Miracle-dz/UniFAR-FTUs huggingface dataset:
Cysteine-scanning Analysis of Helices TM8, TM9a, and TM9b and Intervening Loops in the YgfO Xanthine Permease

Bacterial and fungal members of the ubiquitous nucleobase-ascorbate transporter (NAT/NCS2) family use the NAT signature motif, a conserved 11-amino acid sequence between amphipathic helices TM9a and TM9b, to define function and selectivity of the purine binding site. To examine the role of flanking helices TM9a, TM9b, and TM8, we employed Cys-scanning analysis of the xanthine-specific homolog YgfO from Escherichia coli. Using a functional mutant devoid of Cys residues (C-less), each amino acid residue in sequences 259FLVVGTIYLLSVLEAVGDITATAMVSRRPIQGEEYQSRLKGGVLADGLVSVIASAV314 and 342TIAVMLVILGLFP354 including these TMs (underlined) was replaced individually with Cys, except the irreplaceable Glu-272 and Asp-304, which had been studied previously. Of 67 single Cys mutants, 55 accumulate xanthine to 35–140% of the steady state observed with C-less, five (I265C, D276C, I277C, G299C, L350C) accumulate to low levels (10–20%) and seven (T278C, A279C, T280C, A281C, G305C, G351C, P354C) show negligible expression in the membrane. Extensive mutagenesis reveals that a carboxyl group is needed at Asp-276 for high activity and that D276E differs from wild type as it recognizes 8-methylxanthine (Ki 79 μm) but fails to recognize 2-thioxanthine, 3-methylxanthine or 6-thioxanthine; bulky replacements of Ala-279 or Thr-280 and replacements of Gly-305, Gly-351, or Pro-354 impair activity or expression. Single Cys mutants V261C, A273C, G275C, and S284C are sensitive to inactivation by N-ethylmaleimide and sensitivity of G275C (IC50 15 μm) is enhanced in the presence of substrate. The data suggest that residues crucial for the transport mechanism cluster in two conserved motifs, at the cytoplasmic end of TM8 (EXXGDXXAT) and in TM9a (GXXXDG).
Edinburgh Research Explorer Beta-AMYLASE4, a noncatalytic protein required for starch breakdown, acts upstream of three active beta-amylases in Arabidopsis chloroplasts

This work investigated the roles of b -amylases in the breakdown of leaf starch. Of the nine b -amylase (BAM)–like proteins encoded in the Arabidopsis thaliana genome, at least four (BAM1, -2, -3, and -4) are chloroplastic. When expressed as recombinant proteins in Escherichia coli , BAM1, BAM2, and BAM3 had measurable b -amylase activity but BAM4 did not. BAM4 has multiple amino acid substitutions relative to characterized b -amylases, including one of the two catalytic residues. Modeling predicts major differences between the glucan binding site of BAM4 and those of active b -amylases. Thus, BAM4 probably lost its catalytic capacity during evolution. Total b -amylase activity was reduced in leaves of bam1 and bam3 mutants but not in bam2 and bam4 mutants. The bam3 mutant had elevated starch levels and lower nighttime maltose levels than the wild type, whereas bam1 did not. However, the bam1 bam3 double mutant had a more severe phenotype than bam3 , suggesting functional overlap between the two proteins. Surprisingly, bam4 mutants had elevated starch levels. Introduction of the bam4 mutation into the bam3 and bam1 bam3 backgrounds further elevated the starch levels in both cases. These data suggest that BAM4 facilitates or regulates starch breakdown and operates independently of BAM1 and BAM3. Together, our ﬁndings are consistent with the proposal that b -amylase is a major enzyme of starch breakdown in leaves, but they reveal unexpected complexity in terms of the specialization of protein function. min, 50% and 50% 5 to 25 min, a concave to 50% A, 10% B, and 40% C (malto-oligosaccharide elution); 32 min, step to 10% B and 90% wash step); 32 36 min, step to 50% A and 50% B (column reequilibration). Peaks were identiﬁed by coelution with known malto-oligosaccharide standards. Peak areas were determined using Chrome- leon software. Susceptibility of the detected compounds to digestion by a -glucosidase conﬁrmed,
Effects of stocking density, flock size and management on the welfare of laying hens in single-tier aviaries

1. Management practices, stocking rate and flock size may affect laying hen welfare but there have been few replicated studies in commercial non-cage systems that investigate this. This study used a broad range of physical and physiological indicators to assess the welfare of hens in 36 commercial flocks. 2. Six laying period treatments were examined with each treatment replicated 6 times. It was not possible to randomly allocate treatments to houses, so treatment and house were largely confounded. 3. Three stocking rates were compared: 7 birds/m2 (n = 2450), 9 birds/m2 (n = 3150) and 12 birds/m2 in either small (n = 2450) or large (n = 4200) flocks. In addition, at 12 birds/m2, in both small and large flocks, birds were subjected to either standard (SM) or modified (MM) management. MM flocks had nipple drinkers and no nest-box lights. 4. Bone strength, fracture incidence, heterophil:lympocyte (H:L) ratio, live weight, organ weights, serum creatine, serum osmolality, muscle pH and faecal corticosterone were measured on samples of birds at the end of the rearing period and at the end of lay. During the laying period, mortality, production and integument condition were recorded at regular intervals. 5 Birds housed at 9 birds/m2 had higher mortality than birds housed at 12 birds/m2 by the end of lay, but not higher than birds housed at 7 birds/m2. Birds housed at 7 and 9 birds/m2 had lower percent liver weight, and worse plumage condition than most of the 12 bird/m2 treatments. Modified management tended to improve plumage condition. There were no clear effects of flock size on the welfare indicators recorded. 6. At the end of the rearing period fracture incidence was almost negligible and H:L ratio was within a normal range. 7. By the end of lay fracture incidence was 60% and H:L ratio was high, with no treatment effect for either measure. This, together with information on faecal corticosterone, feather loss and mortality, suggests that the welfare of birds in all treatments was relatively poor by the end of lay.
Modeling Energy Consumption of Memory Systems

The energy consumption of memory is one of the important metrics to evaluate memory systems. However, previous approaches such as using cycle accurate CPU and memory simulators require a long execution time for simulation. We are developing a model of energy consumption of DRAM-and NVM-based main memory, which allows estimating the energy consumption of a memory subsystem from easily observable performance metrics in real computer systems. In this paper, we conducted preliminary experiments using various types of workloads and observed the correlation of the memory throughput and energy consumption of DRAM. We used hardware performance counters to obtain memory throughput and energy consumption with minimum performance overhead.
Sequence analysis, expression, and deletion of a vaccinia virus gene encoding a homolog of profilin, a eukaryotic actin-binding protein

A 4,500-bp BamHI fragment, located within the HindIII A segment of the vaccinia virus genome, was found to contain eight potential coding regions for polypeptides of 78 to 346 amino acids. The open reading frames with 133, 346, and 125 codons were homologous to profilin (an actin-binding protein), 3-beta-hydroxysteroid dehydrogenase, and Cu-Zn superoxide dismutase, respectively. Sequence alignments indicated that the vaccinia virus and mammalian profilins were more closely related to each other than to known profilins of other eukaryotes. The expression and possible role of the profilin homolog in the virus replicative cycle were therefore investigated. Antibody raised to Escherichia coli expressed vaccinia virus profilin was used to demonstrate the synthesis of the 15-kDa polypeptide at late times after vaccinia virus infection of mammalian cells. The protein accumulated in the cytoplasm, but only trace amounts remained associated with highly purified virions. The isolation of vaccinia virus mutants (in strains WR and IHD-J), with nearly the entire profilin gene replaced by the E. coli gpt gene, indicated that the protein is not essential for infectivity. The characteristic vaccinia virus-induced changes in actin fibers, seen by fluorescence microscopy, occurred in cells infected with the mutant. Moreover, the virus-encoded profilin homolog was not required for actin-associated events, including intracellular virus movement to the periphery of the cell, formation of specialized microvilli, or release of mature virions, as shown by electron microscopy and yields of infectious intra- and extracellular virus.
Human Neuroscience

functional disability and activities of daily living (Katz et al., 1999). Though several therapies have been developed over the last 30 years to treat neglect, addressing the entire range of patients' symptoms and producing consistent improvements across patients remains a challenge. One treatment approach that has shown promise in addressing a broad range of patients' symptoms are behavioral treatments that target tonic and phasic alertness deficits (Robertson et al., 1995; Thimm et al., 2006; for reviews of other treatments see Luaute et al., 2006; Pizzamiglio et al., 2006). Tonic alertness refers to intrinsic arousal that fluctuates on the order of minutes to hours. It is intimately involved in sustaining attention as well as provides the cognitive tone for performing more complicated functions such as working memory and executive control (Sturm et al., 1999; Posner, 2008). Functional MRI studies have shown that tonic alertness is supported by a supramodal network including predominantly right inferior frontal, inferior parietal, and anterior cingulate regions (Sturm and Willmes, 2001; Thiel et al., 2004) whereas neurophysi-ological studies have demonstrated the importance of the locus coeruleus (for a review, see Aston-Jones and Cohen, 2005). Patients with neglect commonly have lesions that involve this network and
Garlic and Onions: Their Cancer Prevention Properties

The Allium genus includes garlic, onions, shallots, leeks, and chives. These vegetables are popular in cuisines worldwide and are valued for their potential medicinal properties. Epidemiologic studies, while limited in their abilities to assess Allium consumption, indicate some associations of Allium vegetable consumption with decreased risk of cancer, particularly cancers of the gastrointestinal tract. Limited intervention studies have been conducted to support these associations. The majority of supportive evidence on Allium vegetables cancer-preventive effects comes from mechanistic studies. These studies highlight potential mechanisms of individual sulfur-containing compounds and of various preparations and extracts of these vegetables, including decreased bioactivation of carcinogens, antimicrobial activities, and redox modification. Allium vegetables and their components have effects at each stage of carcinogenesis and affect many biologic processes that modify cancer risk. This review discusses the cancer-preventive effects of Allium vegetables, particularly garlic and onions, and their bioactive sulfur compounds and highlights research gaps. Cancer Prev Res; 8(3); 181–9. ©2015 AACR.
Highly mutagenic and severely imbalanced dNTP pools can escape detection by the S-phase checkpoint

A balanced supply of deoxyribonucleoside triphosphates (dNTPs) is one of the key prerequisites for faithful genome duplication. Both the overall concentration and the balance among the individual dNTPs (dATP, dTTP, dGTP, and dCTP) are tightly regulated, primarily by the enzyme ribonucleotide reductase (RNR). We asked whether dNTP pool imbalances interfere with cell cycle progression and are detected by the S-phase checkpoint, a genome surveillance mechanism activated in response to DNA damage or replication blocks. By introducing single amino acid substitutions in loop 2 of the allosteric specificity site of Saccharomyces cerevisiae RNR, we obtained a collection of strains with various dNTP pool imbalances. Even mild dNTP pool imbalances were mutagenic, but the mutagenic potential of different dNTP pool imbalances did not directly correlate with their severity. The S-phase checkpoint was activated by the depletion of one or several dNTPs. In contrast, when none of the dNTPs was limiting for DNA replication, even extreme and mutagenic dNTP pool imbalances did not activate the S-phase checkpoint and did not interfere with the cell cycle progression.
Medication errors and adverse drug events in an intensive care unit: Direct observation approach for detection

Objective:To determine the incidence and preventability of medication errors and potential/actual adverse drug events. To evaluate system failures leading to error occurrence. Design:Prospective, direct observation study. Setting:Tertiary care academic medical center. Patients:Patients in a medical/surgical intensive care unit. Interventions:Observers would intervene only in the event that the medication error would cause substantial patient harm or discomfort. Measurements and Main Results:The observers identified 185 incidents during a pilot period and four phases totaling 16.5 days (33 12-hr shifts). Two independent evaluators concluded that 13 of 35 (37%) actual adverse drug events were nonpreventable (i.e., not medication errors). An additional 40 of the remaining 172 medication errors were judged not to be clinically important. Of the 132 medication errors classified as clinically important, 110 (83%) led to potential adverse drug events and 22 (17%) led to actual, preventable adverse drug events. There was one error (i.e., resulting in a potential or actual, preventable adverse drug event) for every five doses of medication administered. The potential adverse drug events mostly occurred in the administration and dispensing stages of the medication use process (34% in each); all of the actual, preventable adverse drug events occurred in the prescribing (77%) and administration (23%) stages. Errors of omission accounted for the majority of potential and actual, preventable adverse drug events (23%), followed by errors due to wrong dose (20%), wrong drug (16%), wrong administration technique (15%), and drug-drug interaction (10%). Conclusions:Using a direct observation approach, we found a higher incidence of potential and actual, preventable adverse drug events and an increased ratio of potential to actual, preventable adverse drug events compared with studies that used chart reviews and solicited incident reporting. All of the potential adverse drug events and approximately two thirds of the actual adverse drug events were judged to be preventable. There was one preventable error for every five doses of medication administered; most errors were due to dose omission, wrong dose, wrong drug, wrong technique, or interactions.
BODY IMPLANT COMMUNICATION – IS IT A REALITY ?

This paper shows how Radio Frequency (RF) communication is possible for implanted medical devices. RF links between implanted medical devices and external monitoring and programming equipment is becoming more common. However, as new RF applications are introduced the battery operating life of the implanted medical device is a concern. This paper describes a technique to prolong battery life. The testing and results of a demonstration implant within a simulated human body are also described.
Chlamydomonas reinhardtii: Biological Rationale for Genomics1

Abstract Chlamydomonas reinhardtii has been the subject of genetic, biochemical, cytological, and molecular analyses for over 50 years. It is an ideal model system for the study of flagella and basal bodies as well as the study of photosynthesis and chloroplast biogenesis, cell-cell recognition and fusion, phototaxis, and secretion. It is clear that many of the genes identified in Chlamydomonas have homologs in land plants as well as animals. Thus, a genomic approach in Chlamydomonas will provide another important avenue for the understanding of important biological processes.
Understanding decay resistance, dimensional stability and strength changes in heat-treated and acetylated wood

Abstract Reductions in hygroscopicity, increased dimensional stability and decay resistance of heat-treated wood depend on decomposition of a large portion of the hemicelluloses in the wood cell wall. In theory, these hemicelluloses are converted to small organic molecules, water and volatile furan-type intermediates that can polymerize in the cell wall. Reductions in hygroscopicity and improved dimensional stability of acetylated wood depend on esterification of the accessible hemicelluloses in the cell wall reducing hydrogen bonding with water and bulking the cell wall back to its green volume. Stability is not 100% since the water molecule is smaller than the acetyl group so water can access hydroxyl sites even when the wood is fully acetylated. The cell-wall moisture content is too low in acetylated wood to support fungal attack so the initial enzymic attack starting the colonization does not take place. Strength properties are reduced in heat-treated wood owing to the degradation of the cell-wall matrix resulting from the hemicellulose loss. Strength properties are not significantly changed in acetylated wood and acetylation results in greatly improved wet strength and wet stiffness properties.
Analysis of BRCA1 and BRCA2 genes in Spanish breast/ovarian cancer patients: A high proportion of mutations unique to Spain and evidence of founder effects

We screened index cases from 410 Spanish breast/ovarian cancer families and 214 patients (19 of them males) with breast cancer for germ‐line mutations in the BRCA1 and BRCA2 genes, using SSCP, PTT, CSGE, DGGE, and direct sequencing. We identified 60 mutations in BRCA1 and 53 in BRCA2. Of the 53 distinct mutations observed, 11 are novel and 12 have been reported only in Spanish families (41.5%). The prevalence of mutations in this set of families was 26.3%, but the percentage was higher in the families with breast and ovarian cancer (52.1%). The lowest proportion of mutations was found in the site‐specific female breast cancer families (15.4%). Of the families with male breast cancer cases, 59.1% presented mutations in the BRCA2 gene. We found a higher frequency of ovarian cancer associated with mutations localized in the 5′ end of the BRCA1 gene, but there was no association between the prevalence of this type of cancer and mutations situated in the ovarian cancer cluster region (OCCR) region of exon 11 of the BRCA2 gene. The mutations 187underscore;188delAG, 330A>G, 5236G>A, 5242C>A, and 589underscore;590del (numbered after GenBank U14680) account for 46.6% of BRCA1 detected mutations whereas 3036underscore;3039del, 6857underscore;6858del, 9254underscore;9258del, and 9538underscore;9539del (numbered after GenBank U43746) account for 56.6% of the BRCA2 mutations. The BRCA1 330A>G has a Galician origin (northwest Spain), and BRCA2 6857underscore;6858del and 9254underscore;9258del probably originated in Catalonia (northeast Spain). Knowledge of the spectrum of mutations and their geographical distribution in Spain will allow a more effective detection strategy in countries with large Spanish populations. Hum Mutat 22:301–312, 2003. © 2003 Wiley‐Liss, Inc.
Insights into the Environmental Resistance Gene Pool from the Genome Sequence of the Multidrug-Resistant Environmental Isolate Escherichia coli SMS-3-5

ABSTRACT The increasing occurrence of multidrug-resistant pathogens of clinical and agricultural importance is a global public health concern. While antimicrobial use in human and veterinary medicine is known to contribute to the dissemination of antimicrobial resistance, the impact of microbial communities and mobile resistance genes from the environment in this process is not well understood. Isolated from an industrially polluted aquatic environment, Escherichia coli SMS-3-5 is resistant to a record number of antimicrobial compounds from all major classes, including two front-line fluoroquinolones (ciprofloxacin and moxifloxacin), and in many cases at record-high concentrations. To gain insights into antimicrobial resistance in environmental bacterial populations, the genome of E. coli SMS-3-5 was sequenced and compared to the genome sequences of other E. coli strains. In addition, selected genetic loci from E. coli SMS-3-5 predicted to be involved in antimicrobial resistance were phenotypically characterized. Using recombinant vector clones from shotgun sequencing libraries, resistance to tetracycline, streptomycin, and sulfonamide/trimethoprim was assigned to a single mosaic region on a 130-kb plasmid (pSMS35_130). The remaining plasmid backbone showed similarity to virulence plasmids from avian-pathogenic E. coli (APEC) strains. Individual resistance gene cassettes from pSMS35_130 are conserved among resistant bacterial isolates from multiple phylogenetic and geographic sources. Resistance to quinolones was assigned to several chromosomal loci, mostly encoding transport systems that are also present in susceptible E. coli isolates. Antimicrobial resistance in E. coli SMS-3-5 is therefore dependent both on determinants acquired from a mobile gene pool that is likely available to clinical and agricultural pathogens, as well, and on specifically adapted multidrug efflux systems. The association of antimicrobial resistance with APEC virulence genes on pSMS35_130 highlights the risk of promoting the spread of virulence through the extensive use of antibiotics.
Relationship Between the Clinical Likelihood of Group A Streptococcal Pharyngitis and the Sensitivity of a Rapid Antigen-Detection Test in a Pediatric Practice

Objective. The sensitivity of a rapid antigen-detection test (RADT) for group A streptococcal (GAS) pharyngitis is critical to whether the test is cost-effective and to whether a confirmatory throat culture is needed. We evaluated a second-generation RADT to determine if its sensitivity varies across the broad clinical spectrum of patients tested for GAS in pediatric outpatient practice. Methods. We used laboratory logbooks from a single pediatric clinic to identify 1184 consecutive patient visits at which an RADT was performed. In a blinded chart review, we calculated McIsaac scores to separately estimate the pretest clinical likelihood of GAS pharyngitis for visits at which the RADT result was positive (n = 384) and for visits at which the result proved to be false-negative (n = 65). Positive RADT results were assumed to be true positives, and test sensitivity was estimated by dividing the number of positive results by the sum of positives and false-negatives. Results. As the clinical likelihood of GAS increased, there were stepwise increases in RADT sensitivity (from 0.67 to 0.88). Sensitivity was low (0.73; 95% confidence interval [CI]: 0.62–0.86) in patients clinically unlikely to have GAS (McIsaac score ≤2) and high (0.94; 95% CI: 0.89–0.99) in patients <15 years old who had tonsillar exudate and no cough. False-negative RADT results were associated with lighter growth of GAS than found on specimens obtained from a random sample of clinic patients who had only primary throat cultures ordered. Conclusions. For pediatric patients who are clinically unlikely to have GAS pharyngitis, as indicated by a McIsaac score ≤2, the sensitivity of a second-generation RADT may drop below thresholds reported for cost-effectiveness. For children who have tonsillar exudate and no cough, the test may be sensitive enough to meet current pediatric practice guidelines for stand-alone testing.