bluuebunny/crossref_metadata_2025_split huggingface dataset:
Data for Care (D4C) Alabama: Clinic-Wide Risk Stratification With Enhanced Personal Contacts for Retention in HIV Care via the Alabama Quality Management Group
Authors: Sohail Maira , Rastegar Jeremiah , Long Dustin , Rana Aadia , Levitan Emily B. , Reed-Pickens Harriette , Batey David Scott , Ross-Davis Kelly , Gaddis Kathy , Tarrant Ashley , Parmar Jitesh , Raper James L. , Mugavero Michael J. 
Published: November 2019

Background:
The Alabama Quality Management Group (AQMG), a consortium of 9 Ryan White–funded part C and D clinics, distributed statewide was established in 2006 under the guidance from the Health and Resources Services Administration with a clinical quality improvement (CQI) focus.

Methods:
We describe the origins and evolution of the AQMG, including requisite shifts from aggregate clinic-wide to de-identified individual-level data reporting for implementation of the Data for Care (D4C-AL) Alabama program. The D4C-AL strategy uses a clinic-wide risk stratification of all patients based on missed clinic visits in the previous 12 months. Intermediate (1–2 missed visits) and high-risk patients (>3 missed visits) receive the evidence-informed Retention through Enhanced Personal Contact intervention. We report on a pilot of the D4CAL program in 4 of 33 primary HIV care clinics at the UAB 1917 Clinic.

Results:
Among 3859 patients seen between April 2018 and February 2019, the missed visit rate was not significantly different between the D4C-1917 (19.2%) and non-D4C clinics (20.5%) in a preintervention period (May 2017–April 2018). However, a significantly lower missed visit rate was observed in the D4C-1917 vs. non–D4C-1917 clinics during the intervention period (April 2018–February 2019, P = 0.049).

Conclusions:
The AQMG has been transformed into a health service research and implementation science platform, building on a shared vision, mission, data reporting, and quality improvement focus. Moreover, CQI may be viewed as an implementation strategy that seeks to enhance uptake and sustained use of effective interventions with D4C-AL representing a prototype for future initiatives embedded within extant quality improvement consortia.
Seeing Is Believing? Unique Capabilities of Internet-Only Studies as a Tool for Implementation Research on HIV Prevention for Men Who Have Sex With Men: A Review of Studies and Methodological Considerations
Authors: Grov Christian , Westmoreland Drew , Rendina H. Jonathon , Nash Denis 
Published: November 2019

Background:In 2014, Grov et al published a comprehensive review cataloguing both men who have sex with men's (MSM's) sexual behavior transitions in online environments from the 1990s through 2013, as well as researchers' efforts in tandem to use the internet to engage MSM into research, treatment, and prevention.Methods:In this article, we discuss historical events and research having occurred in the half decadesincethe Grov et al publication.Results:Notable transitions include MSM's expanded use of geosocial networking apps, as well as other forms of social media accessed primarily through mobile devices, as well as the addition ofbiomedicalprevention strategies (eg, pre-exposure prophylaxis and undetectable = untransmittable) to the proverbial HIV prevention toolkit. In tandem, researchers have rapidly expanded their employment of internet-mediated methods for the recruitment and engagement of key populations for HIV research, treatment, and prevention. In this article, we discuss methodological considerations for using the internet to conduct HIV prevention research with MSM: (1) sources of recruitment (eg, geosocial apps, Facebook, crowdsourced online panels); (2) design (eg, cross sectional, longitudinal, diaries); (3) incentives (including disincentivizing fraudulent participants and/or spam bots); (4) confidentiality; and (5) representativeness.Conclusion:We conclude by discussing future directions in HIV prevention research in light of forthcoming technologies such as fifth generation (5G) mobile networks, combined use of self-collected biological data alongside self-report, and the utility of metadata and metaresearch to document, evaluate, and inform best practices.
Comparison of Three-Dimensional Printing and Computer-aided Engineering in Presurgical Volumetric Assessment of Bilateral Alveolar Clefts
Authors: Chen Shuxiu , Liu Bing , Liu Jing , Yin Ningbei , Wang Yongqian 
Published: November 2019

Abstract
This study aimed to evaluate 2 advanced methods for presurgical calculation of bilateral alveolar cleft defect volume using 3-dimensional (3D) printing and computer-aided engineering (CAE) software. Twelve patients with bilateral alveolar cleft (4 females, 8 males, age range 8–11 years) were enrolled in the study. All patients underwent preoperative helical computed tomography scans, and the digital imaging and communications in medicine (DICOM) data of the computed tomography images were analyzed using 3D printing and CAE software. The 3D-printed model used a simulated graft, and graft volume was measured by water displacement. The CAE software used a subtractive method to calculate volume. Simulated graft volumes and CAE-software-derived volumes were compared using Pearson's correlation test and paired Student's t-test. The average volume of the simulated bone grafts obtained using 3D-printed models was 1.45 mL, which was lower than the CAE-software-derived mean volume of 1.52 mL. The mean calculation time using the 3D-printed model was 51.5 minutes, which was 32.1 minutes longer than the average 19.4 minutes when using CAE software. Paired Student's t-test revealed no statistically significant difference between the volumes derived from these methods. The results of this study further validated the use of 3D printing and CAE technique in bilateral alveolar defect repair. The CAE software is more cost-effective in presurgical volumetric assessment. Moreover, 3D models overcome limitations of 3D visualizations by providing tactile feedback and superior appreciation of visuospatial relationships among anatomical structures.
Primary Cleft Rhinoplasty: Surgical Outcomes and Complications Using Three Techniques for Unilateral Cleft Lip Nose Repair
Authors: Rossell-Perry Percy 
Published: November 2019

Background:
This study represents a single surgeon's 10 years of experience addressing unilateral cleft lip and palate nose deformity. The purpose was to compare surgical outcomes and related complications using 3 different techniques to improve nasal shape in primary unilateral cleft rhinoplasty.

Methods:
This retrospective study with Institutional Ethical Committee approval compares 3 groups of patients with unilateral cleft lip nose and palate who were operated on using different techniques from 2007 to 2017. Surgical outcomes were analyzed by physical examination at least 1 year after primary rhinoplasty. Anthropometric measurements were obtained for the cleft and noncleft sides of the nose.

Results:
Approach with general analysis indicated differences among the 3 techniques. The author's comparative study revealed differences in nose symmetry and related complications, including increased recurrence of nose deformity using the modified McComb technique. Better short-term nose symmetry was observed using Potter technique and the V-Y-Z rhinoplasty.

Conclusions:
Potter approach and the V-Y-Z techniques achieve better short-term nose symmetry than the McComb method. Complications were less common in the group of patients operated on using the modified McComb technique. Additional studies are required to evaluate functional and long-term outcomes after primary rhinoplasty using the proposed methods.
The Influence of Epigenetic Factors in Four Pairs of Twins With Non-Syndromic Craniosynostosis
Authors: Farooq Saadia , Morton Jenny , Lloyd Mark , Krishna Sandhya Trichinopoly 
Published: November 2019

AbstractThe aims of this retrospective case series were to investigate whether twins born with craniosynostosis mirrored each other regarding operative surgery performed, age of undertaking surgery; outcomes in speech, language, and developmental milestones and what environmental factors were present for each set of twins.Case selection was based on clinical and radiographical evidence of craniosynostosis amongst twin sets. The twin sets included were those with craniosynostosis who had different sutures affected or those with the same suture affected but with a varying degree of severity.The presence of the following factors may have played an influential role in the clinical presentation of the twins; these were as follows: a maternal history of smoking, breech presentation, and genetic mutations. It was notable that the overall outcomes for the twins in this study were similar.These cases highlight the multifactorial nature in the development of craniosynostosis and how this influenced the phenotypic presentation of the twins.
National Database Reported Outcomes Following Craniosynostosis Reconstruction
Authors: Massenburg Benjamin B. , Nassar Amer H. , Hopper Richard A. 
Published: November 2019

Background:
While there has been ample interest and literature published regarding craniosynostosis surgical technique, there are few reports on adverse hospital and health system outcomes. The purpose of this study was to describe rate of and risk factors for complications, and adverse outcomes following craniosynostosis reconstruction.

Methods:
This study retrospectively reviewed the American College of Surgeons National Surgical Quality Improvement Program (NSQIP) Pediatric database and identified all patients undergoing craniosynostosis repair from 2012 to 2016. Univariate logistic regression analysis was used to identify significant associations between preoperative risk factors and adverse outcomes. Multivariate logistic regression analysis was then used to identify independent risk factors and causes of prolonged operative times, transfusions, reoperation, prolonged length of hospital stays, and readmission.

Results:
There were 3924 patients included who underwent craniosynostosis repair, of whom 1732 underwent frontoorbital advancement and 2192 underwent cranial vault remodeling. Transfusion was the most common NSQIP reportable outcome, occurring for 66.5% of all patients. The incidence of reoperation was 2.4% and readmission was 3.0%.

Conclusion:
This study provides a large descriptive analysis of craniosynostosis repair throughout the United States. Largely nonmodifiable patient risk factors lead to worse health system metrics, with young age, gastrointestinal comorbidities, American Society of Anesthesiologist scores of 3 and greater, reoperation, and a prolonged length of stay as independent risk factors for readmission. This analysis can be used to identify the standard of practice in synostosis care and enhance the implementation of ancillary care services to provide safe and cost-effective care for patients undergoing craniosynostosis repair.
The Consequences of Aging On the Response to Injury and Critical Illness
Authors: Joseph Bellal , Scalea Thomas 
Published: November 2019

ABSTRACTChanging demographic trends have led to an increase in the overall geriatric trauma patient volume. Furthermore, the intersection of aging and injury can be problematic because geriatric patients have multiple comorbidities, geriatric-specific syndromes, and reduced physiological reserve. Despite mounting evidence that frail geriatric patients have inferior outcomes following trauma, very few studies have examined the effect of aging on the biological response to injury. In the present article, we review the current literature and explore the pathophysiological rationale underlying observed data, available evidence, and future directions on this topic.
Influence of Different Partial Pressures of Oxygen During Continuous Hypothermic Machine Perfusion in a Pig Kidney Ischemia-reperfusion Autotransplant Model
Authors: Darius Tom , Vergauwen Martial , Smith Thomas B. , Patel Kamlesh , Craps Julie , Joris Virginie , Aydin Selda , Ury Benoît , Buemi Antoine , De Meyer Martine , Nath Jay , Ludwig Christian , Dessy Chantal , Many Marie-Christine , Gianello Pierre , Mourad Michel 
Published: November 2019

Background.
The optimal perfusate partial pressure of oxygen (Po
2) during hypothermic machine perfusion (HMP) is unknown. The aims of the study were to determine the functional, metabolic, structural, and flow dynamic effects of low and high perfusate Po
2 during continuous HMP in a pig kidney ischemia-reperfusion autotransplant model.

Methods.
The left kidneys of a ±40 kg pigs were exposed to 30 minutes of warm ischemia and randomized to receive 22-hour HMP with either low perfusate Po
2 (30% oxygen, low oxygenated HMP [HMPO2]) (n = 8) or high perfusate Po
2 (90% oxygen, HMPO2high) (n = 8), before autotransplantation. Kidneys stored in 22-hour standard HMP (n = 6) and 22-hour static cold storage (n = 6) conditions served as controls. The follow-up after autotransplantation was 13 days.

Results.
High Po
2 resulted in a 3- and 10-fold increase in perfusate Po
2 compared with low HMPO2 and standard HMP, respectively. Both HMPO2 groups were associated with superior graft recovery compared with the control groups. Oxygenation was associated with a more rapid and sustained decrease in renal resistance. While there was no difference in functional outcomes between both HMPO2 groups, there were clear metabolic differences with an inverse correlation between oxygen provision and the concentration of major central metabolites in the perfusion fluid but no differences were observed by oxidative stress and metabolic evaluation on preimplantation biopsies.

Conclusions.
While this animal study does not demonstrate any advantages for early graft function for high perfusate Po
2, compared with low perfusate Po
2, perfusate metabolic profile analysis suggests that aerobic mechanism is better supported under high perfusate Po
2 conditions.
Structural modularity of the XIST ribonucleoprotein complex
Authors: Lu Zhipeng , Guo Jimmy K. , Wei Yuning , Dou Diana R. , Zarnegar Brian , Ma Qing , Li Rui , Zhao Yang , Liu Fan , Choudhry Hani , Khavari Paul A. , Chang Howard Y. 
Published: November 2019

SUMMARYLong noncoding RNAs are thought to regulate gene expression by organizing protein complexes through unclear mechanisms. XIST controls the inactivation of an entire X chromosome in female placental mammals. Here we develop and integrate several orthogonal structure-interaction methods to demonstrate that XIST RNA-protein complex folds into an evolutionarily conserved modular architecture. Chimeric RNAs and clustered protein binding in fRIP and eCLIP experiments align with long-range RNA secondary structure, revealing discrete XIST domains that interact with distinct sets of effector proteins. CRISPR-Cas9-mediated permutation of the Xist A-repeat location shows that A-repeat serves as a nucleation center for multiple Xist-associated proteins and m6A modification. Thus modular architecture plays an essential role, in addition to sequence motifs, in determining the specificity of RBP binding and m6A modification. Together, this work builds a comprehensive structure-function model for the XIST RNA-protein complex, and suggests a general strategy for mechanistic studies of large ribonucleoprotein assemblies.
Neglecting model selection alters phylogenetic inference
Authors: Gerth Michael 
Published: November 2019

ABSTRACTMolecular phylogenetics is a standard tool in modern biology that informs the evolutionary history of genes, organisms, and traits, and as such is important in a wide range of disciplines from medicine to palaeontology. Maximum likelihood phylogenetic reconstruction involves assumptions about the evolutionary processes that underlie the dataset to be analysed. These assumptions must be specified in forms of an evolutionary model, and a number of criteria may be used to identify the best-fitting from a plethora of available models of DNA evolution. Using many empirical and simulated nucleotide sequence alignments, Abadi et al.1 have recently found that phylogenetic inferences using best models identified by six different model selection criteria are, on average, very similar to each other. They further claimed that using the model GTR+I+G4 without prior model-fitting results in similarly accurate phylogenetic estimates, and consequently that skipping model selection entirely has no negative impact on many phylogenetic applications. Focussing on this claim, I here revisit and re-analyse some of the data put forward by Abadi et al. I argue that while the presented analyses are sound, the results are misrepresented and in fact - in line with previous work - demonstrate that model selection consistently leads to different phylogenetic estimates compared with using fixed models.
Single cell RNA sequencing of calvarial and long bone endocortical cells
Authors: Ayturk Ugur M. , Scollan Joseph P. , Vesprey Alexander , Jacobsen Christina M. , Pajevic Paola Divieti , Warman Matthew L. 
Published: November 2019

ABSTRACTSingle cell RNA-seq (scRNA-seq) is emerging as a powerful technology to examine transcriptomes of individual cells. We determined whether scRNA-seq could be used to detect the effect of environmental and pharmacologic perturbations on osteoblasts. We began with a commonly used in vitro system in which freshly isolated neonatal mouse calvarial cells are expanded and induced to produce a mineralized matrix. We used scRNA-seq to compare the relative cell type abundances and the transcriptomes of freshly isolated cells to those that had been cultured for 12 days in vitro. We observed that the percentage of macrophage-like cells increased from 6% in freshly isolated calvarial cells to 34% in cultured cells. We also found that Bglap transcripts were abundant in freshly isolated osteoblasts but nearly undetectable in the cultured calvarial cells. Thus, scRNA-seq revealed significant differences between heterogeneity of cells in vivo and in vitro. We next performed scRNA-seq on freshly recovered long bone endocortical cells from mice that received either vehicle or Sclerostin-neutralizing antibody for 1 week. Bone anabolism-associated transcripts were also not significantly increased in immature and mature osteoblasts recovered from Sclerostin-neutralizing antibody treated mice; this is likely a consequence of being underpowered to detect modest changes in gene expression, since only 7% of the sequenced endocortical cells were osteoblasts, and a limited portion of their transcriptomes were sampled. We conclude that scRNA-seq can detect changes in cell abundance, identity, and gene expression in skeletally derived cells. In order to detect modest changes in osteoblast gene expression at the single cell level in the appendicular skeleton, larger numbers of osteoblasts from endocortical bone are required.
The direction of associations: prior knowledge promotes hippocampal separation, but cortical assimilation
Authors: Bein Oded , Reggev Niv , Maril Anat 
Published: November 2019

SummaryWhat does it mean to say, “a new association is learned”? And how is this learning different when adding new information to already-existing knowledge? Here, participants associated pairs of faces while undergoing fMRI, under two different conditions: a famous, highly-familiar face with a novel face or two novel faces. We examined multivoxel activity patterns corresponding to individual faces before and after learning. In the hippocampus, paired novel faces became more similar to one another through learning. In striking contrast, members of famous-novel pairs became distinct. In the cortex, prior knowledge led to integration, but in a specific direction: the representation of the novel face became similar to that of the famous face before learning, but less so vice versa, suggesting assimilation of new into old memories. We propose that hippocampal separation might resolve interference between existing and newly learned information, allowing cortical assimilation. Associations are formed through divergent but specific neural codes, that are adaptively shaped by the internal state of the system – its prior knowledge.
Rapid diagnosis of SCA36 in a three-generation family using short-read whole genome sequencing data
Authors: Rafehi Haloom , Szmulewicz David J. , Pope Kate , Wallis Mathew , Christodoulou John , White Susan M , Delatycki Martin B , Lockhart Paul J , Bahlo Melanie 
Published: November 2019

AbstractBackgroundSpinocerebellar ataxias (SCA) are often caused by expansions of short tandem repeats (STRs). Recent methodological advances have made repeat expansion (RE) detection with whole genome sequencing (WGS) feasible.ObjectivesTo determine the genetic basis of ataxia in a multigenerational Australian pedigree, with autosomal dominant inheritance.Methods and ResultsWGS was performed on three affected relatives. The sequence data was screened for known pathogenic REs using two repeat expansion detection tools: exSTRa and ExpansionHunter. This screen provided a clear and rapid diagnosis (<five days from receiving the sequencing data) of SCA36, a rare form of ataxia caused by an intronic GGCCTG RE in NOP56.Conclusionsthe that diagnosis of rare ataxias caused by REs is highly feasible and cost effective with WGS. We propose that WGS be implemented as the frontline, cost effective methodology for molecular testing of individuals with a clinical diagnosis of ataxia.
MetaEuk – sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics
Authors: Karin Eli Levy , Mirdita Milot , Söding Johannes 
Published: November 2019

AbstractBackgroundMetagenomics is revolutionizing the study of microorganisms and their involvement in biological, biomedical, and geochemical processes, allowing us to investigate by direct sequencing a tremendous diversity of organisms without the need for prior cultivation. Unicellular eukaryotes play essential roles in most microbial communities as chief predators, decomposers, phototrophs, bacterial hosts, symbionts and parasites to plants and animals. Investigating their roles is therefore of great interest to ecology, biotechnology, human health, and evolution. However, the generally lower sequencing coverage, their more complex gene and genome architectures, and a lack of eukaryote-specific experimental and computational procedures have kept them on the sidelines of metagenomics.ResultsMetaEuk is a toolkit for high-throughput, reference-based discovery and annotation of protein-coding genes in eukaryotic metagenomic contigs. It performs fast searches with 6-frame-translated fragments covering all possible exons and optimally combines matches into multi-exon proteins. We used a benchmark of seven diverse, annotated genomes to show that MetaEuk is highly sensitive even under conditions of low sequence similarity to the reference database. To demonstrate MetaEuk’s power to discover novel eukaryotic proteins in large-scale metagenomic data, we assembled contigs from 912 samples of the Tara Oceans project. MetaEuk predicted >12,000,000 protein-coding genes in eight days on ten 16-core servers. Most of the discovered proteins are highly diverged from known proteins and originate from very sparsely sampled eukaryotic supergroups.ConclusionThe open-source (GPLv3) MetaEuk software (https://github.com/soedinglab/metaeuk) enables large-scale eukaryotic metagenomics through reference-based, sensitive taxonomic and functional annotation.