bluuebunny/crossref_metadata_2025_split huggingface dataset:
Uromodulin–SlpA binding dictates Lactobacillus acidophilus uptake by intestinal epithelial M cells
Authors: Yanagihara Sae , Kanaya Takashi , Fukuda Shinji , Nakato Gaku , Hanazato Misaho , Wu Xue-Ru , Yamamoto Naoyuki , Ohno Hiroshi 
Published: July 2017

Abstract
Bacterial access to the gut immune system is a crucial process to promote host immune responses. The probiotic L-92 strain of Lactobacillus acidophilus exerts anti-allergic immunomodulatory effects upon oral administration in mice. Here, we show that microfold cells (M cells) are responsible for L-92 internalization for evoking L-92-mediated immune responses. L-92 specifically bound to uromodulin, a glycosylphosphatidylinositol-anchored protein expressed exclusively on M cells among intestinal epithelial cells. Internalization of L-92 into M cells was significantly reduced in uromodulin-deficient (Umod−/−) mice compared to Umod+/+ mice. Furthermore, the binding of L-92 to uromodulin was significantly decreased after removal of surface layer protein A (SlpA) from the bacteria. Our study thus revealed a crucial role of uromodulin on the M-cell surface for the uptake of SlpA-positive lactic acid bacteria into M cells, possibly leading to subsequent delivery of the bacteria to dendritic cells closely associated with M cells for immunomodulation. Our study also shed light on the possibility that SlpA and uromodulin could be used as vehicle and target, respectively, for efficient mucosal vaccine delivery.
In Vitro Compatibility of Contact Lenses With Corneal Epithelial Cells
Authors: Vijay Ajay K. , Fadli Zohra , Lakkis Carol , Coles-Brennan Chantal , Willcox Mark D. P. 
Published: July 2017

Purpose:
To determine the interaction of contact lenses of different materials with corneal epithelial cells grown in tissue culture.

Methods:
Two different corneal epithelial cell lines were grown to confluence in culture media. Two hydrogel contact lenses with and without polyvinylpyrrolidone (PVP) {1-DAY ACUVUE MOIST (1-Day ACUVUE [hydrogel lenses]) and a silicone hydrogel contact lens, AIR OPTIX NIGHT & DAY} were removed from their blister packs, washed in phosphate-buffered saline, and applied to the cells. After exposure for 24 hr at 37°C, lenses were removed, and the corneal cells and supernatants processed. Supernatants from the cell assays were used to quantify the amount of 17 different cytokines that were produced using a multiplex bead assay. Cells were stained to assess amount of cell death (apoptosis or necrosis) or stained to determine the level of mitochondrial activity. Stimulants of necrotic death (latex) or apoptotic death (sorbitol) were used as positive controls.

Results:
Cells produced cytokines during normal growth. Exposure of cells to the hydrogel lenses resulted in only minimal changes to normal production of cytokines, but latex or sorbitol produced the most change. Exposure of the cells to all three lenses caused 4% to 23% reduction in mitochondrial activity, whereas exposure to the positive controls caused 71% to 98% reduction in mitochondrial activity. Exposure of the corneal epithelial cells to contact lenses produced minimal morphological changes, whereas exposure to latex or sorbitol produced significant changes to the human corneal epithelial cell line.

Conclusions:
Exposure of corneal epithelial cells to contact lenses had minimal impact on their physiology. There was no difference in epithelial cell responses to hydrogel with or without PVP compared with the silicone hydrogel contact lens.
Osteoarticular Infections Caused by Streptococcus pneumoniae in Children in the Post–Pneumococcal Conjugate Vaccine Era
Authors: Olarte Liset , Romero Jose , Barson William , Bradley John , Lin Philana Ling , Givner Laurence , Tan Tina , Hoffman Jill , Hultén Kristina G. , Mason Edward O. , Kaplan Sheldon L. 
Published: July 2017

Background:
Pneumococcal osteoarticular infections (OAIs) are an uncommon manifestation of invasive pneumococcal disease (IPD). We describe the demographic characteristics, hospitalization rate, serotype distribution and antibiotic susceptibility of children with pneumococcal OAI over a 16-year period.

Methods:
We identified patients ≤18 years old with pneumococcal OAI at 8 children’s hospitals in the United States (2000–2015). Pneumococcal isolates were collected prospectively. Serotyping and antibiotic susceptibility were performed in a central laboratory.

Results:
We identified 97 (3.3%) patients with pneumococcal OAI out of 2943 patients with IPD. Over 60% of the children were <2 years old. Septic arthritis (56.7%, 55/97) was the most common pneumococcal OAI, followed by osteomyelitis (25.8%, 25/97) and septic arthritis with concomitant osteomyelitis (17.5%, 17/97). Hospitalization for pneumococcal OAI overall decreased from 6.8 [95% confidence interval (CI): 5.2–8.6] to 4.4 (95% CI: 3.0–6.3) per 100,000 admissions from 2000–2009 to 2010–2015 (–35%, P = 0.05). Hospitalization for pneumococcal OAI caused by PCV13 serotypes decreased from 4.6 (95% CI: 3.4–6.2) to 0.9 (95% CI: 0.3–1.9) per 100,000 admissions from 2000–2009 to 2010–2015 (–87%, P < 0.0001). Overall, 12% of isolates had a penicillin minimal inhibitory concentration> 2 µg/mL, 3% a ceftriaxone minimal inhibitory concentration> 1 µg/mL and 15% were clindamycin resistant; these proportions remained unchanged after the introduction of PCV13. Serotypes 19A and 35B were responsible for penicillin and ceftriaxone nonsusceptible isolates in 2010–2015.

Conclusions:
Pneumococcal OAI represents 3% of all IPD, affecting mainly healthy infants and young children. Hospitalization for pneumococcal OAI caused by PCV13 serotypes dramatically decreased (–87%) after the introduction of PCV13.
Marked Underreporting of Pertussis Requiring Hospitalization in Infants as Estimated by Capture–Recapture Methodology, Germany, 2013–2015
Authors: Schielke Anika , Takla Anja , von Kries Rüdiger , Wichmann Ole , Hellenbrand Wiebke 
Published: July 2017

Background:
In Germany, pertussis became notifiable in eastern federal states in 2002 and nationwide in March 2013. Infants are at greatest risk for severe disease, with a high proportion requiring hospitalization. We implemented enhanced hospital-based surveillance to estimate the incidence of pertussis requiring hospitalization among infants in Germany and to determine the proportion of infants hospitalized with pertussis too young to have been vaccinated.

Methods:
Enhanced surveillance was implemented within a nationwide hospital surveillance network (ESPED). We defined cases as children less than 1 year of age hospitalized due to laboratory-confirmed pertussis with disease onset from 01/07/2013-30/06/2015. We matched cases to those ascertained in the national statutory notification system, and estimated incidence using capture-recapture methodology.

Results:
The estimated annual incidence of pertussis requiring hospitalization in infants was 52/100,000 infants (95% confidence interval [CI] 48-57/100,000), with 39% under-reporting to the national notification system. During the two epidemiologic years under-reporting decreased from 46% to 32% and was lower in eastern than western federal states (21% vs. 40%). Within ESPED, 154 of 240 infants (64%) were younger than or still at the age recommended for the first vaccine dose; 55 (23%) could have received one or more vaccine doses. Median length of hospitalization was 9 days (IQR 5-13 days) and 18% required intensive care treatment.

Conclusions:
Our study revealed a high burden of pertussis in infants with marked under-reporting, especially in western federal states where notification was only recently established. Strategies for the prevention of severe pertussis.
Effect of E-Bike Versus Bike Commuting on Cardiorespiratory Fitness in Overweight Adults: A 4-Week Randomized Pilot Study
Authors: Höchsmann Christoph , Meister Steffen , Gehrig Damiana , Gordon Elisa , Li Yanlei , Nussbaumer Monique , Rossmeissl Anja , Schäfer Juliane , Hanssen Henner , Schmidt-Trucksäss Arno 
Published: July 2017

Objective:
To assess if active commuting with an electrically assisted bicycle (e-bike) during a 4-week period can induce increases in cardiorespiratory fitness measured as peak oxygen uptake (V̇o
2peak) in untrained, overweight individuals, and if these changes are comparable with those induced by a conventional bicycle.

Design:
Four-week randomized pilot study.

Setting:
Controlled laboratory.

Participants:
Thirty-two volunteers (28 men) participated. Seventeen {median age 37 years [interquartile range (IQR) 34, 45], median body mass index [BMI] 29 kg/m2 [IQR 27, 31]} were randomized to the E-Bike group and 15 [median age 43 years (IQR 38, 45), median BMI 28 kg/m2 (IQR 26, 29)] to the Bike group.

Interventions:
Participants in both groups were instructed to use the bicycle allocated to them (e-bike or conventional bicycle) for an active commute to work in the Basel (Switzerland) area at a self-chosen speed on at least 3 days per week during the 4-week intervention period.

Main Outcome Measures:
V̇o
2peak was assessed before and after the intervention in an all-out exercise test on a bicycle ergometer.

Results:
V̇o
2peak increased by an average of 3.6 mL/(kg·min) [SD 3.6 mL/(kg·min)] in the E-Bike group and by 2.2 mL/(kg·min) [SD 3.5 mL/(kg·min)] in the Bike group, with an adjusted difference between the 2 groups of 1.4 mL/(kg·min) [95% confidence interval, −1.4-4.1; P = 0.327].

Conclusions:
E-bikes may have the potential to improve cardiorespiratory fitness similar to conventional bicycles despite the available power assist, as they enable higher biking speeds and greater elevation gain.
Growth and Nutritional Biomarkers of Preterm Infants Fed a New Powdered Human Milk Fortifier
Authors: Rigo Jacques , Hascoët Jean‐Michel , Billeaud Claude , Picaud Jean‐Charles , Mosca Fabio , Rubio Amandine , Saliba Elie , Radkë Michaël , Simeoni Umberto , Guillois Bernard , de Halleux Virginie , Jaeger Jonathan , Ameye Laurent , Hays Nicholas P. , Spalinger Johannes 
Published: July 2017

ABSTRACTObjectives:The aim of this study was to assess growth and nutritional biomarkers of preterm infants fed human milk (HM) supplemented with a new powdered HM fortifier (nHMF) or a control HM fortifier (cHMF). The nHMF provides similar energy content, 16% more protein (partially hydrolyzed whey), and higher micronutrient levels than the cHMF, along with medium‐chain triglycerides and docosahexaenoic acid.Methods:In this controlled, multicenter, double‐blind study, a sample of preterm infants ⩽32 weeks or ⩽1500 g were randomized to receive nHMF (n = 77) or cHMF (n = 76) for a minimum of 21 days. Weight gain was evaluated for noninferiority (margin = –1 g/day) and superiority (margin = 0 g/day). Nutritional status and gut inflammation were assessed by blood, urine, and fecal biochemistries. Adverse events were monitored.Results:Adjusted mean weight gain (analysis of covariance) was 2.3 g/day greater in nHMF versus cHMF; the lower limit of the 95% CI (0.4 g/day) exceeded both noninferiority (P < 0.001) and superiority margins (P = 0.01). Weight gain rate (unadjusted) was 18.3 (nHMF) and 16.8 g · kg−1 · day−1 (cHMF) between study days 1 and 21 (D1–D21). Length and head circumference (HC) gains between D1 and D21 were not different. Adjusted weight‐for‐age z score at D21 and HC‐for‐age z score at week 40 corrected age were greater in nHMF versus cHMF (P = 0.013, P = 0.003 respectively). nHMF had higher serum blood urea nitrogen, pre‐albumin, alkaline phosphatase, and calcium (all within normal ranges; all P ⩽ 0.019) at D21 versus cHMF. Both HMFs were well tolerated with similar incidence of gastrointestinal adverse events.Conclusions:nHMF providing more protein and fat compared to a control fortifier is safe, well‐tolerated, and improves the weight gain of preterm infants.
Sociodemographic Predictors of Anal Cancer Screening and Follow-up in Human Immunodeficiency Virus–Infected Individuals
Authors: Wells Jessica S. , Holstad Marcia M. , Watkins Bruner Deborah 
Published: July 2017

Background:
Anal cancer in the United States is generally rare; however, human immunodeficiency virus (HIV)–infected individuals are 28 times more likely to be given a diagnosis of anal cancer than the general population.

Objective:
The aim of this study was to examine the rates and sociodemographic predictors of anal cancer screening and follow-up anoscopy in a sample of HIV-infected individuals.

Methods:
Data for this study (n = 200) were derived from a retrospective chart review of randomly selected HIV-infected individuals. Data analyses included Pearson's correlation coefficient statistic to examine bivariate associations and logistic regression modeling for prediction of anal Papanicolaou test screening and follow-up anoscopy.

Results:
Screening rates and follow-up after an abnormal anal Pap test were low. Women were less likely to be screened for anal cancer (odds ratio [OR], 0.244; P = .007). Men who have sex with men were almost 4 times more likely to be screened for anal cancer (OR, 3.7; P = .02). Men who have sex with men were 6 times more likely to have follow-up after an abnormal anal Pap test compared with heterosexual men or women of any sexual orientation (OR, 6.88; P = .002).

Conclusions:
High-risk groups for anal cancer should be targeted for preventative measures as part of a cancer prevention plan to decrease the personal and clinical burden associated with anal cancer.

Implications for Practice:
Cancer prevention is a multistep process that requires screening and follow-up efforts, where healthcare providers play a vital role in these efforts. Findings from this study can inform strategies to improve screening and follow-up rates in HIV-infected individuals.
Cervical spine evaluation and clearance in the intoxicated patient: A prospective Western Trauma Association Multi-Institutional Trial and Survey
Authors: Martin Matthew J. , Bush Lisa D. , Inaba Kenji , Byerly Saskya , Schreiber Martin , Peck Kimberly A. , Barmparas Galinos , Menaker Jay , Hazelton Joshua P. , Coimbra Raul , Zielinski Martin D. , Brown Carlos V.R. , Ball Chad G. , Cherry-Bukowiec Jill R. , Burlew Clay Cothren , Dunn Julie , Minshall C. Todd , Carrick Matthew M. , Berg Gina M. , Demetriades Demetrios , Long William 
Published: July 2017

BACKGROUND
Intoxication often prevents clinical clearance of the cervical spine (Csp) after trauma leading to prolonged immobilization even with a normal computed tomography (CT) scan. We evaluated the accuracy of CT at detecting clinically significant Csp injury, and surveyed participants on related opinions and practice.

METHODS
A prospective multicenter study (2013–2015) at 17 centers. All adult blunt trauma patients underwent structured clinical examination and imaging including a Csp CT, with follow-up thru discharge. alcohol- and drug-intoxicated patients (TOX+) were identified by serum and/or urine testing. Primary outcomes included the incidence and type of Csp injuries, the accuracy of CT scan, and the impact of TOX+ on the time to Csp clearance. A 36-item survey querying local protocols, practices, and opinions in the TOX+ population was administered.

RESULTS
Ten thousand one hundred ninety-one patients were prospectively enrolled and underwent CT Csp during the initial trauma evaluation. The majority were men (67%), had vehicular trauma or falls (83%), with mean age of 48 years, and mean Injury Severity Score (ISS) of 11. The overall incidence of Csp injury was 10.6%. TOX+ comprised 30% of the cohort (19% EtOH only, 6% drug only, and 5% both). TOX+ were significantly younger (41 years vs. 51 years; p < 0.01) but with similar mean Injury Severity Score (11) and Glasgow Coma Scale score (13). The TOX+ cohort had a lower incidence of Csp injury versus nonintoxicated (8.4% vs. 11.5%; p < 0.01). In the TOX+ group, CT had a sensitivity of 94%, specificity of 99.5%, and negative predictive value (NPV) of 99.5% for all Csp injuries. For clinically significant injuries, the NPV was 99.9%, and there were no unstable Csp injuries missed by CT (NPV, 100%). When CT Csp was negative, TOX+ led to longer immobilization versus sober patients (mean, 8 hours vs. 2 hours; p < 0.01), and prolonged immobilization (>12 hrs) in 25%. The survey showed marked variations in protocols, definitions, and Csp clearance practices among participating centers, although 100% indicated willingness to change practice based on these data.

CONCLUSION
For intoxicated patients undergoing Csp imaging, CT scan was highly accurate and reliable for identifying clinically significant spine injuries, and had a 100% NPV for identifying unstable injuries. CT-based clearance in TOX+ patients appears safe and may avoid unnecessary prolonged immobilization. There was wide disparity in practices, definitions, and opinions among the participating centers.

LEVEL OF EVIDENCE
Diagnostic tests or criteria, level II.
Access to Heart Transplantation: A Proper Analysis of the Competing Risks of Death and Transplantation Is Required to Optimize Graft Allocation
Authors: Cantrelle Christelle , Legeai Camille , Latouche Aurélien , Tuppin Philippe , Jasseron Carine , Sebbag Laurent , Bastien Olivier , Dorent Richard 
Published: July 2017

Background
Heart allocation systems are usually urgency-based, offering grafts to candidates at high risk of waitlist mortality. In the context of a revision of the heart allocation rules, we determined observed predictors of 1-year waitlist mortality in France, considering the competing risk of transplantation, to determine which candidate subgroups are favored or disadvantaged by the current allocation system.

Methods
Patients registered on the French heart waitlist between 2010 and 2013 were included. Cox cause-specific hazards and Fine and Gray subdistribution hazards were used to determine candidate characteristics associated with waitlist mortality and access to transplantation.

Results
Of the 2053 candidates, 7 variables were associated with 1-year waitlist mortality by the Fine and Gray method including 4 candidate characteristics related to heart failure severity (hospitalization at listing, serum natriuretic peptide level, systolic pulmonary artery pressure, and glomerular filtration rate) and 3 characteristics not associated with heart failure severity but with lower access to transplantation (blood type, age, and body mass index). Observed waitlist mortality for candidates on mechanical circulatory support was like that of others.

Conclusions
The heart allocation system strongly modifies the risk of pretransplant mortality related to heart failure severity. An in-depth competing risk analysis is therefore a more appropriate method to evaluate graft allocation systems. This knowledge should help to prioritize candidates in the context of a limited donor pool.
OPUS-CSF: A C-atom-based Scoring Function for Ranking Protein Structural Models
Authors: Xu Gang , Ma Tianqi , Zang Tianwu , Wang Qinghua , Ma Jianpeng 
Published: July 2017

SummaryWe report aC-atom-basedscoringfunction, named OPUS-CSF, for ranking protein structural models. Rather than using traditional Boltzmann formula, we built a scoring function (CSF score) based on the native distributions (analyzed through entire PDB) of coordinate components of mainchain C atoms on selected residues of peptide segments of 5, 7, 9, and 11 residues in length. In testing OPUS-CSF on decoy recognition, it maximally recognized 257 native structures out of 278 targets in 11 commonly used decoy sets, significantly more than other popular all-atom empirical potentials. The average correlation coefficient with TM-score was also comparable with those of other potentials. OPUS-CSF is a highly coarse-grained scoring function, which only requires input of partial mainchain information, and very fast. Thus it is suitable for applications at early stage of structural building.
Mono-ubiquitination of syntaxin 3 leads to retrieval from the basolateral plasma membrane and facilitates cargo recruitment to exosomes
Authors: Giovannone Adrian J. , Reales Elena , Bhattaram Pallavi , Fraile-Ramos Alberto , Weimbs Thomas 
Published: July 2017

AbstractSyntaxin 3 (Stx3), a SNARE protein located and functioning at the apical plasma membrane of epithelial cells, is required for epithelial polarity. A fraction of Stx3 is localized to late endosomes / lysosomes though how it traffics there and its function in these organelles is unknown. Here we report that Stx3 undergoes mono - ubiquitination in a conserved polybasic domain. Stx3 present at the basolateral – but not the apical - plasma membrane is rapidly endocytosed, targeted to endosomes, internalized into intraluminal vesicles (ILVs) and excreted in exosomes. A non - ubiquitinatable mutant of Stx3 (Stx3 - 5R) fails to enter this pathway and leads to the inability of the apical exosomal cargo protein GPRC5B to enter the ILV / exosomal pathway. This suggests that ubiquitination of Stx3 leads to removal from the basolateral membrane to achieve apical polarity, that Stx3 plays a role in the recruitment of cargo to exosomes, and that the Stx3 - 5R mutant acts as a dominant - negative inhibitor. Human cytomegalovirus (HCMV) acquires its membrane in an intracellular compartment and we show that Stx3 - 5R strongly reduces the number of excreted infectious viral particles. Altogether these results suggest that Stx3 functions in the transport of specific proteins to apical exosomes and that HCMV exploit this pathway for virion excretion.
unitas: the universal tool for annotation of small RNAs
Authors: Gebert Daniel , Hewel Charlotte , Rosenkranz David 
Published: July 2017

AbstractBackgroundNext generation sequencing is a key technique in small RNA biology research that has led to the discovery of functionally different classes of small non-coding RNAs in the past years. However, reliable annotation of the extensive amounts of small non-coding RNA data produced by high-throughput sequencing is time-consuming and requires robust bioinformatics expertise. Moreover, existing tools have a number of shortcomings including a lack of sensitivity under certain conditions, limited number of supported species or detectable sub-classes of small RNAs.ResultsHere we introduce unitas, an out-of-the-box ready software for complete annotation of small RNA sequence datasets, supporting the wide range of species for which non-coding RNA reference sequences are available in the Ensembl databases (currently more than 800). unitas combines high quality annotation and numerous analysis features in a user-friendly manner. A complete annotation can be started with one simple shell command, making unitas particularly useful for researchers not having access to a bioinformatics facility. Noteworthy, the algorithms implemented in unitas are on par or even outperform comparable existing tools for small RNA annotation that base on available ncRNA sequence information.Conclusionsunitas brings together annotation and analysis features that hitherto required the installation of numerous different bioinformatics tools which can pose a challenge for the non-expert user. With this, unitas overcomes the problem of read normalization. Moreover, the high quality of sequence annotation and analysis, paired with the ease of use, make unitas a valuable tool for researchers in all fields connected to small RNA biology.