bluuebunny/crossref_metadata_2025_split huggingface dataset:
CD226 regulates natural killer cell antitumor responses via phosphorylation-mediated inactivation of transcription factor FOXO1
Authors: Du Xiangnan , de Almeida Patricia , Manieri Nick , de Almeida Nagata Denise , Wu Thomas D. , Harden Bowles Kristin , Arumugam Vidhyalakshmi , Schartner Jill , Cubas Rafael , Mittman Stephanie , Javinal Vincent , Anderson Keith R. , Warming Søren , Grogan Jane L. , Chiang Eugene Y. 
Published: December 2018

Significance
CD226 is an important activating receptor involved in mediating natural killer (NK) cell responses against tumors, but how CD226 exerts control over NK cell function is not fully understood. CD226 belongs to the poliovirus receptor (PVR)-nectin family that includes TIGIT and CD96, with TIGIT garnering much attention as a key checkpoint in T cell and NK cell antitumor responses and as an immunotherapy target. Thus, it is imperative to determine how CD226 counteracts the actions of TIGIT and CD96 with which it competes for binding to its ligands such as CD155 (PVR). We demonstrate that CD226 engagement of CD155 is required for phosphorylation of transcription factor FOXO1, resulting in inactivation of its negative regulatory control over NK cell effector function.
Parental Participation in Juvenile Justice Institutions: Parents’ Perspectives on Facilitating and Hindering Factors
Authors: Simons Inge , van der Vaart Wander , Vermeiren Robert , Rigter Henk , Breuk René , van Domburgh Lieke , Mulder Eva 
Published: December 2018

Background: Participation of parents during their adolescent’s detention is important for achieving positive treatment outcomes for youths and their families. To improve parental participation, insight in facilitating or hindering factors is necessary. To this end, we studied the perspectives of parents of adolescents detained in two juvenile justice institutions in the Netherlands. Methods: Data were collected from 19 purposefully selected parents through semi-structured interviewing. The interviews were transcribed verbatim and imported into ATLAS.ti where data were coded and analyzed. Results: Parental participation is influenced by a variety of factors that could be categorized based on the following themes: (1) practical facilitating or obstructing factors; (2) parent-related emotional and mental factors; and (3) factors concerning issues of the parent-adolescent relationship. Discussion: Insight into the factors which facilitate and obstruct participation might help JJI staff understand differences in parental participation. This may enable them to tailor solutions which would improve parental participation during their adolescent’s detention.
GEMPROT: visualization of the impact on the protein of the genetic variants found on each haplotype
Authors: Cuppens Tania , Ludwig Thomas E , Trouvé Pascal , Genin Emmanuelle 
Published: December 2018

Abstract

Summary
When analyzing sequence data, genetic variants are considered one by one, taking no account of whether or not they are found in the same individual. However, variant combinations might be key players in some diseases as variants that are neutral on their own can become deleterious when associated together. GEMPROT is a new analysis tool that allows, from a phased vcf file, to visualize the consequences of the genetic variants on the protein. At the level of an individual, the program shows the variants on each of the two protein sequences and the Pfam functional protein domains. When data on several individuals are available, GEMPROT lists the haplotypes found in the sample and can compare the haplotype distributions between different sub-groups of individuals. By offering a global visualization of the gene with the genetic variants present, GEMPROT makes it possible to better understand the impact of combinations of genetic variants on the protein sequence.

Availability and implementation
GEMPROT is freely available at https://github.com/TaniaCuppens/GEMPROT. An on-line version is also available at http://med-laennec.univ-brest.fr/GEMPROT/.

Supplementary information
Supplementary data are available at Bioinformatics online.
Protein–protein interaction sites prediction by ensemble random forests with synthetic minority oversampling technique
Authors: Wang Xiaoying , Yu Bin , Ma Anjun , Chen Cheng , Liu Bingqiang , Ma Qin 
Published: December 2018

Abstract

Motivation
The prediction of protein–protein interaction (PPI) sites is a key to mutation design, catalytic reaction and the reconstruction of PPI networks. It is a challenging task considering the significant abundant sequences and the imbalance issue in samples.

Results
A new ensemble learning-based method, Ensemble Learning of synthetic minority oversampling technique (SMOTE) for Unbalancing samples and RF algorithm (EL-SMURF), was proposed for PPI sites prediction in this study. The sequence profile feature and the residue evolution rates were combined for feature extraction of neighboring residues using a sliding window, and the SMOTE was applied to oversample interface residues in the feature space for the imbalance problem. The Multi-dimensional Scaling feature selection method was implemented to reduce feature redundancy and subset selection. Finally, the Random Forest classifiers were applied to build the ensemble learning model, and the optimal feature vectors were inserted into EL-SMURF to predict PPI sites. The performance validation of EL-SMURF on two independent validation datasets showed 77.1% and 77.7% accuracy, which were 6.2–15.7% and 6.1–18.9% higher than the other existing tools, respectively.

Availability and implementation
The source codes and data used in this study are publicly available at http://github.com/QUST-AIBBDRC/EL-SMURF/.

Supplementary information
Supplementary data are available at Bioinformatics online.
Prevalence of Human Papillomavirus, Human Immunodeficiency Virus, and Other Sexually Transmitted Infections Among Men Who Have Sex With Men in Togo: A National Cross-sectional Survey
Authors: Ferré Valentine Marie , Gbeasor-Komlanvi Fifonsi A , Collin Gilles , Dagnra Anoumou Claver , Le Hingrat Quentin , Jaquet Antoine , Salou Mounerou , Descamps Diane , Charpentier Charlotte , Ekouevi Didier Koumavi 
Published: December 2018

Abstract

Background
Sub-Saharan Africa is a region of both high human immunodeficiency virus (HIV) and anal cancer incidence. We conducted the first national study in Togo to assess human papillomavirus (HPV), HIV, and other sexually transmitted infection (STI) prevalence among men who have sex with men (MSM).

Methods
A multicentric cross-sectional study was conducted among MSM recruited in 4 Togolese cities. Anal swabs were collected to test HPV, herpes simplex virus (HSV), and 7 STIs.

Results
Among the 207 MSM, HIV and high-risk HPV (hrHPV) overall prevalence were 26.1% and 44.9%, respectively. The most common hrHPV types were HPV-35 (15.0%) and HPV-16 (13.0%). Prevalence of hrHPV and multiple HPV infections were higher among HIV-infected than among HIV-uninfected MSM (85.2% vs 30.7%, P < 10–5 and 85.2% vs 28.7%, P < 10–5, respectively). Other STIs, except hepatitis B virus, were also more prevalent among HIV-infected MSM (Neisseria gonorrhoeae, P = .03; Mycoplasma genitalium, P = .04; HSV-2, P = .001; and a trend for Chlamydia trachomatis, P = .06). In multivariate analysis (adjusted odds ratio [95% confidence interval]), HIV (10.1 [4.0–25.6]), living in Lomé (2.8 [1.1–7.1]), HSV-2 excretion (26.7 [2.9–244.3]), C. trachomatis (11.7 [2.3–58.9]), and M. genitalium infection (9.6 [3.1–29.9]) were associated with increased risk of hrHPV infection.

Conclusions
We report a high burden of anal STIs with an unusual hrHPV type distribution among MSM, highlighting the critical need of implementation of a national strategy regarding prevention of STIs and vaccination against HPV.
Blood Viral Load in Symptomatic Congenital Cytomegalovirus Infection
Authors: Marsico Concetta , Aban Immaculada , Kuo Huichien , James Scott H , Sanchez Pablo J , Ahmed Amina , Arav-Boger Ravit , Michaels Marian G , Ashouri Negar , Englund Janet A , Estrada Benjamin , Jacobs Richard F , Romero José R , Sood Sunil K , Whitworth Suzanne , Jester Penelope M , Whitley Richard J , Kimberlin David W ,   Collaborative Antiviral Study Group (CASG)
Published: December 2018

AbstractBackgroundViral loads (VLs) frequently are followed during treatment of symptomatic congenital cytomegalovirus disease, but their predictive value is unclear.MethodsPost hoc analysis of 2 antiviral studies was performed. Seventy-three subjects were treated for 6 weeks and 47 subjects were treated for 6 months. Whole blood VL was determined by real-time polymerase chain reaction before and during therapy.ResultsHigher baseline VL was associated with central nervous system involvement (3.82 log, range 1–5.65 vs 3.32 log, range 1–5.36; P = .001), thrombocytopenia (3.68 log, range 1–5.65 vs 3.43 log, range 1–5.36; P = .03), and transaminitis at presentation (3.73 log, range 1–5.60 vs 3.39 log, range 1–5.65; P = .009), but with overlap in the amount of virus detected between groups. In subjects treated for 6 months, lower VL at presentation correlated with better hearing outcomes at 12 months, but VL breakpoints predictive of hearing loss were not identified. Sustained viral suppression during 6 months of therapy correlated with better hearing outcomes at 6, 12, and 24 months (P = .01, P = .0007, P = .04), but a majority without viral suppression still had improved hearing.ConclusionsIn infants with symptomatic congenital cytomegalovirus disease, higher whole blood VL before initiation of antiviral therapy has no clinically meaningful predictive value for long-term outcomes.
Validation of the St. Paul’s Endoscopy Comfort Scale (SPECS) for Colonoscopy
Authors: Telford Jennifer , Tavakoli Iran , Takach Oliver , Kwok Ricky , Harris Natasha , Yonge Jordan , Galorpart Cherry , Whittaker Scott , Amar Jack , Rosenfeld Gregory , Ko Hin Hin , Lam Eric , Ramji Alnoor , Bressler Brian , Enns Robert 
Published: December 2018

Abstract

Aims
Patient comfort during colonoscopy is an important measure of quality, which can improve patient satisfaction and compliance with future procedures. Our aim was to develop and validate a pain assessment tool based on objective behavioural cues tailored to outpatients undergoing colonoscopy: St. Paul’s endoscopy comfort score (SPECS).

Methods
A single-centre, prospective study was conducted in consecutive adults undergoing planned outpatient colonoscopy. Patient comfort was independently assessed by the physician, nurse and a research assistant (observer) using the SPECS and the Gloucester scale (GS). In addition, the nurse-assessed patient comfort score (NAPCOMS), nonverbal pain Assessment tool (NPAT) and Richmond agitation sedation scale (RASS) were completed by the observer. Data on subject demographics, sedation dose and duration of the procedure were collected. Following the procedure, patients completed a patient satisfaction questionnaire, including a visual analogue scale (VAS) to measure their overall perceived pain during the procedure.

Results
The study enrolled 350 subjects. The SPECS showed excellent inter-rater reliability among all three raters with an intra-class coefficient (ICC) of 0.81 (95% CI, 0.78–0.84), while the GS showed good reliability with an ICC of 0.77 (95% CI, 0.73–0.80). The SPECS demonstrated moderate agreement with the patient-reported VAS ratings.

Conclusions
The St. Paul’s endoscopy comfort score was successfully validated, demonstrating excellent inter-rater reliability.
Unequivocal identification of an underestimated opportunistic yeast species, Cyberlindnera fabianii, and its close relatives using a dual-function PCR and literature review of published cases
Authors: Arastehfar Amir , Fang Wenjie , Al-Hatmi Abdullah M S , Afsarian Mohammad Hosein , Daneshnia Farnaz , Bakhtiari Mina , Sadati Sara Khanjari , Badali Hamid , Khodavaisy Sadegh , Hagen Ferry , Liao Wanqing , Pan Weihua , Zomorodian Kamiar , Boekhout Teun 
Published: December 2018

Abstract
Although Cyberlindnera fabinaii is a rare opportunist yeast species, its ability to cause septicemia, produce biofilm, and rapid acquisition of resistance to fluconazole and voriconazole, reinforced the urge for its identification from its closely related species. Widely used biochemical assays mainly identify Cyberlindnera fabinaii as Cyberlindnera jadinii and Wickerhamomyces anomalus, resulting in underestimation of this yeast in clinical settings. Moreover, the urge for a reliable molecular means of identification remains unsolved for 28 years. In order to unequivocally differentiate Cy. fabianii, Cy. mississipiensis, Cy. jadinii, and W. anomalus, we designed a dual-function multiplex polymerase chain reaction (PCR) assay. Challenging our dual-function multiplex PCR assay with 30 most clinically important yeast species, proved its specificity. Although conventional PCR could differentiate four target species, the real-time PCR counterpart due to Tm overlap misidentified Cy. mississipiensis as Cy. jadinii. Alongside of presenting a comprehensive literature review of published cases of Cy. fabianii from 1990 to 2018, we collected various clinical isolates from Tehran, Shiraz, and Fasa (July 1, 2017, to December 31, 2017) to find a passive relative distribution of these closely-related species in Iran. Subjecting our Iranian collection of yeast isolates to matrix-assisted laser desorption/ionization–time of flight (MALDI-TOF) MS and LSU and ITS rDNA sequencing revealed six isolates of Cy. fabianii (central venous catheter n = 2 and vaginal swabs n = 4) and one isolate of Cy. jadinii (vaginal swabs). Due to the use of biochemical assays in global ARTEMIS study, we encourage reidentification of clinical isolates of Cy. jadinii and Cy. jadinii using MALDI-TOF or Sanger sequencing that might lead to correcting the distribution of this fungus.
The association of health-related quality of life and cognitive function in patients receiving memantine for the prevention of cognitive dysfunction during whole-brain radiotherapy
Authors: Laack Nadia N , Pugh Stephanie L , Brown Paul D , Fox Sherry , Wefel Jeffrey S , Meyers Christina , Choucair Ali , Khuntia Deepak , Suh John H , Roberge David , Wendland Merideth M , Bruner Deborah 
Published: December 2018

Abstract

Background
This study evaluated the association between health-related quality of life (HRQOL) and cognition in patients receiving memantine for prevention of cognitive dysfunction during whole-brain radiotherapy (WBRT).

Methods
Adult patients with brain metastases received WBRT and were randomized to receive placebo or memantine, 20 mg per day, within 3 days of initiating radiotherapy, for 24 weeks. The Functional Assessment of Cancer Therapy-Brain module (FACT-Br) and Medical Outcomes Scale-Cognitive Functioning Scale (MOS-C) were completed in coordination with serial standardized tests of cognitive function.

Results
Of the 508 eligible patients, 442 (87%) consented to participate in the HRQOL portion and contributed to baseline analyses. Evaluable patients at 24 weeks (n = 246) included surviving patients completing FACT-Br, MOS-C, and objective cognitive assessments (n = 146, 59%) and patients alive at time of missed assessment (n = 100, 41%). Baseline cognitive function correlated significantly with FACT-Br and MOS-C self-reports. All domains of objective cognitive function showed declines over time. Neither FACT-Br nor MOS-C differed between the treatment arms. Emotional and functional well-being subscales of the FACT improved over time while the remainder of the FACT-Br domains remained stable. MOS-C scores declined over time.

Conclusion
Baseline cognitive function correlated significantly with FACT-Br and MOS-C scores. No by-arm differences in HRQOL were observed despite differences in objective cognitive function. Patient attrition and poor testing compliance remain significant problems in studies of cognitive function of brain metastases patients and further effort is needed to improve compliance with testing and sensitivity of patient-reported measures.
The use of ultrasound to measure muscle depth and area in postmortem Holstein dairy calves
Authors: Davis Jessica H , Rossow Heidi A 
Published: December 2018

Abstract
Monitoring growth of neonatal dairy calves is a useful management tool to assist producers in achieving goals for reproduction and performance. The goal of this study was to examine ultrasound as an in vivo tool to quantify longissimus dorsi muscle (ribeye) linear depth and extensor carpi radialis (ECR) and semitendinosus (ST) muscle cross-sectional areas in postmortem preweaned Holstein calves. Postmortem preweaned calves (n = 137, age 13.1 d ± 15.5 SD, body weight 36.5 kg ± 7.2 SD) were obtained from two California calf ranches between April and July 2013. Two operators collected ultrasound images of the ribeye, ECR, and ST muscles using an Aloka 500V equipped with a 5-cm 7.5-MHz linear transducer. Ultrasound ribeye linear depth and ECR and ST cross-sectional areas were calculated using the Ultrasound Image Capture System. Ultrasound measurements were compared to dissected (carcass) measures. Carcass ribeye linear depth was estimated using a ruler. Dissected ECR and ST muscle cross-sectional areas were estimated by tracing muscle cross sections onto transparency paper and then photocopying, cutting out, and weighing individual paper muscle tracings. Weights of the tracings were then converted to areas using the known area of a standard 8.5 × 11 inch paper. Data were analyzed by regressing carcass estimates on observed ultrasound measurements. The coefficient of determination (R2) indicated that ultrasound measurements were most closely associated with carcass measurements for the ST muscle (R2 = 0.60, 0.62 for operator 1 and 2, respectively) when compared to the ribeye and ECR muscles (R2 = 0.27, 0.41 for ribeye and 0.43, 0.32 for ECR for operator 1 and 2, respectively). The mean bias showed consistent underestimation by the ultrasound measurements when predicting carcass measurements for all three muscles and for both operators (ribeye bias = 0.15, 0.40; ECR bias = 0.95, 1.15; and ST bias = 0.73, 0.27 for operator 1 and 2, respectively). Operator contributed significantly in explaining a proportion of the variation in the regression equation for the ST muscle only, whereas calf body weight contributed significantly in explaining a proportion of the variation in the regression equation for all three muscles. The results of this study demonstrated that ultrasound measurements of the ST were the most accurate for quantifying the cross-sectional area when compared to both the ECR and ribeye in postmortem Holstein calves.
Prospective Evaluation of a Rapid Functional Assay for Heparin-Induced Thrombocytopenia Diagnosis in Critically Ill Patients*
Authors: Gkalea Vasiliki , Khaterchi Amir , Levy Pierre , Jourdi Georges , Elalamy Ismail 
Published: December 2018

Objectives:
Overdiagnosis of heparin-induced thrombocytopenia remains an unresolved issue in the ICU leading to the unjustified switch from heparin to alternative anticoagulants or delays in anticoagulation. Platelet function assays significantly improve the specificity of heparin-induced thrombocytopenia diagnosis, but they are not readily available, involve technical difficulties and have a long turnaround time. We evaluated the performance of a rapid and easy to perform functional assay for heparin-induced thrombocytopenia diagnosis in ICU patients, known as “heparin-induced multiple electrode aggregometry.”

Design:
In this observational prospective study patients were tested with the immunoglobulin G enzyme-linked immunosorbent assay, the serotonin release assay and heparin-induced multiple electrode aggregometry. Heparin-induced multiple electrode aggregometry was assessed against heparin-induced thrombocytopenia diagnosis (clinical picture in favor, serotonin release assay, and immunoglobulin G enzyme-linked immunosorbent assay positive) and serotonin release assay.

Setting:
Medical or surgical ICU of 35 medical centers.

Patients:
Patients suspected for heparin-induced thrombocytopenia hospitalized in medical or surgical ICU from January 2013 to May 2013.

Interventions:
None.

Measurements and Main results:
Heparin-induced thrombocytopenia diagnosis was retained in 12 patients (14%). Using heparin-induced thrombocytopenia diagnosis as reference, heparin-induced multiple electrode aggregometry showed an excellent negative predictive value and sensitivity, at 98% and 92% respectively. Its positive predictive value and specificity were 100%. Receiver operating characteristic analysis with the serotonin release assay as reference showed an optimal heparin-induced multiple electrode aggregometry cut-off at 1,300 AU × minutes (specificity, 100%; sensitivity, 90%; area under the curve, 0.98; 95% CI, 0.95–1.0). The Kappa coefficient between heparin-induced multiple electrode aggregometry and the serotonin release assay was at 0.90%.

Conclusions:
Heparin-induced multiple electrode aggregometry performed very well in heparin-induced thrombocytopenia diagnosis in ICU patients and agreed with the gold standard test for heparin-induced thrombocytopenia diagnosis, the serotonin release assay. Heparin-induced multiple electrode aggregometry is a reliable and rapid platelet functional assay that could decrease heparin-induced thrombocytopenia overdiagnosis in the ICU setting.
Prediction of ICU Delirium: Validation of Current Delirium Predictive Models in Routine Clinical Practice*
Authors: Green Cameron , Bonavia William , Toh Candice , Tiruvoipati Ravindranath 
Published: December 2018

Objectives:
To investigate the ability of available delirium risk assessment tools to identify patients at risk of delirium in an Australian tertiary ICU.

Design:
Prospective observational study.

Setting:
An Australian tertiary ICU.

Patients:
All patients admitted to the study ICU between May 8, 2017, and December 31, 2017, were assessed bid for delirium throughout their ICU stay using the Confusion Assessment Method for ICU. Patients were included in this study if they remained in ICU for over 24 hours and were excluded if they were delirious on ICU admission, or if they were unable to be assessed using the Confusion Assessment Method for ICU during their ICU stay. Delirium risk was calculated for each patient using the prediction of delirium in ICU patients, early prediction of delirium in ICU patients, and Lanzhou models. Data required for delirium predictor models were obtained retrospectively from patients medical records.

Interventions:
None.

Measurements and Main Results:
There were 803 ICU admissions during the study period, of which 455 met inclusion criteria. 35.2% (n = 160) were Confusion Assessment Method for ICU positive during their ICU admission. Delirious patients had significantly higher Acute Physiology and Chronic Health Evaluation III scores (median, 72 vs 54; p < 0.001), longer ICU (median, 4.8 vs 1.8 d; p < 0.001) and hospital stay (16.0 vs 8.16 d; p < 0.001), greater requirement of invasive mechanical ventilation (70% vs 21.4%; p < 0.001), and increased ICU mortality (6.3% vs 2.4%; p = 0.037). All models included in this study displayed moderate to good discriminative ability. Area under the receiver operating curve for the prediction of delirium in ICU patients was 0.79 (95% CI, 0.75–0.83); recalibrated prediction of delirium in ICU patients was 0.79 (95% CI, 0.75–0.83); early prediction of delirium in ICU patients was 0.72 (95% CI, 0.67–0.77); and the Lanzhou model was 0.77 (95% CI, 0.72–0.81).

Conclusions:
The predictive models evaluated in this study demonstrated moderate to good discriminative ability to predict ICU patients’ risk of developing delirium. Models calculated at 24-hours post-ICU admission appear to be more accurate but may have limited utility in practice.