Miracle-dz/UniFAR-FTUs huggingface dataset:
Transcriptional regulation of delta-aminolevulinic acid dehydratase synthesis by oxygen in Bradyrhizobium japonicum and evidence for developmental control of the hemB gene

An increased demand for cytochromes is associated with symbiotic development and microaerobic metabolism in the bacterium Bradyrhizobium japonicum, and evidence suggests that hemB, rather than hemA, is the first essential bacterial heme synthesis gene in symbiosis with soybean. Steady-state levels of mRNA and protein encoded by hemB were strongly and rapidly induced by O2 deprivation as determined by RNase protection and immunoblot analyses, but hemH message was not induced. Oxygen limitation resulted in a greater-than-10-fold increase in the rate of hemB mRNA synthesis as determined by transcriptional runoff experiments, whereas hemH transcription was unaffected by the O2 status. Thus, hemB is a regulated gene in B. japonicum and is transcriptionally controlled by O2. Unlike the expression in parent strain I110, hemB expression was not affected by O2 in the fixJ strain 7360, and O2-limited cultures of the mutant contained quantities of hemB mRNA and protein that were comparable to uninduced levels found in aerobic cells. In addition, spectroscopic analysis of cell extracts showed that increases in b- and c-type cytochromes and the disappearance of cytochrome aa3 in response to microaerobic growth in wild-type cells were not observed in the fixJ mutant. FixJ is a key transcriptional regulator that mediates O2-dependent differentiation in rhizobia, and therefore hemB expression is under developmental control. Furthermore, the data suggest a global control of cytochrome expression and heme biosynthesis in response to the cellular O2 status.
Replication Publication

I n December 2003, PLoS Biology published a research article reporting evidence of an association between a gene called GAD2 and susceptibility to obesity (DOI: 10.1371/ journal.pbio.0000068). Although the genetic data were suggestive rather than conclusive, the editors and reviewers supported publication because unambiguous evidence in association studies is notoriously diffi cult to obtain and obesity is such a major burden on public health. Enthusiasm was heightened because GAD2 lies in a region of human Chromosome 10 that is thought to contain a gene infl uencing obesity, and GAD2 itself is involved in the synthesis of a neurotransmitter implicated in the regulation of food intake. Publication would allow others to test just how important the connection between GAD2 and obesity might be—and the enticing prospect was that insight into the role of GAD2 in this disease might lead ultimately to new therapeutic approaches. In this issue of PLoS Biology, we publish a follow-up to the original study, from a separate team of researchers based at the University of California at San Francisco (DOI: 10.1371/journal. pbio.0030315). Swarbrick et al. looked at different and much larger patient populations and analyzed variation within GAD2 more comprehensively, but disappointingly, the new study was not able to replicate the initial fi nding. Despite the negative conclusions, however, the reviewers were no less enthusiastic about the publication of this paper than the fi rst. One of the reasons for this is related to a problem that has beset the fi eld of complex disease genetics for several years—a tendency towards the publication of studies that show an association. Diseases are termed complex when their etiology is infl uenced by many factors, both genetic and environmental. These diseases include obesity, diabetes, mental illness, and many more common ailments. But fi nding the genes that are involved with these diseases is an extremely diffi cult problem: individual genes have only a limited effect, which means that large patient populations need to be studied; specifi c genes might have effects only in certain ethnic groups; and statistical artifacts can be hard to eliminate. These and other problems mean that success stories are few and far between, whereas false leads have been plentiful. High-profi le journals, in particular, have therefore tended to publish the positive results, whereas negative data often end up in specialist literature or, much worse, don't get published at all. Because the identifi cation of a complex …
Fluid dynamics of syringe-based irrigation to optimise anti-biofilm efficacy in root-canal disinfection

A mature bacterial biofilm is composed of multiple layers of bacteria embedded in a self-made matrix formed of extracellular polymeric substance. This substance has the potential to modify the response of the resident bacteria to antimicrobials by acting as a shield against the chemical effects of antimicrobials. There is also a localised high density of bacterial cells in a biofilm structure. This spatial arrangement will expose the cells in the deeper layers of the biofilm to less nutrients and redox potential than the cells on the biofilm surface. Since the degree of nutrient and gas gradients increases with the thickness and maturity of a biofilm, the influence of growth rate and oxygen on the antimicrobial resistance is particularly marked in aged biofilm. The resistance associated with biofilm bacteria is further associated with the slow growth rate (starvation) and/or due to the adoption of resistant phenotypes in bacteria residing in a biofilm. It is recognised that no single mechanism may account for the general resistance to antimicrobials in a biofilm. It is apparent that different mechanisms may act in concert within the biofilm, and amplify the effect of small variations in the susceptible phenotypes (Dunne et al. 1993; Costerton et al. 1994). Thus from a clinical perspective, bacteria are observed to demonstrate considerably high resistance to antimicrobials when they are in a biofilm (Kishen 2012).
Conducted EMI from motor drive system of electric vehicle under load operation

A complete test for conducted EMI from the direct current fed (DC-fed) alternating current (AC) motor drive system in an electric vehicle (EV) under load conditions is set up to analyze the conducted voltage and current of high voltage DC cables in a frequency range of 150 kHz–108 MHz at 500rpm and 2500rpm with 50Nm load torque of the EV motor with space vector pulse width-modulation (SVPWM) control. The effect of the motor speed increased form 500rpm to 2500rpm on conducted EMI are presented and verified by simulation and experiment. The comparison between the conducted EMI from three bridge legs and that of one bridge leg in the power inverter is presented.
Selective cyclooxygenase-2 inhibitor ameliorates cholecystokinin-octapeptide-induced acute pancreatitis in rats.

AIM To investigate the effect of selective Cycloo-xygenase-2 (COX-2) inhibitor 4-[5-(4-Chloro-phenyl)-3-(trifluoromethyl)-1H-pyrazol-1-yl] benzenesulfonamide (SC-236), on the cholecystokinin (CCK)-octapeptide-induced acute pancreatitis (AP) in rats. METHODS Wistar rat weighing 240 g to 260 g were divided into three groups. (1) Normal DMSO treated group, (2) SC-236 at 4 mg/kg treated group; SC-236 systemically administered via the intravenous (i.v.) catheter, followed by 75 microg/kg CCK octapeptide subcutaneously three times, after 1, 3 and 5 h. This whole procedure was repeated for 5 d. (3) Dimethyl sulfoxide (DMSO) treated group: an identical protocol was used in this group as in the SC-236 cohort (see 2. above). Repeated CCK octapeptide treatment resulted in a typical experimentally induced pancreatitis in the Wistar rats. RESULTS SC-236 improved the severity of CCK-octapeptide-induced AP as measured by laboratory criteria [the pancreatic weight/body weight (p.w/b.w) ratio, the level of serum amylase and lipase]. The SC-236 treated group showed minimal histologic evidence of pancreatitis and a significant reduction in myeloperoxidase activity. SC-236 also increased heat shock protein (HSP)-60 and HSP72 compared with the DMSO-treated group in the CCK-octapeptide-induced AP and also reduced the pancreatic levels of COX-2. Furthermore, SC-236 reduced proinflammatory cytokine synthesis and inhibited NF-kappaB activation compared with the DMSO-treated group in the CCK-octapeptide-induced AP. CONCLUSION Our results suggested that COX-2 plays pivotal role in the development of AP and COX-2 inhibitors may play a beneficial role in preventing AP.
WHAAM: A mobile application for ubiquitous monitoring of ADHD behaviors

Attention Deficit Hyperactivity Disorder (ADHD) is one of the most common psychiatric conditions in childhood. Observation of the behavior of the young person plays a key role in Cognitive-Behavioural (CB) approaches to the treatment of ADHD, but traditional pen and pen-and-paper based methods have a number of disadvantages which inhibit their use in realworld situations. The WHAAM mobile application (WMA) provides teachers, parents and health experts with features to easily monitor behaviors in a Specific, Measurable, Attainable, Realistic and Timely (SMART) way.
Red cells for transfusion.

The current innovation in the preservation of red cells for transfusion is adenine. Adenine in the storage medium increases ATP content and enhances red-cell viability. A formula called citrate phosphate dextrose adenine (CPDA-1) has a bright new FDA license permitting its use for the storage of whole blood or red cells for as long as 35 days.1 During World War II, the red cells left after the plasma from citrated blood was harvested were stored in corn syrup before use. The anticoagulant was modified later to provide pure dextrose and to lower the pH, and acid citrate dextrose (ACD) solutions .
A sigma factor that modifies the circadian expression of a subset of genes in cyanobacteria.

We isolated mutants affected in the circadian expression of the psbAI gene in Synechococcus sp. strain PCC 7942 using a strategy that tags the genomic locus responsible for the mutant phenotype. The search identified one short period (22 h) mutant (M2) and two low amplitude mutants, one of which showed apparent arhythmia (M11) and one that was still clearly rhythmic (M16). We characterized the disrupted locus of the low amplitude but still rhythmic mutant (M16) as the rpoD2 gene, a member of a gene family that encodes sigma70‐like transcription factors in Synechococcus. We also inactivated rpoD2 in a number of reporter strains and showed that the circadian expression of some genes is not modified by the loss of this sigma factor. Therefore, we conclude that rpoD2 is a component of an output pathway of the biological clock that affects the circadian expression of a subset of genes in Synechococcus. This work demonstrates a direct link between a transcription factor and the manifestation of circadian gene expression.
Risk factors for treatment-related death in elderly patients with aggressive non-Hodgkin's lymphoma: results of a multivariate analysis.

PURPOSE It has been suggested that age is associated with chemotherapy-related death in patients with non-Hodgkin's lymphoma (NHL) treated with doxorubicin-containing chemotherapy. The purpose of this study was to evaluate the relative influence of increasing age and other clinical parameters on the occurrence of treatment-related death in elderly patients with intermediate- or high-grade NHL treated with cyclophosphamide, doxorubicin, vincristine, and prednisone (CHOP) chemotherapy. METHODS A retrospective study of patients 60 years of age or older with intermediate- or high-grade NHL treated with CHOP chemotherapy in a single cancer center. The following variables were recorded: age (60 to 69, 70 to 79, and 80 to 94 years), histology (Working Formulation [WF] D, E, F, G, and H), Ann Arbor stage, B symptoms, extranodal involvement, bulky disease (> 7 cm), performance status (Eastern Cooperative Oncology Group [ECOG] scale), International Prognostic Index (IPI score), serum lactate dehydrogenase (LDH) level and doxorubicin relative dose-intensity (RDI). The relationship between these features and treatment-related death was assessed in univariate and multivariate logistic regression analysis. RESULTS From 1982 to 1991, 267 consecutive patients were treated. Median age was 70 years (range, 60 to 94 years). There were 35 toxic deaths. Sixty-three percent of the deaths occurred after the first cycle. Infection accounted for 82% of the toxic deaths. In the univariate analysis, the features associated with an increased risk of toxic death were ECOG performance status 2 to 4 (relative risk [RR], 7.82), B symptoms (RR, 3.38), diffuse large-cell histology (RR, 3.06), bulky disease (RR, 2.58), serum levels of LDH (RR, 2.53), and IPI score (RR, 2.46). The age groups did not show significance. In the regression model, performance status 2 to 4 was the only independent predictor of treatment-related death (RR, 3.52; 95% confidence interval [CI], 2.98 to 4.06). CONCLUSION Our results show that in elderly patients with NHL treated with doxorubicin-based chemotherapy the risk for treatment-related death is associated with poor performance status rather than with increasing chronologic age.
Cross-Entropy and Iterative Decoding

In this correspondence, the relationship between iterative decoding and techniques for minimizing cross-entropy is explained. It is shown that minimum cross-entropy (MCE) decoding is an optimal lossless decoding algorithm but its complexity limits its practical implementation. Use of a maximum a posteriori (MAP) symbol estimation algorithm instead of the true MCE algorithm provides practical algorithms that are identical to those proposed in the literature. In particular, turbo decoding is shown to be equivalent to an optimal algorithm for iteratively minimizing cross-entropy under an implicit independence assumption.
Persistent mechanical stretch-induced calcium overload and MAPK signal activation contributed to SCF reduction in colonic smooth muscle in vivo and in vitro

Abstract Gastrointestinal (GI) distention is a common pathological characteristic in most GI motility disorders (GMDs), however, their detail mechanism remains unknown. In this study, we focused on Ca2+ overload of smooth muscle, which is an early intracellular reaction to stretch, and its downstream MAPK signaling and also reduction of SCF in vivo and in vitro. We successfully established colonic dilation mouse model by keeping incomplete colon obstruction for 8 days. The results showed that persistent colonic dilation clearly induced Ca2+ overload and activated all the three MAPK family members including JNK, ERK and p38 in smooth muscle tissues. Similar results were obtained from dilated colon of patients with Hirschsprung's disease and stretched primary mouse colonic smooth muscle cells (SMCs). Furthermore, we demonstrated that persistent stretch-induced Ca2+ overload was originated from extracellular Ca2+ influx and endoplasmic reticulum (ER) Ca2+ release identified by treating with different Ca2+ channel blockers, and was responsible for the persistent activation of MAPK signaling and SCF reduction in colonic SMCs. Our results suggested that Ca2+ overload caused by smooth muscle stretch led to persistent activation of MAPK signaling which might contribute to the decrease of SCF and development of the GMDs.
UHF Dipole-AMC Combination for RFID Applications

The design of a novel dipole-artificial magnetic conductor (AMC) combination for UHF radio frequency identification (RFID) band, showing proper performance in the proximity of metallic surfaces, surrounding a metallic can and being conformed around the human wrist is presented. The prototypes of the dipole antenna alone and dipole antenna combined with the AMC are manufactured using laser micromachining. To the authors' knowledge , this is the first letter presenting the actual functionality of antennas and AMCs at UHF RFID frequency in order to insulate the user's body from undesired exposure to electromagnetic radiation. The experimental results of the manufactured prototypes in terms of return loss and radiation pattern measurements in an anechoic chamber are shown for comparison.
Leader protein of foot-and-mouth disease virus is required for cleavage of the p220 component of the cap-binding protein complex

Suppression of host protein synthesis in cells infected by poliovirus and certain other picornaviruses involves inactivation of the cap-binding protein complex. Inactivation of this complex has been correlated with the proteolytic cleavage of p220, a component of the cap-binding protein complex. Since picornaviral RNA is not capped, it continues to be translated as the cap-binding protein complex is inactivated. The cleavage of p220 can be induced to occur in vitro, catalyzed by extracts from infected cells or by reticulocyte lysates translating viral RNA. Expression of polioviral protease 2A is sufficient to induce p220 cleavage, and the presence in 2A of an 18-amino-acid sequence representing a putative cysteine protease active site correlates with the ability of different picornaviruses to induce p220 cleavage. Foot-and-mouth disease virus (FMDV) infection induces complete cleavage of p220, yet the FMDV genome codes for a 2A protein of only 16 amino acids, which does not include the putative cysteine protease active site. Using cDNA plasmids encoding various regions of the FMDV genome, we have determined that the leader protein is required to initiate p220 cleavage. This is the first report of a function for the leader protein, other than that of autocatalytic cleavage from the FMDV polyprotein.
Individual differences in distance travelled by serial burglars

This paper uses police data on a sample of 41 serial burglars committed in the city of St John's, Canada and surrounding areas, to examine individual differences in distances travelled. In accord with findings from studies in other locations, results show that serial burglary is a localised activity. Differences between serial burglars in distances they travel are related to the burglars' age, method of transportation and value of property stolen. These results are discussed in terms of existing explanations of distances that serial burglars travel to select targets and implications for police decision-making. Copyright © 2004 John Wiley & Sons, Ltd.
Stroke rehabilitation: should physiotherapy intervention be provided at a primary health care centre or the patients’ place of domicile?

Abstract Purpose: This randomized controlled trial compared the outcomes of physiotherapy intervention on selected indices of recovery for stroke survivors treated at a primary health centre group (PHCG) with those treated in their respective places of domicile group (DG). Methods: Participants were 52 individuals comprising 24 males and 28 females who had suffered a stroke and were recently discharged from two inpatient health facilities in Ibadan, Nigeria. They were randomly assigned into either the PHCG (n = 25) or DG (n = 27) and treated twice weekly for 10 consecutive weeks using a physiotherapy intervention protocol comprising a battery of task-specific exercises. The outcomes measured were motor function, balance and handicap assessed using the modified motor assessment scale (MMAS), short-form postural assessment scale for stroke (SF-PASS) and reintegration to normal living index (RNLI), respectively, as well as walking speed which was assessed using a standard technique. Results: Between-group comparison using the General Linear Model revealed no statistically significant difference in both the pre- and post-intervention scores of the two groups on the MMAS, SF-PASS, RNLI and walking speed in both PHCG and DG (p > 0.05). However, within-group comparison yielded a statistically significant difference in each of the indices of stroke recovery measured across the 10-week period in both groups. Conclusion: Physiotherapy intervention at the primary health care centre and respective homes of stroke survivors similarly improved clinical outcomes. Treatment at any of these locations may enhance access to physiotherapy after stroke in a low-income community like Nigeria. Implications for Rehabilitation Physiotherapy protocol comprising 10-week task-specific battery of exercises produced significant improvement in walking speed, balance, motor function and community reintegration of stroke survivors. Physiotherapy post-stroke can be provided at either a primary health centre or the domicile of the individual. In a low-income country like Nigeria, this will enhance access to this important service.
A genes eye view of ontogeny: de novo assembly and profiling of the Gryllus rubens transcriptome

Crickets (Orthoptera:Gryllidae) are widely used model organisms for developmental, evolutionary, neurobiological and behavioural research. Here, we developed a de novo transcriptome from pooled RNA‐seq Illumina data spanning seven stages in the life cycle of Gryllus rubens. Approximately 705 Mbp of data was assembled and filtered to form 27 312 transcripts. We were able to annotate 52% of our transcripts using BLAST and assign at least one gene ontology term to 41%. Pooled samples from three different ontogenetic stages were used for transcriptomic profiling revealing patterns of differential gene expression that highlight processes in the different life stages. Embryonic and early instar development was enriched for ecdysteroid metabolism, cytochrome P450s and glutathione production. Late instar development was enriched for regulation of gene expression and many of the genes highly expressed during this stage were involved in conserved developmental signalling pathways suggesting that these developmental pathways are active beyond embryonic development. Adults were enriched for fat transport (mostly relating to egg production) and production of octopamine, an important neurohormone. We also identified genes involved in conserved developmental pathways (Hedgehog, Hippo, Wnt, JAK/STAT, TGF‐beta, Notch, and MEK/ERK). This is the first transcriptome spanning ontogeny in Gryllus rubens and a valuable resource for future work on development and evolution in Orthoptera.
Annexin V binds to the actin-based cytoskeleton at the plasma membrane of activated platelets.

Immunocytochemical studies demonstrate that annexin V relocates to the plasma membranes of intact stimulated blood platelets. Anti-annexin V antibodies label the cytoplasmic side of the substrate-adherent plasma membrane of mechanically unroofed, glass-activated platelets and colocalize with actin. In addition, crosslinking experiments using detergent-solubilized membranes of activated platelets have identified an 85-kDa complex containing annexin V. The 85-kDa complex is also recognized by antibodies against actin, suggesting that annexin V interacts with actin. In addition, annexin V was found to associate with filamentous actin in the presence of millimolar Ca(2+). Annexin V was also shown by immunofluorescence microscopy to be associated with platelet cytoskeletons, colocalizing with actin in the presence of micromolar Ca(2+). These findings provide the first evidence for annexin V binding to the plasma membrane and to the actin-based cytoskeleton in activated platelets and indicate that annexin V may function in both cytoskeletal and membrane domains.