Miracle-dz/UniFAR-FTUs huggingface dataset:
Adeno-associated virus DNA replication in vitro: activation by a maltose binding protein/Rep 68 fusion protein

The adeno-associated virus (AAV) nonstructural protein Rep 68 is required for viral DNA replication. An in vitro assay has been developed in which addition of Rep 68 to an extract from uninfected HeLa cells supports AAV DNA replication. In this paper, we report characterization of the replication process when a fusion of the maltose binding protein and Rep 68, expressed in Escherichia coli, was used in the assay. Replication was observed when the template was either linear double-stranded AAV DNA or a plasmid construct containing intact AAV DNA. When the recombinant plasmid construct was used as the template, there was replication of pBR322 DNA as well as the AAV DNA; however, linear pBR322 DNA was not replicated. When the plasmid construct was the template, replication appeared to initiate on the intact plasmid and led to separation of the AAV sequences from those of the vector, a process which has been termed rescue. There was no evidence that replication could initiate on the products of rescue. Rep 68 can make a site-specific nick 124 nucleotides from the 3' end of AAV DNA; the site of the nick has been called the terminal resolution site. Our data are most consistent with initiation occurring at the terminal resolution site and proceeding toward the 3' terminus. When the template was the plasmid construct, either elongation continued past the junction into pBR322 sequences or the newly synthesized sequence hairpinned, switched template strands, and replicated the AAV DNA. Replication was linear for 4 h, during which time 70% of the maximal synthesis took place. An additional finding was that the Rep fusion could resolve AAV dimer length duplex intermediates into monomer duplexes without DNA synthesis.
Drawbacks in the use of unconventional hydrophobic anhydrides for histone derivatization in bottom‐up proteomics PTM analysis

MS‐based proteomics has become the most utilized tool to characterize histone PTMs. Since histones are highly enriched in lysine and arginine residues, lysine derivatization has been developed to prevent the generation of short peptides (<6 residues) during trypsin digestion. One of the most adopted protocols applies propionic anhydride for derivatization. However, the propionyl group is not sufficiently hydrophobic to fully retain the shortest histone peptides in RP LC, and such procedure also hampers the discovery of natural propionylation events. In this work we tested 12 commercially available anhydrides, selected based on their safety and hydrophobicity. Performance was evaluated in terms of yield of the reaction, MS/MS fragmentation efficiency, and drift in retention time using the following samples: (i) a synthetic unmodified histone H3 tail, (ii) synthetic modified histone peptides, and (iii) a histone extract from cell lysate. Results highlighted that seven of the selected anhydrides increased peptide retention time as compared to propionic, and several anhydrides such as benzoic and valeric led to high MS/MS spectra quality. However, propionic anhydride derivatization still resulted, in our opinion, as the best protocol to achieve high MS sensitivity and even ionization efficiency among the analyzed peptides.
A novel in vitro transcription‐translation system: accurate and efficient synthesis of single proteins from cloned DNA sequences.

A system is described which permits the efficient synthesis of single proteins in vitro. The essential element in this expression system is a strong promoter derived from coliphage T5 which produces, with high efficiency, specific RNAs in capped or uncapped form, depending upon the experimental conditions used. The transcription‐coupled capping of RNA allows the direct translation of the RNA in eukaryotic extracts from wheat germ as well as from HeLa cells. The synthesis of three different proteins is reported, including lysozyme, which is shown to be translocated across membranes when appropriate assay conditions are used. The simplicity of the experimental procedure, the high purity and specific activity of the [35S]methionine‐labelled proteins produced offer a number of possibilities for the study of structure‐function relationships of proteins.
Validation of Surrogate Markers in Multiple Randomized Clinical Trials with Repeated Measurements

Part of the recent literature on the validation of biomarkers as surrogate endpoints proposes to undertake the validation exercise in a multi‐trial context which led to a definition of validity in terms of the quality of both trial level and individual level association between the surrogate and the true endpoints (Buyse et al., 2000). These authors concentrated on continuous univariate responses. However, in many randomized clinical studies, repeated measurements are encountered on either or both endpoints. When both the surrogate and true endpoints are measured repeatedly over time, one is confronted with the modelling of bivariate longitudinal data. In this work, we show how such a joint model can be implemented in the context of surrogate marker validation. In addition, another challenge in this setting is the formulation of a simple and meaningful concept of “surrogacy”. We propose the use of a new measure, the so‐called variance reduction factor, to evaluate surrogacy at the trial and individual level. On the other hand, most of the work published in this area assume that only one potential surrogate is going to be evaluated. We also show that this concept will let us evaluate surrogacy when more than one surrogate variable is available for the analysis. The methodology is illustrated on data from a meta‐analysis of five clinical trials comparing antipsychotic agents for the treatment of chronic schizophrenia.
Metoprolol and diltiazem ameliorate ziprasidone-induced prolonged corrected QT interval in rats

Ziprasidone, an atypical antipsychotic agent, has been shown to increase the corrected QT (QTc) interval in some patients. The aim of this study was to reveal the effects of metoprolol and diltiazem on ziprasidone drug-induced prolonged QTc interval. A total of 24 rats were equally divided into the following four groups: the first group was used as the control and received 1 mL/kg saline; 3 mg/kg ziprasidone and saline were administered to the second group; 3 mg/kg ziprasidone and 1 mg/kg metoprolol were administered to the third group and 3 mg/kg ziprasidone and 2 mg/kg diltiazem were administered to the fourth group. Two hours following application of the drugs, the QTc was calculated by performing electrocardiography in derivation (D)I. The duration of QTc interval was compared among the four groups. The mean QTc intervals were significantly increased in the third and fourth groups compared with the second group (p < 0.0005 and p < 0.0001, respectively). The study demonstrated the effectiveness of metoprolol and diltiazem in the prevention of ziprasidone-induced elongation in the QTc interval. Both metoprolol and diltiazem may be considered in the prophylactic therapy of high-risk patients who are using ziprasidone.
Strategy-Proofness and Efficiency of Probabilistic Mechanisms for Excludable Public Good

We study strategy-proof probabilistic mechanisms in a binary excludable public good model. We construct a new class of probabilistic mechanisms satisfying strategy-proofness, called mechanisms. We first show that the mechanisms are second-best efficient. Next, we identify the optimal mechanism with respect to the supremal welfare loss, and show that it improves the inefficiency of the equal cost sharing with maximal participation mechanism [Moulin (1994)] and the anonymous augmented serial mechanisms [Ohseto (2005)].
Lymphedema after breast cancer: incidence, risk factors, and effect on upper body function.

PURPOSE Secondary lymphedema is associated with adverse physical and psychosocial consequences among women with breast cancer (BC). This article describes the prevalence and incidence of lymphedema between 6 and 18 months after BC treatment; personal, treatment, and behavioral correlates of lymphedema status; and the presence of other upper-body symptoms (UBS) and function (UBF). PATIENTS AND METHODS A population-based sample of Australian women (n = 287) with recently diagnosed, invasive BC were evaluated on five occasions using bioimpedance spectroscopy. Lymphedema was diagnosed when the ratio of impedance values, comparing treated and untreated sides, was three standard deviations more than normative data. UBF was assessed using the validated Disability of the Arm, Shoulder, and Hand questionnaire. RESULTS From 6 to 18 months after surgery, 33% (n = 62) of the sample were classified as having lymphedema; of these, 40% had long-term lymphedema. Although older age, more extensive surgery or axillary node dissection, and experiencing one or more treatment-related complication(s) or symptom(s) at baseline were associated with increased odds, lower socioeconomic status, having a partner, greater child care responsibilities, being treated on the dominant side, participation in regular activity, and having good UBF were associated with decreased odds of lymphedema. Not surprisingly, lymphedema leads to reduced UBF; however, BC survivors report high prevalences of other UBS (34% to 62%), irrespective of their lymphedema status. CONCLUSION Lymphedema is a public health issue deserving greater attention. More systematic surveillance for earlier detection and the potential benefits of physical activity to prevent lymphedema and mitigate symptoms warrant further clinical integration and research.
Decreasing laboratory turnaround time and patient wait time by implementing process improvement methodologies in an outpatient oncology infusion unit.

PURPOSE Prolonged patient wait times in the outpatient oncology infusion unit indicated a need to streamline phlebotomy processes by using existing resources to decrease laboratory turnaround time and improve patient wait time. METHODS Using the DMAIC (define, measure, analyze, improve, control) method, a project to streamline phlebotomy processes within the outpatient oncology infusion unit in an academic Comprehensive Cancer Center known as the Comprehensive Treatment Unit (CTU) was completed. Laboratory turnaround time for patients who needed same-day lab and CTU services and wait time for all CTU patients was tracked for 9 weeks. RESULTS During the pilot, the wait time from arrival to CTU to sitting in treatment area decreased by 17% for all patients treated in the CTU during the pilot. A total of 528 patients were seen at the CTU phlebotomy location, representing 16% of the total patients who received treatment in the CTU, with a mean turnaround time of 24 minutes compared with a baseline turnaround time of 51 minutes. CONCLUSIONS Streamlining workflows and placing a phlebotomy station inside of the CTU decreased laboratory turnaround times by 53% for patients requiring same day lab and CTU services. The success of the pilot project prompted the team to make the station a permanent fixture.
ABT-378/ritonavir plus stavudine and lamivudine for the treatment of antiretroviral-naive adults with HIV-1 infection: 48-week results

ObjectiveTo evaluate the safety and antiviral activity of different dose levels of the HIV protease inhibitor ABT-378 combined with low-dose ritonavir, plus stavudine and lamivudine in antiretroviral-naive individuals. DesignProspective, randomized, double-blind, multicenter. MethodsEligible patients with plasma HIV-1 RNA > 5000 copies/ml received ABT-378 200 or 400 mg with ritonavir 100 mg every 12 h; after 3 weeks stavudine 40 mg and lamivudine 150 mg every 12 h were added (group I, n = 32). A second group initiated treatment with ABT-378 400 mg and ritonavir 100 or 200 mg plus stavudine and lamivudine every 12 h (group II, n = 68). ResultsMean baseline HIV-1 RNA was 4.9 log10 copies/ml in both groups and CD4 cell count was 398 × 106/l and 310 × 106/l in Groups I and II respectively. In the intent-to-treat (ITT; missing value = failure) analysis at 48 weeks, HIV-1 RNA was < 400 copies/ml for 91% (< 50 copies/ml, 75%) and 82% (< 50 copies/ml, 79%) of patients in groups I and II respectively. Mean steady-state ABT-378 trough concentrations exceeded the wild-type HIV-1 EC50 (effective concentration to inhibit 50%) by 50–100-fold. The most common adverse events were abnormal stools, diarrhea and nausea. No patient discontinued before 48 weeks because of treatment-related toxicity or virologic rebound. ConclusionsABT-378 is a potent, well-tolerated protease inhibitor. The activity and durable suppression of HIV-1 observed in this study is probably attributable to the observed tolerability profile and the achievement of high ABT-378 plasma concentrations.
Tracking the time-varying sparsity of channel coefficients in shallow water acoustic communications

Sparse estimation techniques typically assume a fixed weighting between the L1 norm of the coefficients to be estimated, and the L2 norm of the estimation error. This weighting reflects the sparsity assumption on the distribution of coefficients being estimated, and therefore, is sensitive to potential mismatch with the actual sparsity of the distribution. In this paper, we address this issue from the perspective of tracking the delay-Doppler spread of the shallow water acoustic channel, where the sparsity of the distribution itself is unknown and changes over time. We justify the need to track the sparsity based on simulation results as well as experimental field data collected at 15 meters depth and 200 meters range under moderate to high wind conditions. We propose a heuristic update to the sparsity weighting based on the normalized prediction error, which measures the mismatch between the predicted observation based on the current estimate and the actual observation in the next time step. The proposed heuristic update for the channel sparsity is designed to adapt towards lower values of the normalized prediction error and thus, by design, ensures that the estimator performance increases, or in the worst case, stays stable as the channel sparsity undergoes changes with time.
Inter turn short circuit detection at higher modulation indexes including six step operation

Inverter fed induction machine drives have become one of the most important part in industrial applications. The devices are usually operated near or at the rated vales. Additionally high dynamic operations, overload cycles and the fast switching inverter are putting additional stress to all machines components. The stator winding system is one of the most critical components. Faults in the winding system of a machine can cause a dramatic damage due to their fast developing behavior. An early detection of winding faults can reduce these consequences. In this paper a method is presented to achieve reliable fault detection on stator winding faults focused on application at higher speed levels where immediate detection is imperative. Higher inverter modulation indexes provide the possibility to estimate the transient leakage inductance in each PWM modulation cycle. This parameter contains the information on machine asymmetries. Specific signal processing steps provide a high sensitive fault indicator.
Bacterial Subfamily of LuxR Regulators That Respond to Plant Compounds

ABSTRACT Pseudomonas fluorescens are rhizobacteria known for their biocontrol properties. Several antimicrobial functions are crucial for this process, and the experiments described here investigate the modulation of their expression during the plant-bacterium interaction. The role of a LuxR family regulator in interkingdom signaling has been investigated using genome-scale transcriptome analysis, gene promoter studies in vivo and in vitro, biocontrol assays, and response to plant compounds. PsoR, a LuxR solo or orphan regulator of P. fluorescens, was identified. PsoR is solubilized and activates a lux-box-containing promoter only in the presence of macerated plants, suggesting the presence of a plant molecule(s) that most likely binds to PsoR. Gene expression profiles revealed that genes involved in the inhibition of plant pathogens were affected by PsoR, including a chitinase gene, iron metabolism genes, and biosynthetic genes of antifungal compounds. 2,4-Diacetylphloroglucinol production is PsoR dependent both in vitro and in vivo. psoR mutants were significantly reduced for their ability to protect wheat plants from root rot, and damping-off caused by Pythium ultimum infection. PsoR most likely senses a molecule(s) in the plant and modulates expression of genes that have a role in biocontrol. PsoR and related proteins form a subfamily of LuxR family regulators in plant-associated bacteria.
Artificial urinary sphincter in patients with neurogenic bladder dysfunction.

OBJECTIVE To assess the role of the artificial urinary sphincter (AUS) in the management of sphincter weakness incontinence in neuropathic patients. PATIENTS AND METHODS Ninety patients (75 male and 15 female, mean age 26 years, range 13-62) with neurogenic bladder dysfunction (71 with congenital and 19 with acquired cord lesions) who underwent implantation of an AUS were reviewed. All patients were followed up for a minimum of one year after the initial implantation of the sphincter (mean 4 years, range 1-10). Pre-operative video-urodynamics demonstrated sphincter weakness incontinence in all patients, with 24 patients having an acontractile-type bladder. Of 66 patients with intermediate-type bladders, 52 underwent cystoplasty. RESULTS Eighty-three patients (92%) were continent both night and day, three were occasionally damp and controlled by pharmacotherapy, and four had a persistent poor result. Of the 66 patients with detrusor hyper-reflexia, 52 (79%) required a cystoplasty to achieve continence and 14 (21%) were controlled with anti-cholinergic therapy. The re-operation rate was 28% (25/90) and complications included six infections, seven erosions, eight system failures, two pump failures, one sheered tube and one rectal and one bladder perforation. Seventy (78%) of the patients currently perform intermittent catheterization to treat high post-voiding residual urine volumes. CONCLUSIONS A rate of continence > 90% was achieved in these neurogenic patients after implantation of an AUS and we recommend a simultaneous cystoplasty in patients with detrusor overactivity.
Frontotemporal dementia: Pathology of gait?

The main diagnostic criteria of the behavioural variant of frontotemporal degeneration (bvFTD) include neurobehavioral and dysexecutive syndromes, but not specific gait characteristics although strong relationship between gait and prefrontal functions are increasingly recognized. Accordingly, we tested the hypothesis that patients with bvFTD would have more gait changes than older healthy controls and demented patients with Alzheimer's disease (AD). Sixty subjects were included in the study: 19 with bvFTD, 19 with AD and 22 healthy controls. Mean values and coefficients of variation (CV) of stride time while just walking (i.e., single tasking) and while walking with backward counting (i.e., dual tasking) were measured using the SMTEC®‐footswitch system. Stride time, mean value, and CV were significantly increased in both patient groups compared with healthy controls during single task or walking alone (P < 0.001) and during dual tasking (P < 0.001). After adjusting for age, Mini‐mental examination, psychoactive drugs, gender, and history of previous fall, only the patients with bvFTD group was associated with an increase of CV of stride time during single walking (P < 0.001) and dual tasking (P < 0.001). These data suggest that gait instability during single and dual tasking could represent a supportive argument for bvFTD. In clinical practice, such a diagnosis should be at least considered in any demented patient with gait instability. © 2010 Movement Disorder Society
Cdc14A and Cdc14B Redundantly Regulate DNA Double-Strand Break Repair

ABSTRACT Cdc14 is a phosphatase that controls mitotic exit and cytokinesis in budding yeast. In mammals, the two Cdc14 homologues, Cdc14A and Cdc14B, have been proposed to regulate DNA damage repair, whereas the mitotic exit and cytokinesis rely on another phosphatase, PP2A-B55α. It is unclear if the two Cdc14s work redundantly in DNA repair and which repair pathways they participate in. More importantly, their target(s) in DNA repair remains elusive. Here we report that Cdc14B knockout (Cdc14B−/−) mouse embryonic fibroblasts (MEFs) showed defects in repairing ionizing radiation (IR)-induced DNA double-strand breaks (DSBs), which occurred only at late passages when Cdc14A levels were low. This repair defect could occur at early passages if Cdc14A levels were also compromised. These results indicate redundancy between Cdc14B and Cdc14A in DSB repair. Further, we found that Cdc14B deficiency impaired both homologous recombination (HR) and nonhomologous end joining (NHEJ), the two major DSB repair pathways. We also provide evidence that Cdh1 is a downstream target of Cdc14B in DSB repair.
3-Deoxyfructose Concentrations are Increased in Human Plasma and Urine in Diabetes

3-Deoxyglucosone (3-DG) is a reactive dicarbonyl sugar thought to be a key intermediate in the nonenzymatic polymerization and browning of proteins by glucose. 3-DG may be formed in vivo from fructose, fructose 3-phosphate, or Amadori adducts to protein, such as NE-fructoselysine (FL), all of which are known to be elevated in body fluids or tissues in diabetes. Modification of proteins by 3-DG formed in vivo is thought to be limited by enzymatic reduction of 3-DG to less reactive species, such as 3-deoxyfructose (3-DF). In this study, we have measured 3-DF, as a metabolic fingerprint of 3-DG, in plasma and urine from a group of diabetic patients and control subjects. Plasma and urinary 3-DF concentrations were significantly increased in the diabetic compared with the control population (0.853 ± 0.189 vs. 0.494 ± 0.072 μM, P < 0.001, and 69.9 ± 44.2 vs. 38.7 ± 16.1 nmol/mg creatinine, P < 0.001, respectively). Plasma and urinary 3-DF concentrations correlated strongly with one another, with HbA1c (P < 0.005 in all cases), and with urinary FL (P < 0.02 and P = 0.005, respectively). The overall increase in 3-DF concentrations in plasma and urine in diabetes and their correlation with other indexes of glycemic control suggest that increased amounts of 3-DG are formed in the body during hyperglycemia in diabetes and then metabolized to 3-DF. These observations are consistent with a role for increased formation of the dicarbonyl sugar 3-DG in the accelerated browning of tissue proteins in diabetes.