICL repair have been characterized more thoroughly in bacteria and yeast than in mammalian cells. Thus, a better understanding of the molecular mechanisms of ICL processing offers the potential to improve the efficacy of these drugs in cancer therapy. In mammalian cells, it is thought that ICLs are repaired by the coordination of proteins from several pathways, including nucleotide excision repair (NER), base excision repair (BER), mismatch repair (MMR), homologous recombination (HR), translesion synthesis (TLS), and proteins involved in Fanconi anemia (FA). In this review, we focus on the potential functions of NER, MMR, and HR proteins in the repair of and response to ICLs in human cells and in mice. We will also discuss a unique approach, using psoralen covalently linked to triplex‐forming oligonucleotides to direct ICLs to specific sites in the mammalian genome. Environ. Mol. Mutagen. 2010. © 2010 Wiley‐Liss, Inc.
Evaluation of Students' Skills in Remote Collaboration for Creative Problem Solving in Computer Graphics

Use of distributed teams of artists and engineers is becoming more prevalent in computer graphics oriented industries. Developing the skills required to work as a team through the complex sequential development and production process of animated films, visual effects, and commercial productions is a part of many academic programs that focus on computer graphics. However, the development of the skills required to communicate and coordinate this kind of work across a distributed team is currently a rare curriculum feature, and may not even be recognized as a separate set of issues from localized collaboration. This paper reports on an effort to assess this problem through pilot projects that focus on discovering how adept students are at working as members of distributed teams. We tightly controlled the tools of communication -email, chat, and video-conferencing- to determine the impact of each modality on creative problem solving while teams of students from four locations attempted to coordinate their work to produce short 30-second computer animations. Assessment by industry professionals of the originality found in the aesthetic and technical results of the student projects suggests that the students, overall, are deficient in two areas that are essential to successful creative collaboration: communication that contributes to awareness among distant partners, and communicating in ways that build consensus and solves problems. Though these issues also exist for co-located teams, their significance is likely heightened in distance collaboration projects. These issues might also impact the manner in which companies that use distributed teams incorporate various modalities of communication technology into their production pipelines.
Field degradation of aminopyralid and clopyralid and microbial community response to application in Alaskan soils

High‐latitude regions experience unique conditions that affect the degradation rate of agrochemicals in the environment. In the present study, data collected from 2 field sites in Alaska, USA (Palmer and Delta) were used to generate a kinetic model for aminopyralid and clopyralid degradation and to describe the microbial community response to herbicide exposure. Field plots were sprayed with herbicides and sampled over the summer of 2013. Quantification was performed via liquid chromatrography/tandem mass spectrometry, and microbial diversity was assessed via next‐generation sequencing of bacterial 16S ribosomal ribonucleic acid (rRNA) genes. Both compounds degraded rapidly via pseudo‐first–order degradation kinetics between 0 d and 28 d (t1/2 = 9.1–23.0 d), and then degradation slowed thereafter through 90 d. Aminopyralid concentration was 0.048 μg/g to 0.120 μg/g at 90 d post application, whereas clopyralid degraded rapidly at the Palmer site but was recovered in Delta soil at a concentraction of 0.046 μg/g. Microbial community diversity was moderately impacted by herbicide treatment, with the effect more pronounced at Delta. These data predict reductions in crop yield when sensitive plants (potatoes, tomatoes, marigolds, etc.) are rotated onto treated fields. Agricultural operations in high‐latitude regions, both commercial and residential, rely heavily on cultivation of such crops and care must be taken when rotating. Environ Toxicol Chem 2016;35:485–493. © 2015 SETAC
Executive dysfunction and domestic violence

Primary objective: To replicate previous studies which have reported a high prevalence of traumatic brain injury (TBI) in partner-abusive men and to extend research in this area by determining the prevalence of executive dysfunctions, which have been linked with both TBI and violent behaviour. Research design: Thirty-eight men with criminal convictions for violence and who were receiving treatment for abusing their partners were assessed. Methods and procedures: Subjects with a self-reported history of TBI (n = 22) were compared to the non-TBI group (n = 16) on various psychological measures. Main outcomes and results: The two groups were not significantly different on the variables of age, pre-morbid IQ, self-esteem and alcohol use. The TBI group scored more poorly than the non-TBI group on a measure of current IQ and two of the three measures of executive functioning. Conclusion: The presence of executive dysfunction has implications for the design of successful intervention programmes with this sub-group of batterers.