Miracle-dz/UniFAR-FTUs huggingface dataset:
Quantitative Analysis of the Binding of Simian Virus 40 Large T Antigen to DNA

ABSTRACT SV40 large T antigen (T-ag) is a multifunctional protein that successively binds to 5′-GAGGC-3′ sequences in the viral origin of replication, melts the origin, unwinds DNA ahead of the replication fork, and interacts with host DNA replication factors to promote replication of the simian virus 40 genome. The transition of T-ag from a sequence-specific binding protein to a nonspecific helicase involves its assembly into a double hexamer whose formation is likely dictated by the propensity of T-ag to oligomerize and its relative affinities for the origin as well as for nonspecific double- and single-stranded DNA. In this study, we used a sensitive assay based on fluorescence anisotropy to measure the affinities of wild-type and mutant forms of the T-ag origin-binding domain (OBD), and of a larger fragment containing the N-terminal domain (N260), for different DNA substrates. We report that the N-terminal domain does not contribute to binding affinity but reduces the propensity of the OBD to self-associate. We found that the OBD binds with different affinities to its four sites in the origin and determined a consensus binding site by systematic mutagenesis of the 5′-GAGGC-3′ sequence and of the residue downstream of it, which also contributes to affinity. Interestingly, the OBD also binds to single-stranded DNA with an ∼10-fold higher affinity than to nonspecific duplex DNA and in a mutually exclusive manner. Finally, we provide evidence that the sequence specificity of full-length T-ag is lower than that of the OBD. These results provide a quantitative basis onto which to anchor our understanding of the interaction of T-ag with the origin and its assembly into a double hexamer.
Long-term results of urinary stress incontinence treated with mid-urethral tape as a standalone operation or in combination with pelvic floor reconstruction

This was a prospective observational study of 124 women who underwent tension-free vaginal tape (TVT) surgery between 1998 and 2003 at a District General Hospital. We compared the long-term outcomes of TVT as a standalone operation (Group 1) with those in TVT in combination with pelvic floor reconstruction (Group 2) during a 5-year follow-up. Subjective cure was similar at 2 years (84.8% Group 1; 78.1% Group 2) and 5 years (80.9% Group 1; 92.8% Group 2). There were no differences in objective cure in both groups at 2 years on cystometry (87.3% Group 1; 85.7% Group 2) and 5 years using a 1-hour pad test (98.3% Group 1; 93.1% Group 2). Similar results were seen for overall satisfaction at 2 years (95.4% Group 1; 84.3% Group 2) and 5 years (93.6% Group 1; 100% Group 2). QoL improvement was reported by 95.4% (Group 1) and 96.8% (Group 2) women at 2 years and by 96.8% (Group 1) and 100% (Group 2) at 5 years. Overall, there were no significant differences in long-term outcomes in both groups.
The Role of the Ankyrin-Binding Protein NrCAM in Node of Ranvier Formation

Molecular events involved in Na+ channel clustering at the node of Ranvier have been investigated during early development. NrCAM, an ankyrinG-binding protein, precedes Na+ channels at cluster sites adjacent to the tips of Schwann cell processes. Both Na+ channel and ankyrinG sequestration at developing nodes are delayed in NrCAM null mutants. The action of NrCAM is manifest locally at individual nodes, rather than affecting overall neuronal expression, and is linked to glial interactions. During remyelination, Na+ channel clusters at new nodes are initially labile, and anchoring to the cytoskeleton appears to grow progressively with time. The distance between Na+ channel clusters across remyelinating Schwann cells (nascent internodes) increases markedly from 83 to 274 μm during node formation, arguing against schemes in which the loci of nodes are fixed in advance by the axon. A hypothesis for node formation in which axonal Na+ channels move by lateral diffusion from regions of Schwann cell contact, with clustering dependent on linkage to the cytoskeleton by ankyrinG, is proposed and tested in a computational model. To match experimental measurements, this latter reaction needs fast kinetics, and the early arrival of NrCAM is postulated to contribute to this requirement.
Coordinates: Probabilistic Forecasting of Presence and Availability

We present methods employed in COORDINATE, a prototype service that supports collaboration and communication by learning predictive models that provide forecasts of users' presence and availability. We describe how data is collected about user activity and proximity from multiple devices, in addition to analysis of the content of users' calendars, the time of day, and day of week. We review applications of presence forecasting embedded in the PRIORITIES application and then present details of the COORDINATE service that was informed by the earlier efforts.
Human Neuroscience Original Research Article When Higher Activations Reflect Lower Deactivations: a Pet Study in Alzheimer's Disease during Encoding and Retrieval in Episodic Memory

The aim of the present study was to explore the cerebral substrates of episodic memory disorders in Alzheimer's disease (AD) and investigate patients' hyperactivations frequently reported in the functional imaging literature. It remains unclear whether some of these hyperactivations reflect real increased activity or deactivation disturbances in the default mode network (DMN). Using positron emission tomography (15 O-H 2 O), cerebral blood flow was measured in 11 AD patients and 12 healthy elderly controls at rest and during encoding and stem-cued recall of verbal items. Subtractions analyses between the target and control conditions were performed and compared between groups. The average signal was extracted in regions showing hyperactivation in AD patients versus controls in both contrasts. To determine whether hyperactivations occurred in regions that were activated or deactivated during the memory tasks, we compared signal intensities between the target conditions versus rest. Our results showed reduced activation in AD patients compared to controls in several core episodic memory regions, including the medial temporal structures, during both encoding and retrieval. Patients also showed hyperactivations compared to controls in a set of brain areas. Further analyses conducted on the signal extracted in these areas indicated that most of these hyperactivations actually reflected a failure of deactivation. Indeed, whereas almost all of these regions were significantly more activated at rest than during the target conditions in controls, only one region presented a similar pattern of deactivation in patients. Altogether, our findings suggest that hyperactivations in AD must be interpreted with caution and may not systematically reflect increased activity. Although there has been evidence supporting the existence of genuine compensatory mechanisms, dysfunction within the DMN may be responsible for part of the apparent hyperactivations reported in the literature on AD.
Observations of energetic ions on the nightside of Venus

Ions with energy greater than 40 eV have been measured on the nightside of Venus by the Pioneer Venus orbiter neutral mass spectrometer (ONMS). For periapsis altitudes beyond 1500 km, they are confined to solar zenith angles greater than 120 deg. The nightside energetic ion composition at 2000 km resembles the nightside thermal ion composition occurring at 1000 km with the dominant species being O(+). Postflight laboratory calibrations performed on the ONMS backup unit have been used to estimate the energetic O(+) ambient flux and density. The direction from which the energetic ions appear to be coming can be determined because the ONMS is mounted at an angle with respect to the spin axis of the spacecraft. Both tailward and antitailward components of the apparent ion flow are exhibited when projected into the ecliptic plane. The major component of the apparent ion flow is observed perpendicular to the ecliptic plane.
LFSR-Reseeding Scheme Achieving Low-Power Dissipation During Test

This paper presents a new low-power test-data-compression scheme based on linear feedback shift register (LFSR) reseeding. A drawback of compression schemes based on LFSR reseeding is that the unspecified bits are filled with random values, which results in a large number of transitions during scan-in, thereby causing high-power dissipation. A new encoding scheme that can be used in conjunction with any LFSR-reseeding scheme to significantly reduce test power and even further reduce test storage is presented. The proposed encoding scheme acts as the second stage of compression after LFSR reseeding. It accomplishes two goals. First, it reduces the number of transitions in the scan chains (by filling the unspecified bits in a different manner). Second, it reduces the number of specified bits that need to be generated via LFSR reseeding. Experimental results indicate that the proposed method significantly reduces test power and in most cases provides greater test-data compression than LFSR reseeding alone
Algorithms for data placement, reconfiguration and monitoring in storage networks

In this thesis we address three problems related to self-management of storage networks - data placement, data reconfiguration and data monitoring. Examples of such storage networks include centrally managed systems like Storage Area Networks and Network Attached Storage devices, or even highly distributed systems like a P2P network or a Sensor Network. One of the crucial functions of a storage system is that of deciding the placement of data within the system. This data placement is dependent on the demand pattern for the data and subject to constraints of the storage system. For instance, if a particular data item is very popular the storage system might want to host it on a disk with high bandwidth or make multiple copies of the item. We present new results for some of these data placement problems. As the demand pattern changes over time, the storage system will have to modify its placement accordingly. Such a modification in placement will typically involve movement of data items from one set of disks to another or changing the number of copies of a data item in the system. For such a modification to be effective, it should be computed and applied quickly since the system is running inefficiently during this reconfiguration. We propose new schemes to reconfigure the data placement to deal with changing demand. To re-compute data placement periodically and to reconfigure the data placement, we need to continuously track of the demand distribution in the storage system and also be able to answer aggregate queries about the demand distribution. The data monitoring portion of the thesis deals with such problems that arise in the context of distributed data management applications. A monitoring system for such a scenario would need to process large amounts of data from a widely distributed set of data sources. The thesis presents new schemes that improve communication-efficiency of existing methods that address these problems.
A Comparison of Measured and Wind-derived Ekman Transport at 11°N in the Atlantic Ocean

Abstract A comparison of measured and wind-derived ageostrophic transport is presented from a zonal transect spanning the Atlantic Ocean along 11°N. The transport per unit depth shows a striking surface maximum that decays to nearly zero at a depth of approximately 100 m. We identify this flow in the upper 100 m as the Ekman transport. The sustained values of wind stress and the penetration depth of the Ekman transport reported here are considerably greater than in previous observations, which were made in conditions of light winds. The transport of 12.0 ± 5.5 × 106 m3 s−1, calculated from the difference of geostrophic shear and shear measured by an acoustic Doppler current profiler, is in good agreement with that estimated from the shipboard winds, 8.8 ± 1.9 × 106 m3 s−1, and from climatology, 13.5 ± 0.3 × 106 m3 s−1. Qualitatively, the horizontal distribution of the wind-driven flow was best predicted by the shipboard winds. The cumulative transport increased linearly over the western three-fourths of t.
Structural basis of ion permeation gating in Slo2.1 K+ channels

The activation gate of ion channels controls the transmembrane flux of permeant ions. In voltage-gated K+ channels, the aperture formed by the S6 bundle crossing can widen to open or narrow to close the ion permeation pathway, whereas the selectivity filter gates ion flux in cyclic-nucleotide gated (CNG) and Slo1 channels. Here we explore the structural basis of the activation gate for Slo2.1, a weakly voltage-dependent K+ channel that is activated by intracellular Na+ and Cl−. Slo2.1 channels were heterologously expressed in Xenopus laevis oocytes and activated by elevated [NaCl]i or extracellular application of niflumic acid. In contrast to other voltage-gated channels, Slo2.1 was blocked by verapamil in an activation-independent manner, implying that the S6 bundle crossing does not gate the access of verapamil to its central cavity binding site. The structural basis of Slo2.1 activation was probed by Ala scanning mutagenesis of the S6 segment and by mutation of selected residues in the pore helix and S5 segment. Mutation to Ala of three S6 residues caused reduced trafficking of channels to the cell surface and partial (K256A, I263A, Q273A) or complete loss (E275A) of channel function. P271A Slo2.1 channels trafficked normally, but were nonfunctional. Further mutagenesis and intragenic rescue by second site mutations suggest that Pro271 and Glu275 maintain the inner pore in an open configuration by preventing formation of a tight S6 bundle crossing. Mutation of several residues in S6 and S5 predicted by homology modeling to contact residues in the pore helix induced a gain of channel function. Substitution of the pore helix residue Phe240 with polar residues induced constitutive channel activation. Together these findings suggest that (1) the selectivity filter and not the bundle crossing gates ion permeation and (2) dynamic coupling between the pore helix and the S5 and S6 segments mediates Slo2.1 channel activation.
Interleukins 6 and 15 Levels Are Higher in Subcutaneous Adipose Tissue, but Obesity Is Associated with Their Increased Content in Visceral Fat Depots

Excess adiposity is associated with chronic inflammation, which takes part in the development of obesity-related complications. The aim of this study was to establish whether subcutaneous (SAT) or visceral (VAT) adipose tissue plays a major role in synthesis of pro-inflammatory cytokines. Concentrations of interleukins (IL): 1β, 6, 8 and 15 were measured at the protein level by an ELISA-based method and on the mRNA level by real-time PCR in VAT and SAT samples obtained from 49 obese (BMI > 40 kg/m2) and 16 normal-weight (BMI 20–24.9 kg/m2) controls. IL-6 and IL-15 protein concentrations were higher in SAT than in VAT for both obese (p = 0.003 and p < 0.0001, respectively) and control individuals (p = 0.004 and p = 0.001, respectively), while for IL-1β this was observed only in obese subjects (p = 0.047). What characterized obese individuals was the higher expression of IL-6 and IL-15 at the protein level in VAT compared to normal-weight controls (p = 0.047 and p = 0.016, respectively). Additionally, obese individuals with metabolic syndrome had higher IL-1β levels in VAT than did obese individuals without this syndrome (p = 0.003). In conclusion, concentrations of some pro-inflammatory cytokines were higher in SAT than in VAT, but it was the increased pro-inflammatory activity of VAT that was associated with obesity and metabolic syndrome.
Design Parameters to Control Synthetic Gene Expression in Escherichia coli

Background Production of proteins as therapeutic agents, research reagents and molecular tools frequently depends on expression in heterologous hosts. Synthetic genes are increasingly used for protein production because sequence information is easier to obtain than the corresponding physical DNA. Protein-coding sequences are commonly re-designed to enhance expression, but there are no experimentally supported design principles. Principal Findings To identify sequence features that affect protein expression we synthesized and expressed in E. coli two sets of 40 genes encoding two commercially valuable proteins, a DNA polymerase and a single chain antibody. Genes differing only in synonymous codon usage expressed protein at levels ranging from undetectable to 30% of cellular protein. Using partial least squares regression we tested the correlation of protein production levels with parameters that have been reported to affect expression. We found that the amount of protein produced in E. coli was strongly dependent on the codons used to encode a subset of amino acids. Favorable codons were predominantly those read by tRNAs that are most highly charged during amino acid starvation, not codons that are most abundant in highly expressed E. coli proteins. Finally we confirmed the validity of our models by designing, synthesizing and testing new genes using codon biases predicted to perform well. Conclusion The systematic analysis of gene design parameters shown in this study has allowed us to identify codon usage within a gene as a critical determinant of achievable protein expression levels in E. coli. We propose a biochemical basis for this, as well as design algorithms to ensure high protein production from synthetic genes. Replication of this methodology should allow similar design algorithms to be empirically derived for any expression system.
Growth patterns and ontogenetic variation of the teeth and jaws of the Middle Jurassic sphenodontian Cynosphenodon huizachalensis (Reptilia: Rhynchocephalia)

Growth patterns in teeth and jaws of the Middle Jurassic sphenodontian Cynosphenodon huizachalensis are compared to those of the extant Sphenodon, showing extreme similarity. Both taxa share the unique presence of a hatchling tooth series divided into anterior uniform size and posterior alternating size tooth regions by the eruption of successional teeth early in life, an ever-growing second-generation successional tooth that becomes a caniniform tooth in adults, and a symphysial region that grows anteriorly but with a differential faster rate in the dorsal margin, enlarging considerably the length between the caniniform tooth and the anterior tip of the dentary, and increasing the angle of the anterior margin of the symphysis. The sister-group relationships of Sphenodon and Cynosphenodon have been supported by the simple presence of a single caniniform tooth, but this tooth is shown to be a complex structure involving several other ontogenetic related synapomorphies as follows: (i) it is a second-generat.
Acute effects of a guided relaxation routine (body scan) on tobacco withdrawal symptoms and cravings in abstinent smokers.

AIMS To examine the acute effects of a guided relaxation routine (body scan) on desire to smoke and tobacco withdrawal symptoms in overnight abstinent smokers. DESIGN Experimental. PARTICIPANTS Thirty individuals reporting to smoke 10 or more cigarettes daily for at least 3 years. INTERVENTION Participants were assigned randomly to complete a 10-minute body scan (experimental group n = 15) or listen to a natural history passage for 10 minutes (control group n = 15). MEASUREMENT Ratings of strength of desire to smoke and smoking withdrawal symptoms were assessed at baseline, immediately after the interventions, and 5, 10 and 15 minutes post-intervention. FINDINGS There was a significant group x time interaction for strength of desire to smoke. The mean desire to smoke rating was significantly lower in the body scan group relative to the control group immediately after the intervention, and 5 minutes post-intervention. The body scan group also reported lower ratings of irritability, tension and restlessness, relative to the controls. CONCLUSION A brief body scan intervention reduces strength of desire to smoke and some tobacco withdrawal symptoms in temporarily abstaining smokers. The body scan may be beneficial as a technique for managing cigarette cravings and withdrawal.
Patient views through the keyhole: new perspectives on single-incision vs. multiport laparoscopic cholecystectomy.

OBJECTIVES Single-incision laparoscopic cholecystectomy (SILC) may be associated with less pain, shorter hospital stay and better cosmetic results than multiport laparoscopic cholecystectomy (MLC). Advocates suggest that patients prefer SILC, although research directly addressing the question of patient preferences is limited. This study aimed to assess patient preferences using currently available evidence. METHODS Patients awaiting elective cholecystectomy were shown a series of postoperative images taken after SILC or MLC and asked which procedure this led them to prefer. This was repeated after patients had completed a questionnaire constructed using published objective data comparing patient-reported outcomes of SILC and MLC. RESULTS The study was completed by 113 consecutive patients. After their initial viewing of the images, 16% of subjects preferred MLC. Younger age, lower body mass index and female sex were associated with choosing SILC. After completing the questionnaire, 88% of patients preferred MLC (P < 0.001). Patients ranked the level of risk for complications and postoperative pain above cosmetic results in determining their choice of procedure. CONCLUSIONS Patients' initial preference when presented with cosmetic appearance was for SILC. When contemporary outcome data were included, the majority chose MLC. This underlines the need to fully inform patients during the consent process and indicates that patient views of SILC may differ from the views of those introducing the technology.
Facies architecture of the felsic lava‐dominated host sequence to the Thalanga massive sulfide deposit, Lower Ordovician, northern Queensland*

The Thalanga volcanic‐hosted massive sulfide deposit occurs in the Cambro‐Ordovician Mt Windsor Subprovince in northern Queensland. The orebody comprises steeply dipping, stratiform, sheet‐like, polymetallic massive sulfide lenses. Overall, the volcanic facies architecture at Thalanga is dominated by quartz‐ and/or feldspar‐phyric lavas and synvolcanic intrusions that comprise coherent facies and in situ and resedimented autoclastic facies. Systematic phenocryst logging (mineralogy, abundance, size) has been used to discriminate separate emplacement units of rhyolite in the footwall and dacite in the hangingwall. Some of the petrographically different rhyolite and dacite types can also be distinguished using immobile‐element geochemistry. Rhyolitic lavas and intrusions in the footwall are weakly to strongly altered. Apparent clastic textures resulting from hydrothermal alteration and metamorphism are widely developed in the coherent facies. Genuine clastic textures are characterised by clasts with randoml.
THE ANALYSIS OF INDIVIDUAL SKILLS OF ICE SLEDGE HOCKEY PLAYERS AT THE TORINO 2006 PARALYMPIC TOURNAMENT

Ice Sledge Hockey is one of the fastest growing winter Paralympic sports. There has been little research performed on ice sledge hockey and consequently the information on performance parameters is scarce. The purpose of this study is to determine the differences in the level of individual ice sledge hockey skills among players of eight teams participating in Paralympic tournament Torino 2006 using observation protocol for assessment of key technical skills in Ice Sledge Hockey (Beckman, Kudlacek & Vanlandewijck, 2007). The players involved in this study were players from Paralympic tournament. Four of the five best players are from Canada and one is from Norway. While we presented clear differences of individual players which are associated with actual standings in the Paralympic tournament we found only significant differences are total scores (F=5.29, p0.01) and skating subscale (F=3.66, p0.05).