bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of MALDI Biotyper Mycobacteria Library v3.0 for Identification of Nontuberculous Mycobacteria
Authors: Rodríguez-Sánchez Belén , Ruiz-Serrano M. Jesús , Ruiz Adrián , Timke Markus , Kostrzewa Markus , Bouza Emilio 
Published: February 2016

ABSTRACT

Matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) has demonstrated its ability to promptly identify nontuberculous mycobacteria using the Mycobacteria Library v2.0. However, some species are particularly difficult to identify reliably using this database, providing a low log(score). In this study, the identification power of an updated Mycobacteria Library (v3.0) has been evaluated. Overall, 109 NTM isolates were analyzed with both databases. The v3.0 database allowed a high-level confidence in the identification [log(score) value, ≥1.8] of 91.7% of the isolates versus 83.5% with the v2.0 version (
P
< 0.01).
gD-Independent Superinfection Exclusion of Alphaherpesviruses
Authors: Criddle A. , Thornburg T. , Kochetkova I. , DePartee M. , Taylor M. P. 
Published: February 2016

ABSTRACT
Many viruses have the capacity to prevent a cell from being infected by a second virus, often termed superinfection exclusion. Alphaherpesviruses, including the human pathogen herpes simplex virus 1 (HSV-1) and the animal herpesvirus pseudorabies virus (PRV), encode a membrane-bound glycoprotein, gD, that can interfere with subsequent virion entry. We sought to characterize the timing and mechanism of superinfection exclusion during HSV-1 and PRV infection. To this end, we utilized recombinant viruses expressing fluorescent protein (FP) markers of infection that allowed the visualization of viral infections by microscopy and flow cytometry as well as the differentiation of viral progeny. Our results demonstrated the majority of HSV-1- and PRV-infected cells establish superinfection exclusion by 2 h postinfection. The modification of viral infections by virion inactivation and phosphonoacetic acid, cycloheximide, and actinomycin D treatments indicated new protein synthesis is needed to establish superinfection exclusion. Primary infection with gene deletion PRV recombinants identified that new gD expression is not required to establish superinfection exclusion of a secondary viral inoculum. We also identified the timing of coinfection events during axon-to-cell spread, with most occurring within a 2-h window, suggesting a role for cellular superinfection exclusion during neuroinvasive spread of infection. In summary, we have characterized a gD-independent mechanism of superinfection exclusion established by two members of the alphaherpesvirus family and identified a potential role of exclusion during the pathogenic spread of infection.

IMPORTANCE
Superinfection exclusion is a widely observed phenomenon initiated by a primary viral infection to prevent further viruses from infecting the same cell. The capacity for alphaherpesviruses to infect the same cell impacts rates of interviral recombination and disease. Interviral recombination allows genome diversification, facilitating the development of resistance to antiviral therapeutics and evasion of vaccine-mediated immune responses. Our results demonstrate superinfection exclusion occurs early, through a gD-independent process, and is important in the directed spread of infection. Identifying when and where in an infected host viral genomes are more likely to coinfect the same cell and generate viral recombinants will enhance the development of effective antiviral therapies and interventions.
The Herpes Simplex Virus Latency-Associated Transcript Gene Is Associated with a Broader Repertoire of Virus-Specific Exhausted CD8
+
T Cells Retained within the Trigeminal Ganglia of Latently Infected HLA Transgenic Rabbits
Authors: Srivastava Ruchi , Dervillez Xavier , Khan Arif A. , Chentoufi Aziz A. , Chilukuri Sravya , Shukr Nora , Fazli Yasmin , Ong Nicolas N. , Afifi Rasha E. , Osorio Nelson , Geertsema Roger , Nesburn Anthony B. , Wechsler Steven L. , BenMohamed Lbachir 
Published: February 2016

ABSTRACT

Persistent pathogens, such as herpes simplex virus 1 (HSV-1), have evolved a variety of immune evasion strategies to avoid being detected and destroyed by the host's immune system. A dynamic cross talk appears to occur between the HSV-1 latency-associated transcript (LAT), the only viral gene that is abundantly transcribed during latency, and the CD8
+
T cells that reside in HSV-1 latently infected human and rabbit trigeminal ganglia (TG). The reactivation phenotype of TG that are latently infected with wild-type HSV-1 or with LAT-rescued mutant (i.e., LAT
+
TG) is significantly higher than TG latently infected with LAT-null mutant (i.e., LAT
−
TG). Whether LAT promotes virus reactivation by selectively shaping a unique repertoire of HSV-specific CD8
+
T cells in LAT
+
TG is unknown. In the present study, we assessed the frequency, function, and exhaustion status of TG-resident CD8
+
T cells specific to 40 epitopes derived from HSV-1 gB, gD, VP11/12, and VP13/14 proteins, in human leukocyte antigen (HLA-A*0201) transgenic rabbits infected ocularly with LAT
+
versus LAT
–
virus. Compared to CD8
+
T cells from LAT
–
TG, CD8
+
T cells from LAT
+
TG (i) recognized a broader selection of nonoverlapping HSV-1 epitopes, (ii) expressed higher levels of PD-1, TIM-3, and CTLA-4 markers of exhaustion, and (iii) produced less tumor necrosis factor alpha, gamma interferon, and granzyme B. These results suggest a novel immune evasion mechanism by which the HSV-1 LAT may contribute to the shaping of a broader repertoire of exhausted HSV-specific CD8
+
T cells in latently infected TG, thus allowing for increased viral reactivation.

IMPORTANCE
A significantly larger repertoire of dysfunctional (exhausted) HSV-specific CD8
+
T cells were found in the TG of HLA transgenic rabbits latently infected with wild-type HSV-1 or with LAT-rescued mutant (i.e., LAT
+
TG) than in a more restricted repertoire of functional HSV-specific CD8
+
T cells in the TG of HLA transgenic rabbits latently infected with LAT-null mutant (i.e., LAT
–
TG). These findings suggest that the HSV-1 LAT locus interferes with the host cellular immune response by shaping a broader repertoire of exhausted HSV-specific CD8
+
T cells within the latency/reactivation TG site.
A Regulatory Element Near the 3′ End of the Adeno-Associated Virus
rep
Gene Inhibits Adenovirus Replication in
cis
by Means of p40 Promoter-Associated Short Transcripts
Authors: Weger Stefan , Hammer Eva , Gonsior Melanie , Stutika Catrin , Heilbronn Regine 
Published: February 2016

ABSTRACT

Adeno-associated virus (AAV) has long been known to inhibit helper adenovirus (Ad) replication independently of AAV Rep protein expression. More recently, replication of Ad serotype 5 (Ad5)/AAV serotype 2 (AAV-2) hybrid vectors was shown to be inhibited in
cis
by a sequence near the 3′ end of AAV
rep
, termed the Rep inhibition sequence for adenoviral replication (RIS-Ad). RIS-Ad functions independently of Rep protein expression. Here we demonstrate that inhibition of adenoviral replication by RIS-Ad requires an active AAV p40 promoter and the 5′ half of the intron. In addition, Ad inhibition is critically dependent on the integrity of the p40 transcription start site (TSS) leading to short p40-associated transcripts. These do not give rise to effector molecules capable of inhibiting adenoviral replication in
trans
, like small polypeptides or microRNAs. Our data point to an inhibitory mechanism in which RNA polymerase II (Pol II) pauses directly downstream of the p40 promoter, leading to interference of the stalled Pol II transcription complex with the adenoviral replication machinery. Whereas inhibition by RIS-Ad is mediated exclusively in
cis
, it can be overcome by providing a replication-competent adenoviral genome in
trans
. Moreover, the inhibitory effect of RIS-Ad is not limited to AAV-2 but could also be shown for the corresponding regions of other AAV serotypes, including AAV-5. These findings have important implications for the future generation of Ad5/AAV hybrid vectors.

IMPORTANCE
Insertion of sequences from the 3′ part of the
rep
gene of adeno-associated virus (AAV) into the genome of its helper adenovirus strongly reduces adenoviral genome replication. We could show that this inhibition is mediated exclusively in
cis
without the involvement of
trans
-acting regulatory RNAs or polypeptides but nevertheless requires an active AAV-2 p40 promoter and p40-associated short transcripts. Our results suggest a novel inhibitory mechanism that has so far not been described for AAV and that involves stalled RNA polymerase II complexes and their interference with adenoviral DNA replication. Such a mechanism would have important implications both for the generation of adenoviral vectors expressing the AAV
rep
and
cap
genes and for the regulation of AAV gene expression in the absence and presence of helper virus.
Prime, Shock, and Kill: Priming CD4 T Cells from HIV Patients with a BCL-2 Antagonist before HIV Reactivation Reduces HIV Reservoir Size
Authors: Cummins Nathan W. , Sainski Amy M. , Dai Haiming , Natesampillai Sekar , Pang Yuan-Ping , Bren Gary D. , de Araujo Correia Maria Cristina Miranda , Sampath Rahul , Rizza Stacey A. , O'Brien Daniel , Yao Joseph D. , Kaufmann Scott H. , Badley Andrew D. 
Published: February 2016

ABSTRACT

Understanding how some HIV-infected cells resist the cytotoxicity of HIV replication is crucial to enabling HIV cure efforts. HIV killing of CD4 T cells that replicate HIV can involve HIV protease-mediated cleavage of procaspase 8 to generate a fragment (Casp8p41) that directly binds and activates the mitochondrial proapoptotic protein BAK. Here, we demonstrate that Casp8p41 also binds with nanomolar affinity to the antiapoptotic protein Bcl-2, which sequesters Casp8p41 and prevents apoptosis. Further, we show that central memory CD4 T cells (T
CM
) from HIV-infected individuals have heightened expression of BCL-2 relative to procaspase 8, possibly explaining the persistence of HIV-infected T
CM
despite generation of Casp8p41. Consistent with this hypothesis, the selective BCL-2 antagonist venetoclax induced minimal killing of uninfected CD4 T cells but markedly increased the death of CD4 T cells and diminished cell-associated HIV DNA when CD4 T cells from antiretroviral therapy (ART)-suppressed HIV patients were induced with αCD3/αCD28 to reactivate HIV
ex vivo
. Thus, priming CD4 T cells from ART suppressed HIV patients with a BCL-2 antagonist, followed by HIV reactivation, achieves reductions in cell-associated HIV DNA, whereas HIV reactivation alone does not.

IMPORTANCE
HIV infection is incurable due to a long-lived reservoir of HIV
+
memory CD4 T cells, and no clinically relevant interventions have been identified that reduce the number of these HIV DNA-containing cells. Since postintegration HIV replication can result in HIV protease generation of Casp8p41, which activates BAK, causing infected CD4 T cell death, we sought to determine whether this occurs in memory CD4 T cells. Here, we demonstrate that memory CD4 T cells can generate Casp8p41 and yet are intrinsically resistant to death induced by diverse stimuli, including Casp8p41. Furthermore, BCL-2 expression is relatively increased in these cells and directly binds and inhibits Casp8p41's proapoptotic effects. Antagonizing BCL-2 with venetoclax derepresses this antagonism, resulting in death, preferentially in HIV DNA containing cells, since only these cells generate Casp8p41. Thus, BCL-2 antagonism is a clinically relevant intervention with the potential to reduce HIV reservoir size in patients.
Ct Evaluation of Acupuncture Needles Inserted into Sacral Foramina
Authors: Katayama Yuichi , Kamibeppu Toyoharu , Nishii Ryuichi , Mukai Shoichiro , Wakeda Hironobu , Kamoto Toshiyuki 
Published: February 2016

Objective To use CT scanning to evaluate the precision with which acupuncture needles can be inserted into sacral foramina to establish sacral nerve modulation by electroacupuncture. Methods The subjects were five adult women (mean age 71.6 years). These five cases were divided into two groups. In the first three subjects (group A) the intention was to insert acupuncture needles in the S3 and S4 foramina; in the remaining two subjects (group B) the intention was to insert acupuncture needles in the S2 and S3 foramina. Results CT scanning showed that in subject 1 of group A, the acupuncture needle intended for insertion in S3 was actually in the S4 foramen, and the acupuncture needle intended for insertion in S4 was actually distal to the sacral body. In subjects 2 and 3, the acupuncture needles were inserted accurately in the S3 and S4 foramina. In the three subjects who had acupuncture needles inserted in the S4 foramen, the tip of the acupuncture needle was an average distance of 6.0 mm from the rectum. The acupuncture needles inserted in subjects 4 and 5 of group B were inserted accurately into the S2 and S3 foramina. Conclusions Inserting acupuncture needles into the sacral foramina of S2 and S3 at an angle of about 60° has the potential to be used for sacral nerve modulation by repeated electroacupuncture stimulation. Needling may be less accurate in subjects with higher body mass index. Because of the potential risk of perforating the rectum with the needle, this technique must be used by specialists only. Trial Registration Number 2013-026
A combination of initial and follow-up physiotherapist examination predicts physician-determined time to return to play after hamstring injury, with no added value of MRI
Authors: Jacobsen Phil , Witvrouw Erik , Muxart Patrice , Tol Johannes L , Whiteley Rod 
Published: February 2016

BackgroundPrevious studies investigating prediction of return to play after acute hamstring injury were limited by examining a single postinjury clinical and MRI evaluation. We evaluated the added value of including follow-up clinical evaluation when predicting return to play.MethodsA range of clinical and MRI parameters were prospectively investigated for an association with the time to return to play in 90 athletes with MRI positive hamstring injuries undergoing a criteria-based rehabilitation programme. Clinical evaluation was performed within 5 days of injury and 7 days after this initial assessment (follow-up clinical evaluation). The association between possible prognostic parameters and the time to return to play was assessed with a multiple linear regression model.ResultsData of 90 athletes were available for analysis. At the first physiotherapy appointment, a combination of three demographic and six clinical variables explained 50% of the variance (±19 days) in the time to return to play. At follow-up assessment (7 days), a combination of 10 clinical and demographic variables explained 97.0% of the variance (±5 days) in time to return to play. In order of importance, the variables were: change in strength during the first week for the ‘mid-range’ test, peak isokinetic knee flexion torque of the uninjured leg, maximum pain at the time of injury, number of days to walk pain free, playing the sport of football, strength performing the ‘inner range’ hamstring test at day 1, presence of pain on a single leg bridge at day 7 or its absence during a single leg bridge, delay in starting treatment and percentage of strength in the ‘outer range’ test compared to the healthy leg. No MRI variables were retained in any of these analyses. MRI variables alone explained 8.6% of the variance—which is unhelpful to players and coaches.SummaryThe combination of initial and 7-day follow-up clinical evaluation is clinically helpful in predicting time to return to play (±5 days) following acute hamstring injury. MRI offered no useful clinical information regarding return to play duration in this cohort.Trial registration numberNCT01812564.
Conducting a fully mobile and randomised clinical trial for depression: access, engagement and expense
Authors: Anguera Joaquin A , Jordan Joshua T , Castaneda Diego , Gazzaley Adam , Areán Patricia A 
Published: February 2016

ImportanceAdvances in mobile technology have resulted in federal and industry-level initiatives to facilitate large-scale clinical research using smart devices. Although the benefits of technology to expand data collection are obvious, assumptions about the reach of mobile research methods (access), participant willingness to engage in mobile research protocols (engagement), and the cost of this research (cost) remain untested.ObjectiveTo assess the feasibility of a fully mobile randomised controlled trial using assessments and treatments delivered entirely through mobile devices to depressed individuals.DesignUsing a web-based research portal, adult participants with depression who also owned a smart device were screened, consented and randomised to 1 of 3 mental health apps for treatment. Assessments of self-reported mood and cognitive function were conducted at baseline, 4, 8 and 12 weeks. Physical and social activity was monitored daily using passively collected phone use data. All treatment and assessment tools were housed on each participant's smart phone or tablet.InterventionsA cognitive training application, an application based on problem-solving therapy, and a mobile-sensing application promoting daily activities.ResultsAccess: We screened 2923 people and enrolled 1098 participants in 5 months. The sample characteristics were comparable to the 2013 US census data. Recruitment via Craigslist.org yielded the largest sample.Engagement: Study engagement was high during the first 2 weeks of treatment, falling to 44% adherence by the 4th week.Cost: The total amount spent on for this project, including staff costs and β testing, was $314 264 over 2 years.Conclusions and relevanceThese findings suggest that mobile randomised control trials can recruit large numbers of participants in a short period of time and with minimal cost, but study engagement remains challenging.Trial registration numberNCT00540865.
Impact of wearable technology on psychosocial factors of osteoarthritis management: a qualitative study
Authors: Belsi Athina , Papi Enrica , McGregor Alison H 
Published: February 2016

ObjectivesTo identify the impact the use of wearable technology could have in patients with osteoarthritis in terms of communication with healthcare providers and patients’ empowerment to manage their condition.DesignQualitative study using focus groups with patients with osteoarthritis; data from patients’ responses were analysed using Framework Methodology.Participants21 patients with knee osteoarthritis from the London area (age range 45–65 years) participated in a total of four focus groups. Recruitment continued until data saturation.SettingThe study was conducted in a university setting.ResultsPatients’ responses suggested a positive attitude on the impact wearable technology could have on the management of osteoarthritis. It was perceived that the use of wearable devices would benefit patients in terms of feeling in control of their condition, providing them with awareness of their progress, empowering in terms of self-management and improving communication with their clinician.ConclusionsThis paper suggests positive patient perspectives on the perceived benefits wearable technology could have on the management of osteoarthritis. The data that could be collected with the use of wearable technology could be beneficial both to patients and clinicians. The information obtained from this study suggests that introducing wearable technology into patient-centred care could enhance patient experience in the field of osteoarthritis and beyond.
Do patients with lung cancer recall physician-initiated discussions about planning for end-of-life care following disclosure of a terminal prognosis?
Authors: Horne Gillian , Payne Sheila , Seymour Jane 
Published: February 2016

BackgroundCommunicating with patients about their prognosis and goals of care, including offering opportunities to engage in advance care planning (ACP) is widely recognised as best practice. Little is known about terminally ill patients’ perceptions of communication and ACP practice following disclosure of their terminal prognosis.ObjectivesTo examine whether terminally ill patients with lung cancer and their relatives recall conversations with disclosing physicians, about their concerns, goals of care or any offers to engage in ACP.MethodsQualitative study using semistructured interviews with patients and their family members. The study setting was a cancer centre and cancer unit in northern England.Results25 patients with advanced lung cancer (18 men and 7 women, aged 47–85) and 19 family members, mainly from lower social economic classes, took part in the study. Participants had little or no recall of physicians initiating discussions about their concerns, or goals of care and did not perceive that they had been provided with either information about or opportunities to engage in ACP. Some participants reported a sense of abandonment following the disclosure of a terminal prognosis. This sense was compounded by a range of difficult emotional experiences following the disclosure.ConclusionsIt may be inappropriate to initiate discussions about end-of-life care planning immediately following the disclosure of a terminal prognosis. To avoid patients feeling abandoned physicians need to consider how they or another appropriate person can provide information and opportunities for terminally ill patients to engage in a process of ACP.Trial registration number06/Q2307/22.
New insulins and newer insulin regimens: a review of their role in improving glycaemic control in patients with diabetes
Authors: Gururaj Setty S , Crasto W , Jarvis J , Khunti K , Davies M J 
Published: February 2016

AbstractThe legacy effect of early good glycaemic control in people with diabetes shows it is associated with reduction of microvascular and macrovascular complications. Insulin therapy is essential and lifesaving in individuals with type 1 diabetes and beneficial for those with type 2 diabetes who fail to achieve optimal glycaemic targets with other classes of glucose-lowering therapies. Since the introduction of insulin analogues, insulin management has changed. This follow-up review attempts to update our earlier publication from 2009 and discusses the role of new insulin analogues and newer insulin regimens. Recognising the advent of new quality and economic initiatives both in the UK and worldwide, this paper reviews current insulin prescribing and the pros and cons of prescribing analogues in comparison to the human insulins that are now gaining more acceptance in everyday clinical practice.