Miracle-dz/UniFAR-FTUs huggingface dataset:
Temperature-Induced Remodeling of the Photosynthetic Machinery Tunes Photosynthesis in the Thermophilic Alga Cyanidioschyzon merolae1

C. merolae acclimates to suboptimal growth temperature by tuning its photosynthetic capacity and by adjusting its machinery for protein folding, degradation, and homeostasis. The thermophilic alga C. merolae thrives in extreme environments (low pH and temperature between 40°C and 56°C). In this study, we investigated the acclimation process of the alga to a colder temperature (25°C). A long-term cell growth experiment revealed an extensive remodeling of the photosynthetic apparatus in the first 250 h of acclimation, which was followed by cell growth to an even higher density than the control (grown at 42°C) cell density. Once the cells were shifted to the lower temperature, the proteins of the light-harvesting antenna were greatly down-regulated and the phycobilisome composition was altered. The amount of PSI and PSII subunits was also decreased, but the chlorophyll to photosystems ratio remained unchanged. The 25°C cells possessed a less efficient photon-to-oxygen conversion rate and require a 2.5 times higher light intensity to reach maximum photosynthetic efficiency. With respect to chlorophyll, however, the photosynthetic oxygen evolution rate of the 25°C culture was 2 times higher than the control. Quantitative proteomics revealed that acclimation requires, besides remodeling of the photosynthetic apparatus, also adjustment of the machinery for protein folding, degradation, and homeostasis. In summary, these remodeling processes tuned photosynthesis according to the demands placed on the system and revealed the capability of C. merolae to grow under a broad range of temperatures.
A framework of adaptive T-S type Rough-Fuzzy Inference Systems (ARFIS)

The rough-fuzzy hybridization scheme has become of research interest in a variety of areas over the past decade. The present paper proposes a general framework for adaptive T-S type rough-fuzzy inference systems (ARFIS) for many practical applications. Rough set theory is utilized to reduce the number of attributes and to obtain a minimal set of decision rules based on input-output data sets. A T-S type fuzzy inference system is constructed by the automatic generation of membership functions and rules by the fuzzy c-means clustering algorithm and the rough set approach, respectively. The generated T-S type rough-fuzzy inference system is then adjusted by the least squares fit and the conjugate gradient descent algorithm towards better performance with a validity checking for the generated minimal set of rules. The proposed framework of ARFIS is able to reduce the number of rules which increases exponentially when more input variables are involved and also to assess the validity of the minimized decision rules. The performance of the proposed framework of ARFIS is compared with other existing approaches in a variety of application areas and shown to be very competitive.
Extracellular Surface Residues of the α1B-Adrenoceptor Critical for G Protein–Coupled Receptor Function

Ligand binding and conformational changes that accompany signaling from G protein–coupled receptors (GPCRs) have mostly focused on the role of transmembrane helices and intracellular loop regions. However, recent studies, including several GPCRs cocrystallized with bound ligands, suggest that the extracellular surface (ECS) of GPCRs plays an important role in ligand recognition, selectivity, and binding, as well as potentially contributing to receptor activation and signaling. This study applied alanine-scanning mutagenesis to investigate the role of the complete ECS of the α1B-adrenoreceptor on norepinephrine (NE) potency, affinity, and efficacy. Half (24 of 48) of the ECS mutations significantly decreased NE potency in an inositol 1-phosphate assay. Most mutations reduced NE affinity (17) determined from [3H]prazosin displacement studies, whereas four mutations at the entrance to the NE binding pocket enhanced NE affinity. Removing the influence of NE affinity and receptor expression levels on NE potency gave a measure of NE efficacy, which was significantly decreased for 11 of 48 ECS mutants. These different effects tended to cluster to different regions of the ECS, which is consistent with different regions of the ECS playing discrete functional roles. Exposed ECS residues at the entrance to the NE binding pocket mostly affected NE affinity, whereas buried or structurally significant residues mostly affected NE efficacy. The broad potential for ECS mutations to affect GPCR function has relevance for the increasing number of nonsynonymous single nucleotide polymorphisms now being identified in GPCRs.
A Highly Available Log Service for Transaction Termination

Distributed transaction processing hinges on enforcing agreement among the involved resource managers on whether to commit or abort transactions (atomicity) and on making their updates permanent (durability). This paper introduces a log service which abstracts these tasks. The service logs commit and abort votes as well as the updates performed by each resource manager. Based on the votes, the log service outputs the transaction's outcome. The service also totally orders non-concurrent transactions and makes the sequence of updates performed by each resource manager available as a means to consistently recover resource managers without relying on their local state. Besides the specification, we overview two highly available implementations of this service and present an experimental performance evaluation.
Surgical Treatment of Infantile Hemangiomas in the Era of Propranolol

Background: Despite the proven efficacy and safety of beta-blockers in the management of infantile hemangiomas (IH), there are still many patients requiring surgical treatment. The aim of our study is to analize the current indications for surgical treatment of IH in the era of propranolol. Methods: This is a retrospective study from 2009 until 2014, including 45 children (38 females and 7 males) referred from other centers to our institution for surgical treatment of an IH. Epidemiological, clinical and treatment data were collected and variables analyzed. Results: Of the 45 patients included in the study, 22 patients were not offered any treatment as it was not considered necessary, 16 were treated with a systemic b-blocker, 3 patients, despite being considered candidates for propranolol therapy, refused it for fear of potential adverse side effects and the remaining 4 received an alternative treatment. The average age of patients at their first visit to surgery consultation was 32.41 months (SD 36.71), the average age of initiation of treatment with propranolol was 10.58 months (SD 7.99) and the average age at time of surgery was 29.11 months (SD 16.10). Conclusion: No indication for propranolol treatment or the delays in its administration are the main current causes of surgical treatment of IH. Therefore it is important to improve protocols to establish more effective and preventative guidelines that would reduce the need for subsequent surgery.
fMRI responses to Jung's Word Association Test: implications for theory, treatment and research.

Jung's Word Association Test was performed under fMRI conditions by 12 normal subjects. Pooled complexed responses were contrasted against pooled neutral ones. The fMRI activation pattern of this generic 'complexed response' was very strong (corrected Z scores ranging from 4.90 to 5.69). The activation pattern in each hemisphere includes mirror neurone areas that track 'otherness' (perspectival empathy), anterior insula (both self-awareness and emotional empathy), and cingulated gyrus (self-awareness and conflict-monitoring). These are the sites described by Siegel and colleagues as the 'resonance circuitry' in the brain which is central to mindfulness (awareness of self) and empathy (sense of the other), negotiations between self awareness and the 'internal other'. But there is also an interhemispheric dialogue. Within 3 seconds, the left hemisphere over-rides the right (at least in our normal subjects). Mindfulness and empathy are central to good psychotherapy, and complexes can be windows of opportunity if left-brain hegemony is resisted. This study sets foundations for further research: (i) QEEG studies (with their finer temporal resolution) of complexed responses in normal subjects (ii) QEEG and fMRI studies of complexed responses in other conditions, like schizophrenia, PTSD, disorders of self organization.
Metabolic costs of force generation for constant‐frequency and catchlike‐inducing electrical stimulation in human tibialis anterior muscle

Metabolic costs of force generation were compared for constant‐frequency and catchlike‐inducing electrical stimulation. Repetitive catchlike‐inducing trains consisted of 2 interpulse intervals (IPIs) at 12.5 ms, 1 IPI at 25 ms, and 5 IPIs at 50 ms. Constant‐frequency trains consisted of 8 IPIs at 37.5 ms. One train was delivered to the peroneal nerve every 2.5 s for 36 times under ischemic conditions. Anaerobic adenosine triphosphate (ATP) turnover was determined using 31‐phosphorus magnetic resonance spectroscopy (P‐MRS) of the human tibialis anterior muscle. Compared with constant‐frequency trains, catchlike‐inducing trains produced a faster force generation and were more effective in maintaining the force–time integral as well as peak force. However, ATP costs of force generation were similar for the catchlike‐inducing and constant‐frequency stimulation (6.7 ± 1.1 and 6.6 ± 1.0 μmol ATP/kg wet weight/N·s, respectively, P = 0.601). This suggests that the positive effects of catchlike‐inducing stimulation on force maintenance are mediated by potentiated Ca2+ release from the sarcoplasmic reticulum rather than by lower metabolic costs of muscle force generation. Our findings also suggest that catchlike‐inducing stimulation produces larger forces in fatigued muscle than constant‐frequency trains and thus may be beneficial for muscle training or rehabilitation when muscle loading needs to be maintained in repetitive contractions. © 2002 Wiley Periodicals, Inc. Muscle Nerve 25: 000–000, 2002
Antimicrobial Resistance, Toxinotype, and Genotypic Profiling of Clostridium difficile Isolates of Swine Origin

ABSTRACT The occurrence of Clostridium difficile infections in patients that do not fulfill the classical risk factors prompted us to investigate new risk factors of disease. The goal of this study was to characterize strains and associated antimicrobial resistance determinants of C. difficile isolated from swine raised in Ohio and North Carolina. Genotypic approaches used include PCR detection, toxinotyping, DNA sequencing, and pulsed-field gel electrophoresis (PFGE) DNA fingerprinting. Thirty-one percent (37/119) of isolates carried both tetM and tetW genes. The ermB gene was found in 91% of isolates that were resistant to erythromycin (68/75). Eighty-five percent (521/609) of isolates were toxin gene tcdB and tcdA positive. A total of 81% (494/609) of isolates were positive for cdtB and carry a tcdC gene (a toxin gene negative regulator) with a 39-bp deletion. Overall, 88% (196/223) of pigs carry a single C. difficile strain, while 12% (27/223) of pigs carried multiple strains. To the best of our knowledge, this is the first report of individual pigs found to carry more than one strain type of C. difficile. A significant difference in toxinotype profiles in the two geographic locations was noted, with a significantly (P < 0.001) higher prevalence of toxinotype V found in North Carolina (84%; 189/224) than in Ohio (55%; 99/181). Overall, the study findings indicate that significant proportions of C. difficile in swine are toxigenic and often are associated with antimicrobial resistance genes, although they are not resistant to drugs that are used to treat C. difficile infections.
Comprehensive Functional Annotation of 77 Prostate Cancer Risk Loci

Genome-wide association studies (GWAS) have revolutionized the field of cancer genetics, but the causal links between increased genetic risk and onset/progression of disease processes remain to be identified. Here we report the first step in such an endeavor for prostate cancer. We provide a comprehensive annotation of the 77 known risk loci, based upon highly correlated variants in biologically relevant chromatin annotations— we identified 727 such potentially functional SNPs. We also provide a detailed account of possible protein disruption, microRNA target sequence disruption and regulatory response element disruption of all correlated SNPs at . 88% of the 727 SNPs fall within putative enhancers, and many alter critical residues in the response elements of transcription factors known to be involved in prostate biology. We define as risk enhancers those regions with enhancer chromatin biofeatures in prostate-derived cell lines with prostate-cancer correlated SNPs. To aid the identification of these enhancers, we performed genomewide ChIP-seq for H3K27-acetylation, a mark of actively engaged enhancers, as well as the transcription factor TCF7L2. We analyzed in depth three variants in risk enhancers, two of which show significantly altered androgen sensitivity in LNCaP cells. This includes rs4907792, that is in linkage disequilibrium () with an eQTL for NUDT11 (on the X chromosome) in prostate tissue, and rs10486567, the index SNP in intron 3 of the JAZF1 gene on chromosome 7. Rs4907792 is within a critical residue of a strong consensus androgen response element that is interrupted in the protective allele, resulting in a 56% decrease in its androgen sensitivity, whereas rs10486567 affects both NKX3-1 and FOXA-AR motifs where the risk allele results in a 39% increase in basal activity and a 28% fold-increase in androgen stimulated enhancer activity. Identification of such enhancer variants and their potential target genes represents a preliminary step in connecting risk to disease process.
DNA sequence and units of transcription of the conjugative transfer gene complex (trs) of Staphylococcus aureus plasmid pGO1

The conjugative transfer genes of 52-kb staphylococcal R plasmid pGO1 were localized to a single BglII restriction fragment and cloned in Escherichia coli. Sequence analysis of the 13,612-base transfer region, designated trs, identified 14 intact open reading frames (ORFs), 13 of which were transcribed in the same direction. Each ORF identified was preceded by a typical staphylococcal ribosomal binding sequence, and 10 of the 14 proteins predicted to be encoded by these ORFs were seen when an E. coli in vitro transcription-translation system was used. Functional transcription units were identified in a Staphylococcus aureus host by complementation of Tn917 inserts that abolished transfer and by Northern (RNA) blot analysis of pGO1 mRNA transcripts. These studies identified three complementation groups (trsA through trsC, trsD through trsK, and trsL-trsM) and four mRNA transcripts (trsA through trsC [1.8 kb], trsA-trsB [1.3 kb], trsL-trsM [1.5 kb], and trsN [400 bases]). No definite mRNA transcript was seen for the largest complementation group, trsD through trsK (10 kb). Comparison of predicted trs-encoded amino acid sequences to those in the data base showed 20% identity of trsK to three related genes necessary for conjugative transfer of plasmids in gram-negative species and 32% identity of trsC to a gene required for conjugative mobilization of plasmid pC221 from staphylococci.
A new regulatory function of the region proximal to the RGG box in the Fragile X mental retardation protein

Fragile X mental retardation protein (FMRP) is required for normal cognition. FMRP has two autosomal paralogs, which although similar to FMRP, cannot compensate for the loss of FMRP expression in brain. The arginine- and glycine-rich region of FMRP (the RGG box) is unique; it is the high-affinity RNA-binding motif in FMRP and is encoded by exon 15. Alternative splicing occurs in the 5′ end of exon 15, which is predicted to affect the structure of the distally encoded RGG box. Here, we provide evidence that isoform 3, which removes 25 amino acids from the 5′ end of exon 15, has an altered conformation that reduces binding of a specific antibody and renders the RGG box unable to efficiently associate with polyribosomes. Isoform 3 is also compromised in its ability to form granules and to associate with a key messenger ribonucleoprotein Yb1 (also known as p50, NSEP1 and YBX1). Significantly, these functions are similarly compromised when the RGG box is absent from FMRP, suggesting an important regulatory role of the N-terminal region encoded by exon 15.
Effect of Exercise Intensity on Isoform-Specific Expressions of NT-PGC-1 α mRNA in Mouse Skeletal Muscle

PGC-1α is an inducible transcriptional coactivator that regulates mitochondrial biogenesis and cellular energy metabolism in skeletal muscle. Recent studies have identified two additional PGC-1α transcripts that are derived from an alternative exon 1 (exon 1b) and induced by exercise. Given that the PGC-1α gene also produces NT-PGC-1α transcript by alternative 3′ splicing between exon 6 and exon 7, we have investigated isoform-specific expression of NT-PGC-1α mRNA in mouse skeletal muscle during physical exercise with different intensities. We report here that NT-PGC-1α-a mRNA expression derived from a canonical exon 1 (exon 1a) is increased by high-intensity exercise and AMPK activator AICAR in mouse skeletal muscle but not altered by low- and medium-intensity exercise and β 2-adrenergic receptor agonist clenbuterol. In contrast, the alternative exon 1b-driven NT-PGC-1α-b (PGC-1α4) and NT-PGC-1α-c are highly induced by low-, medium-, and high-intensity exercise, AICAR, and clenbuterol. Ectopic expression of NT-PGC-1α-a in C2C12 myotube cells upregulates myosin heavy chain (MHC I, MHC II a) and Glut4, which represent oxidative fibers, and promotes the expression of mitochondrial genes (Cyc1, COX5B, and ATP5B). In line with gene expression data, citrate synthase activity was significantly increased by NT-PGC-1α-a in C2C12 myotube cells. Our results indicate the regulatory role for NT-PGC-1α-a in mitochondrial biogenesis and adaptation of skeletal muscle to endurance exercise.
Transcriptional upregulation of nitric oxide synthase II by nuclear factor‐κB promotes apoptotic neuronal cell death in the hippocampus following experimental status epilepticus

Whereas status epilepticus, or the condition of continuous epileptic seizures, produces a characteristic pattern of preferential neuronal cell loss in the hippocampus, the underlying mechanism is still unsettled. Based on an experimental model of temporal lobe status epilepticus, we demonstrated previously that prolonged seizures prompted an overproduction of nitric oxide (NO) by upregulation of NO synthase II (NOS II) in the hippocampal CA3 subfield, followed by the activation of mitochondrial apoptotic signaling cascade. Using the same animal model, the present study evaluated the hypothesis that transcriptional upregulation of NOS II gene by nuclear factor‐κB (NF‐κB) promotes apoptotic neuronal cell death in the hippocampus following status epilepticus. In Sprague‐Dawley rats, significantly augmented nucleus‐bound translocation of NF‐κB p50 and p65 subunits and DNA binding activity of NF‐κB were observed in hippocampal CA3 neurons as early as 30 min after elicitation of sustained seizure activity by microinjection of kainic acid into the CA3 subfield, followed by a progressive elevation that peaked at 90 min. In addition, application bilaterally into the hippocampal CA3 subfield of a selective NF‐κB inhibitor, pyrrolidine dithiocarbamate or double‐stranded κB decoy DNA significantly antagonized the activated NOS II‐peroxynitrite signaling cascade (3 hr) and the associated manifestations of apoptotic cell death (7 days) in the hippocampus. We conclude that activation of NF‐κB in hippocampal CA3 neurons upregulates NOS II gene expression following experimental temporal lobe status epilepticus, leading to apoptotic neuronal cell death in the hippocampus. © 2010 Wiley‐Liss, Inc.
Exploring Wavelets Subband Decomposition Toward a Computer Aided Detection of Microcalcification in Breast Cancer

2-D wavelet transform decomposition is widely used in computer aided detection of microcalcifications in mammograms. The aim of this work is to investigate the better type of wavelet and its optimal potential level of decomposition that gives us better detection. Our algorithm consists of four steps: First, dimension reduction is performed on the mammography images to delimitate the ROI (region of interest). Second, microcalcification profiles are extracted from digital mammograms. Next, a 1-D WT with different families of wavelet is applied on the signal up to the sixth level. Finally, comparison between details coefficients of each level is done to carry out the optimal level. To validate our result, 2-D wavelet transform decomposition and reconstruction with the better wavelet and up to its optimal level is applied on digital mammograms from the DDSM (digital database for screening mammography) to carry out microcalcifications
Effect of Hyperglycemia on Human Monocyte Activation

Our recent study defined the chemokine-induced human monocyte signaling under normoglycemic condition. To explore the hyperglycemia-induced monocyte signaling, we performed adhesion, migration, and transmigration assays on human monocytes obtained from THP-1 cell line in the presence of normal (5 mM) and high (10 and 20 mM) glucose concentrations without chemokines. We observed augmented (P < 0.01) monocyte adhesion to human umbilical vein endothelial cell monolayer at 10 than 5 mM glucose with no further increase at 20-mM glucose concentration (P < 0.07 vs 10 mM; P < 0.01 vs 5 mM). But incremental increases in monocyte migration (P < 0.01), transmigration (P < 0.01), and stress fiber response (P < 0.01) were observed at 10- and 20-mM glucose concentrations in comparison to 5-mM glucose concentrations. We found gradational increase (P < 0.01) in phosphorylation of Akt S473 and glycogen synthase kinase (GSK3βS9) in hyperglycemia (10 and 20 mM) when compared with 5 mM glucose. Furthermore, hyperglycemia (both 10 and 20 mM)-treated monocyte showed up-regulated phosphorylation of p101 and p110γ subunits of PI-3 kinase in comparison to 5 mM glucose. Hyperglycemia-induced monocyte migration was restored to basal levels in the presence of PI-3 kinase inhibitor, LY. These observations imply that modest hyperglycemia per se, as is commonly observed in diabetic individuals, is a potent stimulator of monocyte activity even without chemokines.
Security in an insecure world: An examination of individualism‐collectivism and psychological sense of community at work

Purpose – An exploratory empirical examination was conducted to determine if collectivists experienced a higher psychological sense of community at work than individualists.Design/methodology/approach – Survey data were obtained from 264 non‐supervisory respondents. Correlation and regression analyses were performed to examine the relationship among individualism‐collectivism and psychological sense of community at work, while controlling for age, gender, marital status, education, and position.Findings – Results showed that while controlling for demographic and job related variables, collectivists experience higher levels of psychological sense of community at work than individualists.Research limitations/implications – Because this investigation was a cross‐sectional research design, causality cannot be determined although reverse causality is unlikely due to individualism‐collectivism being a relatively stable individual difference variable.Practical implications – In the uncertainty of our current eco.