Miracle-dz/UniFAR-FTUs huggingface dataset:
Diversity of O-Antigen Repeat Unit Structures Can Account for the Substantial Sequence Variation of Wzx Translocases

ABSTRACT The most common system for synthesis of cell surface polysaccharides is the Wzx/Wzy-dependent pathway, which involves synthesis, on the cytoplasmic face of the cell membrane, of repeat units, which are then translocated to the periplasmic face by a Wzx translocase and then polymerized by Wzy to generate the polysaccharide. One such polysaccharide is O antigen, which is incorporated into lipopolysaccharide (LPS). The O antigen is extremely variable, with over 186 forms in Escherichia coli. Wzx proteins are also very diverse, but they have been thought to be specific only for the first sugar of the repeat units. However, recent studies demonstrated examples in which Wzx translocases have considerable preference for their native repeat unit, showing that specificity can extend well beyond the first sugar. These results appear to be in conflict with the early conclusions, but they involved specificity for side branch residues and could be a special case. Here we take six Wzx translocases that were critical in the earlier studies on the importance of the first sugar and assess their ability to translocate the Escherichia coli O16 and O111 repeat units. We use gene replacements to optimize maintenance of expression level and show that under these conditions the native translocases are the most effective for their native repeat unit, being, respectively, 64-fold and 4-fold more effective than the next best. We conclude that Wzx translocases are commonly adapted to their native repeat unit, which provides an explanation for the great diversity of wzx genes.
Semi-Calibrated Photometric Stereo

While conventional calibrated photometric stereo methods assume that light intensities and sensor exposures are known or unknown but identical across observed images, this assumption easily breaks down in practical settings due to individual light bulb's characteristics and limited control over sensors. This paper studies the effect of unknown and possibly non-uniform light intensities and sensor exposures among observed images on the shape recovery based on photometric stereo. This leads to the development of a “semi-calibrated” photometric stereo method, where the light directions are known but light intensities (and sensor exposures) are unknown. We show that the semi-calibrated photometric stereo becomes a bilinear problem, whose general form is difficult to solve, but in the photometric stereo context, there exists a unique solution for the surface normal and light intensities (or sensor exposures). We further show that there exists a linear solution method for the problem, and develop efficient and stable solution methods. The semi-calibrated photometric stereo is advantageous over conventional calibrated photometric stereo in accurate determination of surface normal, because it relaxes the assumption of known light intensity ratios/sensor exposures. The experimental results show superior accuracy of the semi-calibrated photometric stereo in comparison to conventional methods in practical settings.
Contrast-enhanced MR Delineation of Stunned Myocardium with Administration of MnCl2 in Rats

PURPOSE: To determine whether stunned myocardium can be delineated at magnetic resonance (MR) imaging with differential cellular uptake of manganese ions. MATERIALS AND METHODS: Twenty-one adult Sprague-Dawley rats underwent either (a) a sequence of three episodes of 10 minutes of coronary artery occlusion and 12 minutes of reflow (group 1, n = 9); (b) a single episode of 10 minutes of occlusion followed by reflow (group 2, n = 6), designed to produce different degrees of myocardial stunning; or (c) a single episode of 2 minutes of occlusion followed by reperfusion (group 3, n = 6), designed to produce no stunning. Ventricular wall thickening was measured on spin-echo (SE) MR images. MnCl2 (0.025 mmol/kg) was intravenously infused for 10 minutes. Highly T1-sensitive inversion-recovery (IR) SE images were obtained to detect subtle regional differences in manganese accumulation. Hearts were stained at sacrifice to define area at risk and to test for myocardial infarction. Significance of differences in mean.
Amino Acid Residues in the GerAB Protein Important in the Function and Assembly of the Alanine Spore Germination Receptor of Bacillus subtilis 168

ABSTRACT The paradigm gerA operon is required for endospore germination in response to l-alanine as the sole germinant, and the three protein products, GerAA, GerAB, and GerAC are predicted to form a receptor complex in the spore inner membrane. GerAB shows homology to the amino acid-polyamine-organocation (APC) family of single-component transporters and is predicted to be an integral membrane protein with 10 membrane-spanning helices. Site-directed mutations were introduced into the gerAB gene at its natural location on the chromosome. Alterations to some charged or potential helix-breaking residues within membrane spans affected receptor function dramatically. In some cases, this is likely to reflect the complete loss of the GerA receptor complex, as judged by the absence of the germinant receptor protein GerAC, which suggests that the altered GerAB protein itself may be unstable or that the altered structure destabilizes the complex. Mutants that have a null phenotype for l-alanine germination but retain GerAC protein at near-normal levels are more likely to define amino acid residues of functional, rather than structural, importance. Single-amino-acid substitutions in each of the GerAB and GerAA proteins can prevent incorporation of GerAC protein into the spore; this provides strong evidence that the proteins within a specific receptor interact and that these interactions are required for receptor assembly. The lipoprotein nature of the GerAC receptor subunit is also important; an amino acid change in the prelipoprotein signal sequence in the gerAC1 mutant results in the absence of GerAC protein from the spore.
Transcriptome Analysis of Pseudomonas syringae Identifies New Genes, Noncoding RNAs, and Antisense Activity

ABSTRACT To fully understand how bacteria respond to their environment, it is essential to assess genome-wide transcriptional activity. New high-throughput sequencing technologies make it possible to query the transcriptome of an organism in an efficient unbiased manner. We applied a strand-specific method to sequence bacterial transcripts using Illumina's high-throughput sequencing technology. The resulting sequences were used to construct genome-wide transcriptional profiles. Novel bioinformatics analyses were developed and used in combination with proteomics data for the qualitative classification of transcriptional activity in defined regions. As expected, most transcriptional activity was consistent with predictions from the genome annotation. Importantly, we identified and confirmed transcriptional activity in areas of the genome inconsistent with the annotation and in unannotated regions. Further analyses revealed potential RpoN-dependent promoter sequences upstream of several noncoding RNAs (ncRNAs), suggesting a role for these ncRNAs in RpoN-dependent phenotypes. We were also able to validate a number of transcriptional start sites, many of which were consistent with predicted promoter motifs. Overall, our approach provides an efficient way to survey global transcriptional activity in bacteria and enables rapid discovery of specific areas in the genome that merit further investigation.
The Only EKG Book You'll Ever Need

This is an attractive textbook with a nicely designed soft cover. The breezy title establishes a sense of informality carried through with humorous illustrations and comments that serve to allay the reader's anxiety about the prospects for being able to read electrocardiograms. The attractive overall design of the book is further complemented by the well-executed and appropriately used drawings of the heart and conduction system. The book begins with an introductory chapter and another devoted to hypertrophy and enlargement. The three-chapter section on arrhythmias and conduction disturbances is placed before the chapter on coronary heart disease. There is a chapter called "Finishing Touches" that contains well-chosen examples of miscellaneous conditions with electrocardiographic manifestations, and the book ends with a review chapter containing a simplified method for reading electrocardiograms and a set of review charts. There are a few minor inaccuracies that do not detract from the overall usefulness of the
Home Assessment Visits within the Acute Setting: a Discussion and Literature Review

The emphasis on the effective and efficient use of finite resources within acute hospitals has led to close attention being paid to the length of patients' hospital stay and the assessment of risk in facilitating timely hospital discharge. Occupational therapy home assessment visits are valued by the multidisciplinary team as a means of assessing a patient's level of function and environmental risk to ensure safe discharge from hospital. Occupational therapists' education and training and experience mean that they are well placed to predict levels of function postdischarge and to anticipate any problems that may occur in activities of daily living. However, for patients the home assessment visit can be a stressful and bewildering experience. The short-term focus on equipment provision combined with limited postdischarge intervention may not meet patient and carer expectations or concerns with longer-term issues. Although there is a body of evidence to support this intervention, the requirement for evidence-based practice means that there is a need for additional research around the areas of optimal timing, selection of patient groups, therapist's rationale, patient and carer perspectives and any effect that home assessments may have on readmission rates. This paper discusses the literature in relation to the practice of home assessment visits from the acute setting.
Storyline Representation of Egocentric Videos with an Applications to Story-Based Search

Egocentric videos are a valuable source of information as a daily log of our lives. However, large fraction of egocentric video content is typically irrelevant and boring to re-watch. It is an agonizing task, for example, to manually search for the moment when your daughter first met Mickey Mouse from hours-long egocentric videos taken at Disneyland. Although many summarization methods have been successfully proposed to create concise representations of videos, in practice, the value of the subshots to users may change according to their immediate preference/mood, thus summaries with fixed criteria may not fully satisfy users' various search intents. To address this, we propose a storyline representation that expresses an egocentric video as a set of jointly inferred, through MRF inference, story elements comprising of actors, locations, supporting objects and events, depicted on a timeline. We construct such a storyline with very limited annotation data (a list of map locations and weak knowledge of what events may be possible at each location), by bootstrapping the process with data obtained through focused Web image and video searches. Our representation promotes story-based search with queries in the form of AND-OR graphs, which span any subset of story elements and their spatio-temporal composition. We show effectiveness of our approach on a set of unconstrained YouTube egocentric videos of visits to Disneyland.
Complete Genome Sequence of Klebsiella pneumoniae 1084, a Hypermucoviscosity-Negative K1 Clinical Strain

ABSTRACT We report the complete genome sequence of Klebsiella pneumoniae 1084, a hypermucoviscosity-negative K1 clinical strain. Sequencing and annotation revealed a 5,386,705-bp circular chromosome (57.4% G+C content), which contains 4,962 protein-coding genes, 80 tRNA genes, and 25 rRNA genes.
Genetic Dissection of T4 Lysis

ABSTRACT t is the holin gene for coliphage T4, encoding a 218-amino-acid (aa) protein essential for the inner membrane hole formation that initiates lysis and terminates the phage infection cycle. T is predicted to be an integral membrane protein that adopts an Nin-Cout topology with a single transmembrane domain (TMD). This holin topology is different from those of the well-studied holins S105 (3 TMDs; Nout-Cin) of the coliphage lambda and S68 (2 TMDs; Nin-Cin) of the lambdoid phage 21. Here, we used random mutagenesis to construct a library of lysis-defective alleles of t to discern residues and domains important for holin function and for the inhibition of lysis by the T4 antiholin, RI. The results show that mutations in all 3 topological domains (N-terminal cytoplasmic, TMD, and C-terminal periplasmic) can abrogate holin function. Additionally, several lysis-defective alleles in the C-terminal domain are no longer competent in binding RI. Taken together, these results shed light on the roles of the previously uncharacterized N-terminal and C-terminal domains in lysis and its real-time regulation.
Altering the Ratio of Phenazines in Pseudomonas chlororaphis (aureofaciens) Strain 30-84: Effects on Biofilm Formation and Pathogen Inhibition

ABSTRACT Pseudomonas chlororaphis strain 30-84 is a plant-beneficial bacterium that is able to control take-all disease of wheat caused by the fungal pathogen Gaeumannomyces graminis var. tritici. The production of phenazines (PZs) by strain 30-84 is the primary mechanism of pathogen inhibition and contributes to the persistence of strain 30-84 in the rhizosphere. PZ production is regulated in part by the PhzR/PhzI quorum-sensing (QS) system. Previous flow cell analyses demonstrated that QS and PZs are involved in biofilm formation in P. chlororaphis (V. S. R. K. Maddula, Z. Zhang, E. A. Pierson, and L. S. Pierson III, Microb. Ecol. 52:289-301, 2006). P. chlororaphis produces mainly two PZs, phenazine-1-carboxylic acid (PCA) and 2-hydroxy-PCA (2-OH-PCA). In the present study, we examined the effect of altering the ratio of PZs produced by P. chlororaphis on biofilm formation and pathogen inhibition. As part of this study, we generated derivatives of strain 30-84 that produced only PCA or overproduced 2-OH-PCA. Using flow cell assays, we found that these PZ-altered derivatives of strain 30-84 differed from the wild type in initial attachment, mature biofilm architecture, and dispersal from biofilms. For example, increased 2-OH-PCA production promoted initial attachment and altered the three-dimensional structure of the mature biofilm relative to the wild type. Additionally, both alterations promoted thicker biofilm development and lowered dispersal rates compared to the wild type. The PZ-altered derivatives of strain 30-84 also differed in their ability to inhibit the fungal pathogen G. graminis var. tritici. Loss of 2-OH-PCA resulted in a significant reduction in the inhibition of G. graminis var. tritici. Our findings suggest that alterations in the ratios of antibiotic secondary metabolites synthesized by an organism may have complex and wide-ranging effects on its biology.
The Response Regulator RpaB Binds to the Upstream Element of Photosystem I Genes To Work for Positive Regulation under Low-Light Conditions in Synechocystis sp. Strain PCC 6803

ABSTRACT The coordinated high-light response of genes encoding subunits of photosystem I (PSI) is achieved by the AT-rich region located just upstream of the core promoter in Synechocystis sp. strain PCC 6803. The upstream element enhances the basal promoter activity under low-light conditions, whereas this positive regulation is lost immediately after the shift to high-light conditions. In this study, we focused on a high-light regulatory 1 (HLR1) sequence included in the upstream element of every PSI gene examined. A gel mobility shift assay revealed that a response regulator RpaB binds to the HLR1 sequence in PSI promoters. Base substitution in the HLR1 sequence or decrease in copy number of the rpaB gene resulted in decrease in the promoter activity of PSI genes under low-light conditions. These observations suggest that RpaB acts as a transcriptional activator for PSI genes. It is likely that RpaB binds to the HLR1 sequence under low-light conditions and works for positive regulation of PSI genes and for negative regulation of high-light-inducible genes depending on the location of the HLR1 sequence within target promoters.
Power Cost Reduction in Distributed Data Centers: A Two-Time-Scale Approach for Delay Tolerant Workloads

This paper considers a stochastic optimization approach for job scheduling and server management in large-scale, geographically distributed data centers. Randomly arriving jobs are routed to a choice of servers. The number of active servers depends on server activation decisions that are updated at a slow time scale, and the service rates of the servers are controlled by power scaling decisions that are made at a faster time scale. We develop a two-time-scale decision strategy that offers provable power cost and delay guarantees. The performance and robustness of the approach is illustrated through simulations.
Sinorhizobium meliloti Mutants Lacking Phosphotransferase System Enzyme HPr or EIIA Are Altered in Diverse Processes, Including Carbon Metabolism, Cobalt Requirements, and Succinoglycan Production

ABSTRACT Sinorhizobium meliloti is a member of the Alphaproteobacteria that fixes nitrogen when it is in a symbiotic relationship. Genes for an incomplete phosphotransferase system (PTS) have been found in the genome of S. meliloti. The genes present code for Hpr and ManX (an EIIAMan-type enzyme). HPr and EIIA regulate carbon utilization in other bacteria. hpr and manX in-frame deletion mutants exhibited altered carbon metabolism and other phenotypes. Loss of HPr resulted in partial relief of succinate-mediated catabolite repression, extreme sensitivity to cobalt limitation, rapid die-off during stationary phase, and altered succinoglycan production. Loss of ManX decreased expression of melA-agp and lac, the operons needed for utilization of α- and β-galactosides, slowed growth on diverse carbon sources, and enhanced accumulation of high-molecular-weight succinoglycan. A strain with both hpr and manX deletions exhibited phenotypes similar to those of the strain with a single hpr deletion. Despite these strong phenotypes, deletion mutants exhibited wild-type nodulation and nitrogen fixation when they were inoculated onto Medicago sativa. The results show that HPr and ManX (EIIAMan) are involved in more than carbon regulation in S. meliloti and suggest that the phenotypes observed occur due to activity of HPr or one of its phosphorylated forms.
A general repair, proportional-hazards, framework to model complex repairable systems

A system (machine) is observed to operate in 1 of 2 modes. The most common mode is loaded (or regular) operation. Occasionally the system is placed in an unloaded state, wherein while the system is mechanically still operating, it is assumed that the failure intensity is lower due to this reduction in operating intensity. A proportional hazards framework is used to capture this potential reduction in failure intensity due to switching of operating modes. In either operating condition, analyzed maintenance-records indicate that the system was occasionally shut down, and either a minor or a major repair was undertaken. Furthermore, despite such repairs, it is observed that both modes of operation (loaded or unloaded) resulted in random failures. On failure, 1 of 3 actions are taken: (1) failures were minimally repaired, (2) given a minor repair, or (3) given a major repair. Both minor and major repairs are assumed to impact the intensity following a virtual age process of the general form proposed by Kijima. This research develops a statistical model of such an operating/maintenance environment. Its purpose is to quantify the impacts of performing these repair actions on the failure intensities. Field data from an industrial-setting demonstrate that appropriate parameter estimates for such multiple phenomena can be obtained. Providing a richer, more detailed, modeling of the failure intensity of a system incorporating both operating conditions and repair effects has important ramifications for maintenance planning. This paper refers to related research, in which optimal timing of maintenance repairs depends fundamentally on the failure rate of the system.
Acetyl Coenzyme A Synthetase Is Acetylated on Multiple Lysine Residues by a Protein Acetyltransferase with a Single Gcn5-Type N-Acetyltransferase (GNAT) Domain in Saccharopolyspora erythraea

ABSTRACT Reversible lysine acetylation (RLA) is used by cells of all domains of life to modulate protein function. To date, bacterial acetylation/deacetylation systems have been studied in a few bacteria (e.g., Salmonella enterica, Bacillus subtilis, Escherichia coli, Erwinia amylovora, Mycobacterium tuberculosis, and Geobacillus kaustophilus), but little is known about RLA in antibiotic-producing actinomycetes. Here, we identify the Gcn5-like protein acetyltransferase AcuA of Saccharopolyspora erythraea (SacAcuA, SACE_5148) as the enzyme responsible for the acetylation of the AMP-forming acetyl coenzyme A synthetase (SacAcsA, SACE_2375). Acetylated SacAcsA was deacetylated by a sirtuin-type NAD+-dependent consuming deacetylase (SacSrtN, SACE_3798). In vitro acetylation/deacetylation of SacAcsA enzyme was studied by Western blotting, and acetylation of lysine residues Lys237, Lys380, Lys611, and Lys628 was confirmed by mass spectrometry. In a strain devoid of SacAcuA, none of the above-mentioned Lys residues of SacAcsA was acetylated. To our knowledge, the ability of SacAcuA to acetylate multiple Lys residues is unique among AcuA-type acetyltransferases. Results from site-specific mutagenesis experiments showed that the activity of SacAcsA was controlled by lysine acetylation. Lastly, immunoprecipitation data showed that in vivo acetylation of SacAcsA was influenced by glucose and acetate availability. These results suggested that reversible acetylation may also be a conserved regulatory posttranslational modification strategy in antibiotic-producing actinomycetes.
Acupuncture and traditional Chinese medicine: an overview

Methods of treatment that were once considered “alternative” are more frequently used by patients for the management of pain conditions. This paper provides a basic overview of one of those modalities: acupuncture and traditional Chinese medicine (TCM). Considered “a whole medical system” by the National Center for Complementary and Alternative Medicine, an institute within the National Institutes of Health, acupuncture and TCM have been used for hundreds of years to treat disease. A description of acupuncture and TCM techniques and an introduction to basic TCM theory will be presented as well as information on research into the mechanism of action of acupuncture, conditions treated, and basic practice information.