Miracle-dz/UniFAR-FTUs huggingface dataset:
Genomic and Biochemical Characterization of Acinetobacter Podophage Petty Reveals a Novel Lysis Mechanism and Tail-Associated Depolymerase Activity

ABSTRACT The increased prevalence of drug-resistant, nosocomial Acinetobacter infections, particularly from pathogenic members of the Acinetobacter calcoaceticus-baumannii complex, necessitates the exploration of novel treatments such as phage therapy. In the present study, we characterized phage Petty, a novel podophage that infects multidrug-resistant Acinetobacter nosocomialis and Acinetobacter baumannii. Genome analysis reveals that phage Petty is a 40,431-bp ϕKMV-like phage, with a coding density of 92.2% and a G+C content of 42.3%. Interestingly, the lysis cassette encodes a class I holin and a single-subunit endolysin, but it lacks canonical spanins to disrupt the outer membrane. Analysis of other ϕKMV-like genomes revealed that spaninless lysis cassettes are a feature of phages infecting Acinetobacter within this subfamily of bacteriophages. The observed halo surrounding Petty's large clear plaques indicated the presence of a phage-encoded depolymerase capable of degrading capsular exopolysaccharides (EPS). The product of gene 39, a putative tail fiber, was hypothesized to possess depolymerase activity based on weak homology to previously reported phage tail fibers. The 101.4-kDa protein gene product 39 (gp39) was cloned and expressed, and its activity against Acinetobacter EPS in solution was determined. The enzyme degraded purified EPS from its host strain A. nosocomialis AU0783, reducing its viscosity, and generated reducing ends in solution, indicative of hydrolase activity. Given that the accessibility to cells within a biofilm is enhanced by degradation of EPS, phages with depolymerases may have enhanced diagnostic and therapeutic potential against drug-resistant Acinetobacter strains. IMPORTANCE Bacteriophage therapy is being revisited as a treatment for difficult-to-treat infections. This is especially true for Acinetobacter infections, which are notorious for being resistant to antimicrobials. Thus, sufficient data need to be generated with regard to phages with therapeutic potential, if they are to be successfully employed clinically. In this report, we describe the isolation and characterization of phage Petty, a novel lytic podophage, and its depolymerase. To our knowledge, it is the first phage reported to be able to infect both A. baumannii and A. nosocomialis. The lytic phage has potential as an alternative therapeutic agent, and the depolymerase could be used for modulating EPS both during infections and in biofilms on medical equipment, as well as for capsular typing. We also highlight the lack of predicted canonical spanins in the phage genome and confirm that, unlike the rounding of lambda lysogens lacking functional spanin genes, A. nosocomialis cells infected with phage Petty lyse by bursting. This suggests that phages like Petty employ a different mechanism to disrupt the outer membrane of Acinetobacter hosts during lysis.
Unsupervised learning of action primitives

Action representation is a key issue in imitation learning for humanoids. With the recent finding of mirror neurons there has been a growing interest in expressing actions as a combination meaningful subparts called primitives. Primitives could be thought of as an alphabet for the human actions. In this paper we observe that human actions and objects can be seen as being intertwined: we can interpret actions from the way the body parts are moving, but as well from how their effect on the involved object. While human movements can look vastly different even under minor changes in location, orientation and scale, the use of the object can provide a strong invariant for the detection of motion primitives. In this paper we propose an unsupervised learning approach for action primitives that makes use of the human movements as well as the object state changes. We group actions according to the changes they make to the object state space. Movements that produce the same state change in the object state space are classified to be instances of the same action primitive. This allows us to define action primitives as sets of movements where the movements of each primitive are connected through the object state change they induce.
Akt Inhibitor Akt-IV Blocks Virus Replication through an Akt-Independent Mechanism

ABSTRACT Many viruses activate the phosphatidylinositol 3′-kinase (PI3k)/Akt intracellular signaling pathway to promote viral replication. We have analyzed whether a rapidly replicating rhabdovirus, vesicular stomatitis virus (VSV), requires the PI3k/Akt signaling pathway for its replication. Through the use of chemical inhibitors of PI3k and Akt, we show that VSV replication and cytopathic effects do not require activation of these kinases. Inhibitors that block the activating phosphorylations of Akt at threonine 308 (Thr308) and serine 473 (Ser473) did not inhibit VSV protein expression or the induction of the cytopathic effects of VSV. One compound, Akt inhibitor Akt-IV, inhibited the replication of VSV, respiratory syncytial virus, and vaccinia virus but increased the phosphorylation of Akt at positions Thr308 and Ser473 and did not inhibit Akt kinase activity in vitro. Together, our data suggest that the PI3k/Akt pathway is of limited relevance to the replication of VSV but that Akt inhibitor Akt-IV is a novel broad-spectrum antiviral compound with a mechanism differing from that of its previously reported effect on the PI3k/Akt pathway. Identification of other targets for this compound may define a new approach for blocking virus replication.
Mild Cognitive Impairment. Aging to Alzheimer's disease

Persons with MCI have an increased risk of developing AD. This book addresses the spectrum of issues involved in MCI, and includes chapters on clinical studies, neuropsychology, neuroimaging, neuropathology, biological markers, diagnostic approaches, and treatment. It is intended for individuals interested in aging and cognition, among them neurologists, psychiatrists, geriatricians, clinical psychologists, neuropsychologists, and their students and trainees.
Role of Human Immunodeficiency Virus Type 1 Envelope Structure in the Induction of Broadly Neutralizing Antibodies

ABSTRACT Very soon after the discovery of neutralizing antibodies (NAbs) toward human immunodeficiency virus type 1 (HIV-1) infection, it became apparent that characterization of these NAbs would be an important step in finding a cure for or a vaccine to eradicate HIV-1. Since the initial description of broadly cross-clade NAbs naturally produced in HIV-1 patients, numerous studies have described new viral targets for these antibodies. More recently, studies concerning new groups of patients able to control their viremia, such as long-term nonprogressors (LTNPs) or elite controllers, have described the generation of numerous envelope-targeted NAbs. Recent studies have marked a new stage in research on NAbs with the description of antibodies obtained from a worldwide screening of HIV-positive patients. These studies have permitted the discovery of NAb families with great potential for both neutralization and neutralization breadth, such as PG, PGT, CH, and highly active agonistic anti-CD4 binding site antibodies (HAADs), of which VRC01 and its variants are members. These antibodies are able to neutralize more than 80% of circulating strains without any autoreactivity and can be rapidly integrated into clinical trials in order to test their protective potential. In this review, we will focus on new insights into HIV-1 envelope structure and their implications for the generation of potent NAbs.
QUANTITATIVE ASSESSMENT OF RESIDUAL ANTIDEPOLARIZING BLOCK (PART II)

An attempt to estimate residual neuromuscular blockade after the administration of anti-depolarizing relaxants to anaesthetized patients is described. A train of four supra-maximal nerve stimuli was applied to the ulnar nerve and the twitch response (mechanical or electrical) was recorded. The frequency of the train used was 2–2.4 Hz with an interval of 10 seconds between the trains. Clinical recovery from the relaxant was assessed by the ability to lift the head. The ratio of the height of the fourth response of the train to that of the first (ratio (c)) gave a good indication of the degree of residual neuromuscular block as indicated by this simple clinical test. As ratio (c) increased muscle power improved. Obvious muscle weakness was associated with values of ratio (c) of less than 0.6.
A matching pursuit method for approximating overlapping ultrasonic echoes

Ultrasonic pulse-echo methods have been used extensively in measuring the thickness of layered structures as well as those of thin adhesive interface layers. When acoustically measuring thin layers, the resulting echoes from two successive interfaces overlap in time, limiting the minimum thickness that can be resolved using conventional pulse-echo techniques. In this paper, we propose a method, named support matching pursuit (SMP), for resolving the individual echoes. The method is based on the concept of sparse signal approximation in an overcomplete dictionary composed of Gabor atoms (elementary functions). Although the dictionary enables highly flexible approximations, it is also overcomplete, which implies that the approximation is not unique. We propose a method for approximation in which each ultrasonic echo is principally represented by a single atom and therefore has a physical interpretation. SMP operates similarly to the sparse matching pursuit (MP) method. It iteratively improves the approximation by adding, at each iteration, a single atom to the solution set. However, our atom selection criterion utilizes the time localization nature of ultrasonic echoes, which causes portions of a multi-echo ultrasonic signal to be composed mainly from a single echo. This leads to accurate approximations in which each echo is characterized by a set of physical parameters that represent the composing ultrasonic echoes. In the current research we compare SMP to other sparse approximation methods such as MP and basis pursuit (BP). We perform simulations and experiments on adhesively bonded structures which clearly demonstrate the superior performance of the SMP method over the MP and BP methods.
Reverse Engineering and Evaluation of Prediction Models for Progression to Type 2 Diabetes

Background: Application of novel machine learning approaches to electronic health record (EHR) data could provide valuable insights into disease processes. We utilized this approach to build predictive models for progression to prediabetes and type 2 diabetes (T2D). Methods: Using a novel analytical platform (Reverse Engineering and Forward Simulation [REFS]), we built prediction model ensembles for progression to prediabetes or T2D from an aggregated EHR data sample. REFS relies on a Bayesian scoring algorithm to explore a wide model space, and outputs a distribution of risk estimates from an ensemble of prediction models. We retrospectively followed 24 331 adults for transitions to prediabetes or T2D, 2007-2012. Accuracy of prediction models was assessed using an area under the curve (AUC) statistic, and validated in an independent data set. Results: Our primary ensemble of models accurately predicted progression to T2D (AUC = 0.76), and was validated out of sample (AUC = 0.78). Models of progression to T2D consisted primarily of established risk factors (blood glucose, blood pressure, triglycerides, hypertension, lipid disorders, socioeconomic factors), whereas models of progression to prediabetes included novel factors (high-density lipoprotein, alanine aminotransferase, C-reactive protein, body temperature; AUC = 0.70). Conclusions: We constructed accurate prediction models from EHR data using a hypothesis-free machine learning approach. Identification of established risk factors for T2D serves as proof of concept for this analytical approach, while novel factors selected by REFS represent emerging areas of T2D research. This methodology has potentially valuable downstream applications to personalized medicine and clinical research.
Evidence for Avian and Human Host Cell Factors That Affect the Activity of Influenza Virus Polymerase

ABSTRACT Typical avian influenza A viruses do not replicate efficiently in humans. The molecular basis of host range restriction and adaptation of avian influenza A viruses to a new host species is still not completely understood. Genetic determinants of host range adaptation have been found on the polymerase complex (PB1, PB2, and PA) as well as on the nucleoprotein (NP). These four viral proteins constitute the minimal set for transcription and replication of influenza viral RNA. It is widely documented that in human cells, avian-derived influenza A viral polymerase is poorly active, but despite extensive study, the reason for this blockade is not known. We monitored the activity of influenza A viral polymerases in heterokaryons formed between avian (DF1) and human (293T) cells. We have discovered that a positive factor present in avian cells enhances the activity of the avian influenza virus polymerase. We found no evidence for the existence of an inhibitory factor for avian virus polymerase in human cells, and we suggest, instead, that the restriction of avian influenza virus polymerases in human cells is the consequence of the absence or the low expression of a compatible positive cofactor. Finally, our results strongly suggest that the well-known adaptative mutation E627K on viral protein PB2 facilitates the ability of a human positive factor to enhance replication of influenza virus in human cells.
White Coat Adherence in Pediatric Patients With Type 1 Diabetes Who Use Insulin Pumps

Background: The purpose was to assess the occurrence of white coat adherence, defined as an increase in adherence to treatment regimens prior to a clinic appointment, in children and adolescents with type 1 diabetes (T1D) who use insulin pumps. Methods: Blood glucose monitoring (BGM) data, carbohydrate inputs, and insulin boluses delivered were downloaded from the insulin pumps of children and adolescents, aged 7-19 years with T1D, at 2 consecutive routine diabetes clinic visits. Linear mixed models were used to analyze patterns of BGM, carbohydrate inputs, and insulin boluses delivered in patients who had ≥28 days of data stored in their insulin pumps. Results: In general, younger children engaged in more frequent BGM, carbohydrate inputs, and insulin boluses delivered than older children and adolescents. White coat adherence occurred with frequency of BGM, carbohydrate inputs, and insulin boluses delivered, but only in younger children. Conclusions: Diabetes care providers need to be aware that white coat adherence may occur, particularly in young children. Providers routinely download meter and insulin pump data for the 1- to 2-week period before the clinic visit. For patients exhibiting white coat adherence, their data will overestimate the patient’s actual adherence.
Reverse Genetics Recovery of Lujo Virus and Role of Virus RNA Secondary Structures in Efficient Virus Growth

ABSTRACT Arenaviruses are rodent-borne viruses with a bisegmented RNA genome. A genetically unique arenavirus, Lujo virus, was recently discovered as the causal agent of a nosocomial outbreak of acute febrile illness with hemorrhagic manifestations in Zambia and South Africa. The outbreak had a case fatality rate of 80%. A reverse genetics system to rescue infectious Lujo virus from cDNA was established to investigate the biological properties of this virus. Sequencing the genomic termini showed unique nucleotides at the 3′ terminus of the S segment promoter element. While developing this system, we discovered that reconstructing infectious Lujo virus using the previously reported L segment intergenic region (IGR), comprising the arenaviral transcription termination signal, yielded an attenuated Lujo virus. Resequencing revealed that the correct L segment IGR was 36 nucleotides longer, and incorporating it into the reconstructed Lujo virus restored the growth rate to that of the authentic clinical virus isolate. These additional nucleotides were predicted to more than double the free energy of the IGR main stem-loop structure. In addition, incorporating the newly determined L-IGR into a replicon reporter system enhanced the expression of a luciferase reporter L segment. Overall, these results imply that an extremely stable secondary structure within the L-IGR is critical for Lujo virus propagation and viral protein production. The technology for producing recombinant Lujo virus now provides a method to precisely investigate the molecular determinants of virulence of this newly identified pathogen.
Interplay of Acute and Persistent Infections Caused by Venezuelan Equine Encephalitis Virus Encoding Mutated Capsid Protein

ABSTRACT Venezuelan equine encephalitis virus (VEEV) is a significant human and animal pathogen. The highlight of VEEV replication in vitro, in cells of vertebrate origin, is the rapid development of cytopathic effect (CPE), which is strongly dependent upon the expression of viral capsid protein. Besides being an integral part of virions, the latter protein is capable of (i) binding both the nuclear import and nuclear export receptors, (ii) accumulating in the nuclear pore complexes, (iii) inhibiting nucleocytoplasmic trafficking, and (iv) inhibiting transcription of cellular ribosomal and messenger RNAs. Using our knowledge of the mechanism of VEEV capsid protein function in these processes, we designed VEEV variants containing combinations of mutations in the capsid-coding sequences. These mutations made VEEV dramatically less cytopathic but had no effect on infectious virus production. In cell lines that have defects in type I interferon (IFN) signaling, the capsid mutants demonstrated very efficient persistent replication. In other cells, which have no defects in IFN production or signaling, the same mutants were capable of inducing a long-term antiviral state, downregulating virus replication to an almost undetectable level. However, ultimately, these cells also developed a persistent infection, characterized by continuous virus replication and beta IFN (IFN-β) release. The results of this study demonstrate that the long-term cellular antiviral state is determined by the synergistic effects of type I IFN signaling and the antiviral reaction induced by replicating viral RNA and/or the expression of VEEV-specific proteins. The designed mutants represent an important model for studying the mechanisms of cell interference with VEEV replication and development of persistent infection.
The Crystal Structure of PF-8, the DNA Polymerase Accessory Subunit from Kaposi's Sarcoma-Associated Herpesvirus

ABSTRACT Kaposi's sarcoma-associated herpesvirus is an emerging pathogen whose mechanism of replication is poorly understood. PF-8, the presumed processivity factor of Kaposi's sarcoma-associated herpesvirus DNA polymerase, acts in combination with the catalytic subunit, Pol-8, to synthesize viral DNA. We have solved the crystal structure of residues 1 to 304 of PF-8 at a resolution of 2.8 Å. This structure reveals that each monomer of PF-8 shares a fold common to processivity factors. Like human cytomegalovirus UL44, PF-8 forms a head-to-head dimer in the form of a C clamp, with its concave face containing a number of basic residues that are predicted to be important for DNA binding. However, there are several differences with related proteins, especially in loops that extend from each monomer into the center of the C clamp and in the loops that connect the two subdomains of each protein, which may be important for determining PF-8's mode of binding to DNA and to Pol-8. Using the crystal structures of PF-8, the herpes simplex virus catalytic subunit, and RB69 bacteriophage DNA polymerase in complex with DNA and initial experiments testing the effects of inhibition of PF-8-stimulated DNA synthesis by peptides derived from Pol-8, we suggest a model for how PF-8 might form a ternary complex with Pol-8 and DNA. The structure and the model suggest interesting similarities and differences in how PF-8 functions relative to structurally similar proteins.
The Interactive Effect of Diabetes Family Conflict and Depression on Insulin Bolusing Behaviors for Youth

Objective: Adherence to type 1 diabetes management declines as children enter adolescence. For youth, psychosocial variables including mood and interpersonal relationships play a large role in diabetes maintenance. The current study assessed the unique and interactive roles diabetes family conflict and depression have on insulin bolusing behaviors for youth ages 10-16 years. Methods: Ninety-one youth-parent dyads completed a survey assessing family conflict and depression. Mean daily blood glucose levels, mealtime insulin bolus scores (BOLUS), and glycated hemoglobin (HbA1c) were collected from the medical record as outcome variables. Results: Parent-reported diabetes-related family conflict and youths’ endorsed depression both significantly predicted insulin bolusing behavior, R2 = . 13, F(2, 88) = 6.66, P < . 05. The interaction of diabetes family conflict and youth depression played a significant role in youths’ bolusing behaviors, above and beyond that which was predicted by conflict and depression separately, R2 = . 18, Fchange(1, 87) = 4.63, P < . 05. BOLUS was negatively related to youths’ hemoglobin A1c, r = –. 556, P < . 001 and mean daily blood glucose levels, r = –. 428, P < . 001. Conclusions: Among depressed youth, mealtime insulin BOLUS scores declined with greater diabetes-related family conflict, while there was no change in BOLUS scores among depressed youth living in families reporting less conflict. Findings underscore the importance of screening for depression and family conflict in youth experiencing or at risk for poor adherence to mealtime insulin and higher HbA1c levels.