bluuebunny/crossref_metadata_2025_split huggingface dataset:
Short article: Influence of regulatory NLRC5 variants on colorectal cancer survival and 5-fluorouracil-based chemotherapy
Authors: Catalano Calogerina , da Silva Filho Miguel I. , Jiraskova Katerina , Vymetalkova Veronika , Levy Miroslav , Liska Vaclav , Vycital Ondrej , Naccarati Alessio , Vodickova Ludmila , Hemminki Kari , Vodicka Pavel , Weber Alexander N.R. , Försti Asta 
Published: May 2018

Background
NLRC5 is an interferon γ-inducible protein, which plays a role in immune surveillance with a potential influence on cancer survival.

Objective
We aimed to evaluate the effect of potential regulatory variants in NLRC5 on overall survival and survival after 5-fluorouracil (5-FU)-based therapy of colorectal cancer (CRC) patients.

Patients and methods
We carried out a case-only study in a Czech population of 589 cases; 232 received 5-FU-based therapy. Eleven variants within NLRC5 were selected using in-silico tools. Associations between polymorphisms and survival were assessed by Cox regression analysis adjusting for age at diagnosis, sex, and TNM stage. Survival curves were derived using the Kaplan–Meier method.

Results
Two variants showed a significant association with survival. All patients and metastasis-free patients at the time of diagnosis (pM0) who were homozygous carriers of the minor allele of rs27194 had a decreased overall survival (OSall and OSpM0) and event-free survival (EFSpM0) under a recessive model (OSall
P=0.003, OSpM0
P=0.005, EFSpM0
P=0.01, respectively). OS was also decreased for all patients and for pM0 patients who carried at least one minor allele of rs289747 (OSall
P=0.03 and OSpM0
P=0.003, respectively). Among CRC patients, who underwent a 5-FU-based adjuvant regimen, rs12445252 was associated with OSall, OSpM0 and EFSpM0, according to the dosage of the minor allele T (OSall
P=0.0004, OSpM0
P=0.0001, EFSpM0
P=0.008, respectively).

Conclusion
Our results showed that polymorphisms in NLRC5 may be used as prognostic markers of survival of CRC patients, as well as for survival in response to 5-FU treatment.
Differences in Experiences With Care Between Homeless and Nonhomeless Patients in Veterans Affairs Facilities With Tailored and Nontailored Primary Care Teams
Authors: Jones Audrey L. , Hausmann Leslie R.M. , Kertesz Stefan , Suo Ying , Cashy John P. , Mor Maria K. , Schaefer James H. , Gundlapalli Adi V. , Gordon Adam J. 
Published: May 2018

Background:
Homeless patients describe poor experiences with primary care. In 2012, the Veterans Health Administration (VHA) implemented homeless-tailored primary care teams (Homeless Patient Aligned Care Team, HPACTs) that could improve the primary care experience for homeless patients.

Objective:
To assess differences in primary care experiences between homeless and nonhomeless Veterans receiving care in VHA facilities that had HPACTs available (HPACT facilities) and in VHA facilities lacking HPACTs (non-HPACT facilities).

Research Design:
We used multivariable multinomial regressions to estimate homeless versus nonhomeless patient differences in primary care experiences (categorized as negative/moderate/positive) reported on a national VHA survey. We compared the homeless versus nonhomeless risk differences (RDs) in reporting negative or positive experiences in 25 HPACT facilities versus 485 non-HPACT facilities.

Subjects:
Survey respondents from non-HPACT facilities (homeless: n=10,148; nonhomeless: n=309,779) and HPACT facilities (homeless: n=2022; nonhomeless: n=20,941).

Measures:
Negative and positive experiences with access, communication, office staff, provider rating, comprehensiveness, coordination, shared decision-making, and self-management support.

Results:
In non-HPACT facilities, homeless patients reported more negative and fewer positive experiences than nonhomeless patients. However, these patterns of homeless versus nonhomeless differences were reversed in HPACT facilities for the domains of communication (positive experience RDs in non-HPACT versus HPACT facilities=−2.0 and 2.0, respectively); comprehensiveness (negative RDs=2.1 and −2.3), shared decision-making (negative RDs=1.2 and −1.8), and self-management support (negative RDs=0.1 and −4.5; positive RDs=0.5 and 8.0).

Conclusions:
VHA facilities with HPACT programs appear to offer a better primary care experience for homeless versus nonhomeless Veterans, reversing the pattern of relatively poor primary care experiences often associated with homelessness.
Glucose Requirements of the Developing Human Brain
Authors: Goyal Manu S. , Raichle Marcus E. 
Published: May 2018

ABSTRACTAdequate nutrition is critical for human brain development, which depends particularly upon glucose. The adult human brain accounts for 20% to 25% of total body resting glucose consumption, and studies indicate that the developing brain requires an even greater percentage of glucose. Here we critically review the currently available data on glucose requirements for early childhood brain development. Implications of these findings are then discussed in the context of childhood malnutrition and future areas of investigation.
Correlation of Level of Trauma Activation With Emergency Department Intervention
Authors: Cooper Michael C. , Srivastava Geetanjali 
Published: May 2018

Background
In-hospital trauma team activation criteria are formulated to identify severely injured patients requiring specialized multidisciplinary care. Efficacy of trauma activation (TA) criteria is commonly measured by emergency department (ED) disposition, injury severity score, and mortality. Necessity of critical ED interventions is another measure that has been proposed to evaluate the appropriateness of TA criteria.

Methods
Two-year retrospective cohort study of 1715 patients from our trauma registry at a Level 1 pediatric trauma center. We abstracted data on acute interventions, level and criterion of TA, ED disposition, and mortality. We report odds ratio (OR) with 95% confidence intervals (CIs), positive predictive value, and frequency of acute interventions.

Results
Trauma activation was initiated for 947 (55%) of the 1715 patients. There were 426 ED interventions performed on 235 patients (14%); 67.8% were in level 1 activations; 17.6% in level 2, and 14.6% in level 3. Highest-level activations were highly associated with need for ED interventions (OR, 16.1; 95% CI, 11.5–22.4). The ORs for requiring an ED intervention were low for lower level activations (OR, 0.4; 95% CI, 0.3–0.5), trauma service consults (OR, 0.3; 95% CI, 0.2–0.4), and certain mechanism-based criteria. The ORs for ED intervention for isolated motor vehicle collision (0.2; 95% CI, 0.1–0.7), isolated all-terrain vehicle rollover (0.4; 95% CI, 0.1–1.7), and suspected spinal cord injury (0.5; 95% CI, 0.1–3.7) were significantly lower than 1.

Conclusions
Highest-level activation criteria correlate with high utilization of ED resources and interventions. Lower level activation criteria and trauma service consult criteria are not highly correlated with need for ED interventions. Downgrading isolated motor vehicle collision and all-terrain vehicle rollovers and suspected spinal cord injury to lower level activations could decrease the overtriage rate, and adding age-specific bradycardia as a physiologic criterion could improve our undertriage rate.
Radiology Callbacks to a Pediatric Emergency Department and Their Clinical Impact
Authors: Arora Rajan , Kannikeswaran Nirupama 
Published: May 2018

Background
Clinical impact of radiology callbacks (missed initial radiologic diagnosis) remains largely unknown in the pediatric emergency department (PED).

Objective
The aim of this study was to describe the incidence, nature of radiology callbacks, and the impact on clinical care during the return visit (RV).

Methods
We performed a retrospective chart review of quality assurance database of RVs for radiology callbacks to our PED over a 1-year period.

Results
Return visit rate to our PED was 3% (2765/92,000) of which 1.9% (55/2765) was for radiology callbacks. Radiology misses involved mostly x-ray interpretations (92.7%), occurred after-hours (83.6%), with fractures being the most common missed finding. Majority of patients (94.5%) required 1 or more interventions during the RV; 34.5% of radiology callbacks had a major impact on clinical management; 27.2% of radiology callbacks were false-positive.

Conclusions
Although RVs secondary to radiology callback remain low, one third of them resulted in major changes in diagnosis, treatment, or disposition and impacted patient outcome.
Fast Abdominal Contrast-Enhanced Imaging With High Parallel-Imaging Factors Using a 60-Channel Receiver Coil Setup
Authors: Weiss Jakob , Martirosian Petros , Wolf Steffen , Horger Wilhelm , Taron Jana , Nikolaou Konstantin , Notohamiprodjo Mike , Othman Ahmed E. 
Published: May 2018

Purpose
The aim of this study was to assess a novel 60-channel receiver body coil (B60) setup for accelerated contrast-enhanced abdominal magnetic resonance imaging (MR) imaging with respect to signal-to-noise ratio (SNR) and image quality using high parallel-imaging technique (PAT) factors in comparison to a standard 30-channel coil setup.

Methods
All imaging data were acquired on a 3 T MR scanner using a novel B60 receiver coil setup in comparison to a standard 30-channel setup serving as reference standard. Phantom measurements were performed to systematically evaluate SNR and geometry factor performance in an ex vivo setting. To assess the in vivo application, additional measurements in 5 healthy volunteers and 17 patients were performed using a 3-dimensional T1w gradient-echo sequences with different acceleration factors. At first, the volunteers were examined. In a second step, standard contrast-enhanced abdominal images were acquired in the 17 patients, who were randomly assigned into 2 groups (group A: 60-channel, n = 8; group B: 30-channel, n = 9). Image quality, noise, lesion conspicuity, and artifacts were assessed by 2 radiologists independently on a 5-point Likert scale (5 = excellent).

Results
The phantom study revealed substantial advantages (SNR and geometry factor) of the B60 coil for measurements in the head-to-feet phase encoding direction, whereas only minor differences were found in other directions. Comparison of image quality in volunteers revealed significantly higher ratings of the B60 setup for all acquisitions (P ≤ 0.032), except for PAT = none. In patients, similar results were observed with comparable image quality at lower PAT factors and significantly superior image quality of the B60 setup for higher PAT factors (2 × 2 and 3 × 2; P = 0.008).

Conclusions
The 60-channel coil setup facilitates improved SNR and image quality at high PAT factors with diagnostic image quality, which allows for accelerated contrast-enhanced MR imaging of the abdomen.
Precise and Automatic Patient Positioning in Computed Tomography
Authors: Saltybaeva Natalia , Schmidt Bernhard , Wimmer Andreas , Flohr Thomas , Alkadhi Hatem 
Published: May 2018

Objectives
The aim of this study was to evaluate the accuracy of a 3-dimensional (3D) camera algorithm for automatic and individualized patient positioning based on body surface detection and to compare the results of the 3D camera with manual positioning performed by technologists in routinely obtained chest and abdomen computed tomography (CT) examinations.

Materials and Methods
This study included data of 120 patients undergoing clinically indicated chest (n = 68) and abdomen (n = 52) CT. Fifty-two of the patients were scanned with CT using a table height manually selected by technologists; 68 patients were automatically positioned with the 3D camera, which is based on patient-specific body surface and contour detection. The ground truth table height (TGT) was defined as the table height that aligns the axial center of the patient’s body region in the CT scanner isocenter. Off-centering was defined as the difference between the ground truth table height (TGT) and the actual table position used in all CT examinations. The t test was performed to determine significant differences in the vertical offset between automatic and manual positioning. The χ2 test was used to check whether there was a relationship between patient size and the magnitude of off-centering.

Results
We found a significant improvement in patient centering (offset 5 ± 3 mm) when using the automatic positioning algorithm with the 3D camera compared with manual positioning (offset 19 ± 10 mm) performed by technologists (P < 0.005). Automatic patient positioning based on the 3D camera reduced the average offset in vertical table position from 19 mm to 7 mm for chest and from 18 mm to 4 mm for abdomen CT. The absolute maximal offset was 39 mm and 43 mm for chest and abdomen CT, respectively, when patients were positioned manually, whereas with automatic positioning using the 3D camera the offset never exceeded 15 mm. In chest CT performed with manual patient positioning, we found a significant correlation between vertical offset greater than 20 mm and patient size (body mass index, >26 kg/m2, P < 0.001). In contrast, no such relationship was found for abdomen CT (P = 0.38).

Conclusions
Automatic individualized patient positioning using a 3D camera allows for accurate patient centering as compared with manual positioning, which improves radiation dose utilization.
Temporal Progression of Craniofacial Dysmorphology in Unilateral Coronal Synostosis: A Mechanistic Hypothesis
Authors: Baweja Kirun , Sun Alexander H. , Sawh-Martinez Rajendra , Persing John A. 
Published: May 2018

Aim:
This study chronicles skull base and face development in nonsyndromic unilateral coronal synostosis (UCS) during infancy, to characterize the mechanistic progression of facial dysmorphology.

Methods:
Computed tomography scans from 51 subjects were reviewed (26 UCS, 25 controls) and data were reconstructed. Patients were stratified into 5 age groups. A series of measurements were taken from the reconstructions.

Results:
All patients had a unilaterally fused coronal suture at the time of analysis. Asymmetry of the sphenoid wings was present across all age groups. The sphenoid wing ipsilateral to the fused suture consistently had a more acute angle from the midline. At 19 days of age, ipsilateral nasal root and cribriform plate deviation are noted, as well as increased contralateral zygoma antero-posterior length. Patients younger than 2 months also had elongated posterior cranial bases. At 2 to 3 months of age, the cranial base widens in the anterior portion of the middle cranial fossa with an increased ipsilateral pterion to sella distance. The most delayed change observed was the increase in contralateral orbital rim angle at 7 to 12 months of age compared to normal.

Conclusion:
After suture fusion, sphenoid wing changes are among the earliest restructural malformations to take place. This suggests that the cascade of dysmorphology in UCS originates in the cranial vault, then progresses to the skull base, and lastly to the facial structures. Ipsilateral orbital changes are early facial changes in UCS that begin before 2 months of age. This is then followed by changes in the contralateral face later in development.
Comparison of Bone Grafts From Various Donor Sites in Human Bone Specimens
Authors: Kamal Mohammad , Gremse Felix , Rosenhain Stefanie , Bartella Alexander K. , Hölzle Frank , Kessler Peter , Lethaus Bernd 
Published: May 2018

Abstract
The objective of the current study was to compare the three-dimensional (3D) morphometric microstructure in human cadaveric bone specimens taken from various commonly utilized donor sites for autogenous bone grafting. Autogenous bone grafts can be harvested from various anatomic sites and express heterogeneous bone quality with a specific 3D microstructure for each site. The long-term structural integrity and susceptibility to resorption of the graft depend on the selected donor bone. Micro-computed tomography generates high-resolution datasets of bone structures and calcifications making this modality versatile for microarchitecture analysis and quantification of the bone. Six bone specimens, 10 mm in length, where anatomically possible, were obtained from various anatomical sites from 10 human dentate cadavers (4 men, 6 women, mean age 69.5 years). Specimens were scanned using a micro-computed tomography device and volumetrically reconstructed. A virtual cylindrical inclusion was reconstructed to analyze the bone mineral density and structural morphometric analysis using bone indices: relative bone volume, surface density, trabecular thicknesses, and trabecular separation. Calvarial bone specimens showed the highest mineral density, followed by the chin, then mandibular ramus then the tibia, whereas iliac crest and maxillary tuberosity had lower bone mineral densities. The pairwise comparison revealed statistically significant differences in the bone mineral density and relative bone volume index in the calvaria, mandibular ramus, mandibular symphysis groups when compared with those in the iliac crest and maxillary tuberosity, suggesting higher bone quality in the former groups than in the latter; tibial specimens expressed variable results.
Association Between Duration of Delayed Graft Function, Acute Rejection, and Allograft Outcome After Deceased Donor Kidney Transplantation
Authors: Lim Wai H. , Johnson David W. , Teixeira-Pinto Armando , Wong Germaine 
Published: May 2018

Background
Prolonged duration of delayed graft function (DGF) may be associated with adverse allograft outcomes, but the association between threshold duration of DGF, acute rejection and long-term allograft loss remains undefined. We aimed to determine the impact of DGF duration on allograft outcomes and to assess whether this association was mediated by acute rejection.

Methods
Using data from the Australian and New Zealand Dialysis and Transplant Registry, Cox proportional modeling was used to determine the association between quartiles of DGF duration, acute rejection at 6 months and death-censored graft loss (DCGL). Mediation analysis was conducted to determine whether acute rejection was a causal intermediate between DGF and DCGL.

Results
Of 7668 deceased donor kidney transplants between 1997 and 2014, 1497 (19.5%) recipients experienced DGF requiring dialysis. The median (interquartile range) duration of DGF was 7 (9) days, with 25% requiring dialysis for 14 days or longer. Among recipients who had experienced a DGF duration of 1 to 4 days, the adjusted hazard ratio for duration of 5 to 7, 8 to 13, and 14 days or longer were 1.13 (95% confidence interval [CI], 0.83-1.55; P = 0.43), 1.44 (95% CI, 1.08-1.91; P = 0.013), and 1.99 (95% CI, 1.50-2.65; P < 0.001), respectively, for acute rejection; and were 1.10 (95% CI< 0.73-1.67; P = 0.64), 1.45 (95% CI, 1.00-2.11; P = 0.05) and 1.60 (95% CI, 1.10-2.31; P = 0.01), respectively, for DCGL. On average, 8% of the effects between DGF duration and DCGL were explained by acute rejection.

Conclusions
There was a direct dose-dependent effect between DGF duration and DCGL, with acute rejection explaining less than 10% of the effects between DGF duration and DCGL. Future research identifying other potential modifiable mediators that lies in the causal pathway between DGF duration and allograft loss is essential.
ALEdb 1.0: A Database of Mutations from Adaptive Laboratory Evolution Experimentation
Authors: Phaneuf Patrick V. , Gosting Dennis , Palsson Bernhard O. , Feist Adam M. 
Published: May 2018

ABSTRACTFull genomic sequences are readily available, but their functional interpretation remains a fundamental challenge. Adaptive Laboratory Evolution (ALE) has emerged as an experimental approach to discover causal mutations that confer desired phenotypic functions. Thus, ALE not only represents a controllable experimental approach to systematically discover genotype-phenotype relationships, but it also allows for the revelation of the series of genetic alterations required to acquire the new phenotype. Numerous ALE studies have appeared in the literature providing a strong impetus for developing structured databases to warehouse experimental evolution information and make it retrievable for large-scale analysis. Here, the first step towards establishing this capability is presented: ALEdb (http://aledb.org). This initial release contains over 11,000 mutations that have been discovered in ALE experiments. ALEdb is the first of its kind; (1) it is a web-based platform that comprehensively reports on ALE acquired mutations and their conditions, (2) it reports key mutations using previously established trends, (3) it enables a search-driven workflow to enhance user mutation functional analysis, (4) it allows exporting of mutation query results for custom analysis, (5) it has a bibliome that describes the underlying published literature, and (6) contains experimental evolution mutations from multiple model organisms. Thus, ALEdb is an informative platform which will become increasingly revealing as the number of reported ALE experiments and identified mutations continue to expand.
Estimating parasite load dynamics to reveal novel resistance mechanisms to human malaria
Authors: Bretscher Michael T. , Georgiadou Athina , Lee Hyun Jae , Walther Michael , van Beek Anna E. , Fitriani Fadlila , Wouters Diana , Kuijpers Taco W. , Nwakanma Davis , D’Alessandro Umberto , Riley Eleanor M. , Levin Michael , Coin Lachlan J. , Ghani Azra , Conway David J. , Cunnington Aubrey J. 
Published: May 2018

AbstractImproved methods are needed to identify host mechanisms which directly protect against human infectious diseases in order to develop better vaccines and therapeutics1,2. Pathogen load determines the outcome of many infections3, and is a consequence of pathogen multiplication rate, duration of the infection, and inhibition or killing of pathogen by the host (resistance). If these determinants of pathogen load could be quantified then their mechanistic correlates might be determined. In humans the timing of infection is rarely known and treatment cannot usually be withheld to monitor serial changes in pathogen load and host response. Here we present an approach to overcome this and identify potential mechanisms of resistance which control parasite load inPlasmodium falciparummalaria. Using a mathematical model of longitudinal infection dynamics for orientation, we made individualized estimates of parasite multiplication and growth inhibition in Gambian children at presentation with acute malaria and used whole blood RNA-sequencing to identify their correlates. We identified novel roles for secreted proteases cathepsin G and matrix metallopeptidase 9 (MMP9) as direct effector molecules which inhibitP. falciparumgrowth. Cathepsin G acts on the erythrocyte membrane, cleaving surface receptors required for parasite invasion, whilst MMP9 acts on the parasite. In contrast, the type 1 interferon response and expression ofCXCL10(IFN-γ-inducible protein of 10 kDa, IP-10) were detrimental to control of parasite growth. Natural variation in iron status and plasma levels of complement factor H were determinants of parasite multiplication rate. Our findings demonstrate the importance of accounting for the dynamic interaction between host and pathogen when seeking to identify correlates of protection, and reveal novel mechanisms controlling parasite growth in humans. This approach could be extended to identify additional mechanistic correlates of natural- and vaccine-induced immunity to malaria and other infections.