Miracle-dz/UniFAR-FTUs huggingface dataset:
Orderly Replication and Segregation of the Four Replicons of Burkholderia cenocepacia J2315

Bacterial genomes typically consist of a single chromosome and, optionally, one or more plasmids. But whole-genome sequencing reveals about ten per-cent of them to be multipartite, with additional replicons which by size and indispensability are considered secondary chromosomes. This raises the questions of how their replication and partition is managed without compromising genome stability and of how such genomes arose. Vibrio cholerae, with a 1 Mb replicon in addition to its 3 Mb chromosome, is the only species for which maintenance of a multipartite genome has been investigated. In this study we have explored the more complex genome of Burkholderia cenocepacia (strain J2315). It comprises an extra replicon (c2) of 3.21 Mb, comparable in size to the3.87Mb main chromosome (c1), another extra replicon(c3) of 0.87 Mb and a plasmid of 0.09 Mb. The replication origin of c1 is typically chromosomal and those of c2 and c3 are plasmid-like; all are replicated bidirectionally. Fluorescence microscopy of tagged origins indicates that all initiate replication at mid-cell and segregate towards the cell quarter positions sequentially, c1-c2-p1/c3. c2 segregation is as well-phased with the cell cycle as c1, implying that this plasmid-like origin has become subject to regulation not typical of plasmids; in contrast, c3 segregates more randomly through the cycle. Disruption of individual Par systems by deletion of parAB or by addition of parS sites showed each Par system to govern the positioning of its own replicon only. Inactivation of c1, c2 and c3 Par systems not only reduced growth rate, generated anucleate cells and compromised viability but influenced processes beyond replicon partition, notably regulation of replication, chromosome condensation and cell size determination. In particular, the absence of the c1 ParA protein altered replication of all three chromosomes, suggesting that the partition system of the main chromosome is a major participant in the choreography of the cell cycle.
Combined radiofrequency and alcohol injection for percutaneous hepatic tumor ablation.

OBJECTIVE We sought to determine if alcohol potentiates radiofrequency energy by obtaining larger ablative volumes in 30 liver tumors in human patients. SUBJECTS AND METHODS We compared two groups of patients: one group treated with radiofrequency ablation alone (radiofrequency-alone group), and a second group treated with radiofrequency ablation and immediate prior injection of alcohol (combined group). The radiofrequency-alone group comprised 20 ablations (mean diameter, 8.4 cm; colorectal cancer metastases [n = 15]; other metastases [n = 5]). The combined group consisted of 30 radiofrequency ablations (mean diameter, 8.8 cm; metastatic colorectal cancer [n = 17]; other metastases [n = 8]; and hepatocellular carcinoma [n = 5]) treated with alcohol injection immediately before radiofrequency ablation. The amount of alcohol injected was determined by the size and location of tumors. Preprocedural laboratory tests (complete blood cell count with differential, liver function tests, and coagulation parameters) were performed in all patients, along with pre- and postprocedural CT, MRI, and PET. Measurements of tissue necrosis were obtained on the postprocedural CT scans and MR images. Volumes of necrosis calculated in each group were corrected for the number of radiofrequency applications and were statistically compared using the Student's t test. In addition, tissue impedances obtained during the radiofrequency ablation procedure were compared between the two groups. RESULTS The mean ablation volumes for the radiofrequency-alone group were 32.3 cm(2) (median, 28.6 cm(2); range, 14.4-61.8 cm(2)) and for the combined group, 84.6 cm(2) (median, 78.3 cm(2); range, 34.6-149 cm(2)). The difference in the necrosis volumes was significantly larger (p < 0.0001) in the combined group. Overall, the combined treatment group underwent fewer radiofrequency applications per session. Tissue impedance during radiofrequency ablation was higher in the combined group (mean, 62.7 vs 57.3 Omega in the radiofrequency alone group; p = 0.0005) at comparable times during the ablations. No major complications were seen in either group. CONCLUSION Percutaneous radiofrequency ablation appears to be potentiated by immediate prior alcohol injection into the tumor. Consistently larger lesions are obtainable in fewer sessions, without any increase of complications, using the combined method.
Determination of Residues Responsible for Substrate and Product Specificity of Solanum habrochaites Short-Chain cis-Prenyltransferases1[W][OPEN]

The relative positions of aromatic amino acids and adjacent residues within domain II of short-chain cis-prenyltransferases contributes to the evolution of volatile terpene biosynthesis in Solanum species trichomes. Isoprenoids are diverse compounds that have their biosynthetic origin in the initial condensation of isopentenyl diphosphate and dimethylallyl diphosphate to form C10 prenyl diphosphates that can be elongated by the addition of subsequent isopentenyl diphosphate units. These reactions are catalyzed by either cis-prenyltransferases (CPTs) or trans-prenyltransferases. The synthesis of volatile terpenes in plants typically proceeds through either geranyl diphosphate (C10) or trans-farnesyl diphosphate (C15), to yield monoterpenes and sesquiterpenes, respectively. However, terpene biosynthesis in glandular trichomes of tomato (Solanum lycopersicum) and related wild relatives also occurs via the cis-substrates neryl diphosphate (NPP) and 2Z,6Z-farnesyl diphosphate (Z,Z-FPP). NPP and Z,Z-FPP are synthesized by neryl diphosphate synthase1 (NDPS1) and Z,Z-farnesyl diphosphate synthase (zFPS), which are encoded by the orthologous CPT1 locus in tomato and Solanum habrochaites, respectively. In this study, comparative sequence analysis of NDPS1 and zFPS enzymes from S. habrochaites accessions that synthesize either monoterpenes or sesquiterpenes was performed to identify amino acid residues that correlate with the ability to synthesize NPP or Z,Z-FPP. Subsequent structural modeling, coupled with site-directed mutagenesis, highlighted the importance of four amino acids located within conserved domain II of CPT enzymes that form part of the second α-helix, for determining substrate and product specificity of these enzymes. In particular, the relative positioning of aromatic amino acid residues at positions 100 and 107 determines the ability of these enzymes to synthesize NPP or Z,Z-FPP. This study provides insight into the biochemical evolution of terpene biosynthesis in the glandular trichomes of Solanum species.
Computed Tomography Workup of Patients Suspected of Acute Ischemic Stroke: Perfusion Computed Tomography Adds Value Compared With Clinical Evaluation, Noncontrast Computed Tomography, and Computed Tomography Angiogram in Terms of Predicting Outcome

Background and Purpose— To determine whether perfusion computed tomography (PCT) adds value to noncontrast head CT (NCT), CT angiogram (CTA), and clinical assessment in patients suspected of acute ischemic stroke. Methods— We retrospectively reviewed 165 patients with acute ischemic stroke. PCT was used to calculate the volumes of infarct core and ischemic penumbra on admission. Other imaging data included Alberta Score Program Early CT Score, site of occlusion, and collateral flow. Clinical data included age, time, National Institutes of Health Stroke Scale at baseline, treatment type, and modified Rankin score (mRS) at 90 days. Recanalization status was assessed on follow-up imaging. In a first multivariate regression analysis, we assessed whether volumes of PCT penumbra and infarct core could be predicted from clinical variables, NCT, or CTA, or whether they represented independent information. In a second multivariate regression analysis, we used mRS at 90 days as outcome and determined which variables predicted it best. Results— Of 165 patients identified, 76 had a mRS score of 0 to 2 at 90 days, 89 had a mRS score >2. PCT infarct could be predicted by clinical data, NCT, CTA, and combinations of this data (P<0.05). PCT penumbra could not be predicted by clinical data, NCT, and CTA. All of the variables but NCT and CTA were significantly associated with 90-day mRS outcome. The single most important predictor was recanalization status (P<0.001). PCT penumbra volume (P=0.001) was also a predictor of clinical outcome, especially when considered in conjunction with recanalization through an interaction term (P<0.001). Conclusions— PCT penumbra represents independent information, which cannot be predicted by clinical, NCT, and CTA data. PCT penumbra is an important determinant of clinical outcome and adds relevant clinical information compared with a stroke CT workup, including NCT and CTA.
Epidemiology of atrial fibrillation: European perspective

In the last 20 years, atrial fibrillation (AF) has become one of the most important public health problems and a significant cause of increasing health care costs in western countries. The prevalence of AF is increasing due to our greater ability to treat chronic cardiac and noncardiac diseases, and the improved ability to suspect and diagnose AF. At the present time, the prevalence of AF (2%) is double that reported in the last decade. The prevalence of AF varies with age and sex. AF is present in 0.12%–0.16% of those younger than 49 years, in 3.7%–4.2% of those aged 60–70 years, and in 10%–17% of those aged 80 years or older. In addition, it occurs more frequently in males, with a male to female ratio of 1.2:1. The incidence of AF ranges between 0.21 and 0.41 per 1,000 person/years. Permanent AF occurs in approximately 50% of patients, and paroxysmal and persistent AF in 25% each. AF is frequently associated with cardiac disease and comorbidities. The most common concomitant diseases are coronary artery disease, valvular heart disease, and cardiomyopathy. The most common comorbidities are hypertension, diabetes, heart failure, chronic obstructive pulmonary disease, renal failure, stroke, and cognitive disturbance. Paroxysmal AF occurs in younger patients and with a reduced burden of both cardiac disease and comorbidities. Generally, the history of AF is long, burdened by frequent recurrences, and associated with symptoms (in two thirds of patients). Patients with AF have a five-fold and two-fold higher risk of stroke and death, respectively. We estimate that the number of patients with AF in 2030 in Europe will be 14–17 million and the number of new cases of AF per year at 120,000–215,000. Given that AF is associated with significant morbidity and mortality, this increasing number of individuals with AF will have major public health implications.
Lime Stabilization of Black Cotton Soil Using Bagasse Ash as Admixture

Laboratory studies to investigate the effect of Bagasse Ash (BA) admixture on the engineering properties of lime treated black cotton soil was carried out. Black cotton soil is classified as A-7-6 or CH respectively. Bagasse ash is obtained from burning the fibrous residue from the extraction of sugar juice from sugarcane. The results obtained show that the moisture density relationship follows a trend of increasing optimum moisture content (OMC)/decreasing maximum dry density (MDD) at the Standard Proctor compaction energy. California bearing ratio (CBR) values obtained are lower than the 80% CBR criterion for untreated base course materials. The peak CBR value obtained was 31% at 8 %lime/ 4%BA. This value meets the recommended criteria for subgrade materials. The Unconfined compressive strength (UCS) at 7 days is lower than the 1034.25kN/m2 evaluation criterion for adequate lime stabilization. On the basis of the soaked CBR and durability values, it is recommended that black cotton soil can be stabilized for road construction using a 8 % lime/ 4 % BA blend of admixture at standard proctor compaction. However, due to the relative high cost of lime and large quantity that shall be required to achieve stabilization, further study and consideration should therefore be given to the use another additive such as cement to augment and lower the percentage of lime and thus the cost of stabilization.
Representation of Haptic Objects during Mental Rotation in Congenital Blindness

The representation of haptic objects by three groups of participants (sighted, blindfolded, and congenitally blind) was studied in a mental-rotation task. Three models were tested. The participants explored a standard object continuously with the left hand and tried to find the mirror object among two alternatives explored sequentially with the right hand. Sighted participants were tested in the visual version of the task. The accuracy of judgments was very high (>95%) for all groups, and the blind group had the highest identification times. Correlation analyses were performed between (both single-trial and average) identification times and angular differences. The identification times of the sighted and blindfolded groups increased as linear functions of the angular difference between the mirror and the standard stimuli, supporting the classical model. The identification times of the blind group changed non-monotonically and were consistent with an antiparallel image (180° rotation superimposed) in the mental representation. The dual code model did not fit the data well for any participant group. The performance differences between the blindfolded and blind groups may be attributed to a modified mapping function from the object-properties-processing sub-system to the visual buffer, which was conjectured to be available also to the blind group while processing haptic objects.
A comparison of 1850 (50 mCi) and 3700 MBq (100 mCi) 131-iodine administered doses for recombinant thyrotropin-stimulated postoperative thyroid remnant ablation in differentiated thyroid cancer.

OBJECTIVE Recently, a multicenter study in differentiated thyroid cancer (DTC) patients showed that 3700 MBq 131-iodine ((131)I) after recombinant human TSH (rhTSH) had a successful thyroid ablation rate similar to that obtained after thyroid hormone withdrawal. We investigated whether 1850 MBq (131)I had a similar successful rate to 3700 MBq in patients prepared with rhTSH. DESIGN A total of 72 patients with DTC were randomly assigned to receive 1850 (group A, n = 36) or 3700 MBq (group B, n = 36) (131)I after rhTSH. One injection of 0.9 mg rhTSH was administered for 2 consecutive days; (131)I therapy was delivered 24 h after the last injection, followed by a posttherapy whole-body scan. Successful ablation was assessed 6-8 months later. RESULTS Successful ablation (no visible uptake in the diagnostic whole-body scan after rhTSH stimulation) was achieved in 88.9% of group A and B patients. Basal and rhTSH-stimulated serum thyroglobulin was undetectable (<1 ng/ml) in 78.9% of group A and 66.6% of group B patients (P = 0.46). Similar rates of ablation were obtained in both groups also in patients with node metastases. CONCLUSION Therapeutic (131)I activities of 1850 MBq are equally effective as 3700 MBq for thyroid ablation in DTC patients prepared with rhTSH, even in the presence of node metastases.
Inhibition of Nox2 Oxidase Activity Ameliorates Influenza A Virus-Induced Lung Inflammation

Influenza A virus pandemics and emerging anti-viral resistance highlight the urgent need for novel generic pharmacological strategies that reduce both viral replication and lung inflammation. We investigated whether the primary enzymatic source of inflammatory cell ROS (reactive oxygen species), Nox2-containing NADPH oxidase, is a novel pharmacological target against the lung inflammation caused by influenza A viruses. Male WT (C57BL/6) and Nox2−/y mice were infected intranasally with low pathogenicity (X-31, H3N2) or higher pathogenicity (PR8, H1N1) influenza A virus. Viral titer, airways inflammation, superoxide and peroxynitrite production, lung histopathology, pro-inflammatory (MCP-1) and antiviral (IL-1β) cytokines/chemokines, CD8+ T cell effector function and alveolar epithelial cell apoptosis were assessed. Infection of Nox2−/y mice with X-31 virus resulted in a significant reduction in viral titers, BALF macrophages, peri-bronchial inflammation, BALF inflammatory cell superoxide and lung tissue peroxynitrite production, MCP-1 levels and alveolar epithelial cell apoptosis when compared to WT control mice. Lung levels of IL-1β were ∼3-fold higher in Nox2−/y mice. The numbers of influenza-specific CD8+DbNP366+ and DbPA224+ T cells in the BALF and spleen were comparable in WT and Nox2−/y mice. In vivo administration of the Nox2 inhibitor apocynin significantly suppressed viral titer, airways inflammation and inflammatory cell superoxide production following infection with X-31 or PR8. In conclusion, these findings indicate that Nox2 inhibitors have therapeutic potential for control of lung inflammation and damage in an influenza strain-independent manner.
OSTIA : An operational, high resolution, real time, global sea surface temperature analysis system

A new global, operational, high-resolution, combined sea surface temperature (SST) and sea ice analysis system (OSTIA) has been developed at the Met Office. The output is a daily, global coverage 1/20deg (~6 km) combined SST and sea ice concentration product, which is generated in near-real time. The analysis has been designed to meet the needs of applications requiring high-resolution space-time scales including global numerical weather prediction (NWP) and operational ocean models and to prepare for future high-resolution global and regional forecast systems.
Immobilizing the Moving Parts of Voltage-Gated Ion Channels

Voltage-gated ion channels have at least two classes of moving parts, voltage sensors that respond to changes in the transmembrane potential and gates that create or deny permeant ions access to the conduction pathway. To explore the coupling between voltage sensors and gates, we have systematically immobilized each using a bifunctional photoactivatable cross-linker, benzophenone-4-carboxamidocysteine methanethiosulfonate, that can be tethered to cysteines introduced into the channel protein by mutagenesis. To validate the method, we first tested it on the inactivation gate of the sodium channel. The benzophenone-labeled inactivation gate of the sodium channel can be trapped selectively either in an open or closed state by ultraviolet irradiation at either a hyperpolarized or depolarized voltage, respectively. To verify that ultraviolet light can immobilize S4 segments, we examined its relative effects on ionic and gating currents in Shaker potassium channels, labeled at residue 359 at the extracellular end of the S4 segment. As predicted by the tetrameric stoichiometry of these potassium channels, ultraviolet irradiation reduces ionic current by approximately the fourth power of the gating current reduction, suggesting little cooperativity between the movements of individual S4 segments. Photocross-linking occurs preferably at hyperpolarized voltages after labeling residue 359, suggesting that depolarization moves the benzophenone adduct out of a restricted environment. Immobilization of the S4 segment of the second domain of sodium channels prevents channels from opening. By contrast, photocross-linking the S4 segment of the fourth domain of the sodium channel has effects on both activation and inactivation. Our results indicate that specific voltage sensors of the sodium channel play unique roles in gating, and suggest that movement of one voltage sensor, the S4 segment of domain 4, is at least a two-step process, each step coupled to a different gate.
Invitation Cards during Pregnancy Enhance Male Partner Involvement in Prevention of Mother to Child Transmission (PMTCT) of Human Immunodeficiency Virus (HIV) in Blantyre, Malawi: A Randomized Controlled Open Label Trial

Introduction Male involvement (MI) is vital for the uptake of Prevention of Mother to Child Transmission (PMTCT) of Human Immunodeficiency Virus (HIV) interventions. Partner notification (PN) is among the strategies identified for MI in PMTCT services. The purpose of this randomized controlled trial was to evaluate the efficacy of an invitation card to the male partners as a strategy for MI in PMTCT services by comparing the proportion of pregnant women that were accompanied by their partners between the intervention and the non-intervention study groups. Methods Pregnant women attending antenatal care without a male partner at South Lunzu and Mpemba health centres in Blantyre, Malawi, were enrolled in the study from June to December 2013. In an intention-to-treat analysis, we compared all participants that were randomized in the invitation card group with the standard of care (SoC) group. Risk ratios (RR) with 95% confidence intervals (CI) were computed to assess the efficacy of the invitation card. Results Of the 462 randomized women, 65/230 (28.26%) of the women in the invitation card group reported to the antenatal care clinic with their partners compared to 44/232 (18.97%) women in the SoC group. In an unadjusted intention-to-treat analysis women in the invitation card group were 50% more likely to be accompanied by their male partners than those in the SoC group RR: 1.49 (95% CI: 1.06-2.09); p = 0.02. Our random effects analysis showed that there was no clustering by site of recruitment with an inter cluster correlation coefficient (ICC) of 1.98x 10-3, (95% CI: 1.78 x10-7 - 0.96 x 10-1); p =0.403. Conclusion An invitation card significantly increased the proportion of women who were accompanied by their male partners for the PMTCT services. An invitation card is a feasible strategy for MI in PMTCT.
Learning Language-Visual Embedding for Movie Understanding with Natural-Language

Learning a joint language-visual embedding has a number of very appealing properties and can result in variety of practical application, including natural language image/video annotation and search. In this work, we study three different joint language-visual neural network model architectures. We evaluate our models on large scale LSMDC16 movie dataset for two tasks: 1) Standard Ranking for video annotation and retrieval 2) Our proposed movie multiple-choice test. This test facilitate automatic evaluation of visual-language models for natural language video annotation based on human activities. In addition to original Audio Description (AD) captions, provided as part of LSMDC16, we collected and will make available a) manually generated re-phrasings of those captions obtained using Amazon MTurk b) automatically generated human activity elements in "Predicate + Object" (PO) phrases based on "Knowlywood", an activity knowledge mining model. Our best model archives Recall@10 of 19.2% on annotation and 18.9% on video retrieval tasks for subset of 1000 samples. For multiple-choice test, our best model achieve accuracy 58.11% over whole LSMDC16 public test-set.
CAMA: a multi-valued satisfiability solver

This paper presents the multi-valued SAT solver CAMA. CAMA generalizes the recently developed speed-up techniques used in state-of-the-art binary SAT solvers, such as the two-literal-watching scheme for Boolean constraint propagation (BCP), conflict-based learning with identifying the first unique implication point (UIP), and non-chronological back-tracking. In addition, a novel minimum value set (MVS) technique is introduced for improving the efficiency of conflict-based learning. By analyzing the conflict clauses, MVS can potentially prune conflicting space that has not been searched before. Two different decision heuristics are discussed and evaluated. Finally the performance of CAMA is compared with Chaff using on a one-hot-encoding scheme. The experimental results show that, for MV-SAT problems with large variable domains, CAMA outperforms Chaff.