bluuebunny/crossref_metadata_2025_split huggingface dataset:
Surgical and Patient-Reported Outcomes in Patients With PEEK Versus Titanium Cranioplasty Reconstruction
Authors: Asaad Malke , Taslakian Editt N. , Banuelos Joseph , Abu-Ghname Amjed , Bite Uldis , Mardini Samir , Van Gompel Jamie J. , Sharaf Basel 
Published: October 2020

Background:
Several materials are available for cranioplasty reconstruction and consensus regarding the ideal material is lacking. The goal of this study is to present surgical and patient-reported outcomes with PEEK versus Titanium alloplastic cranioplasty.

Methods:
A retrospective review of all patients who underwent alloplastic cranioplasty with PEEK or Titanium from 2010 to 2017 was conducted. Patient demographics and complications were abstracted and analyzed. Information regarding patient-reported outcomes was collected through a telephone survey.

Results:
A total of 72 patients (median age 55 years) who underwent 77 cranioplasties were identified (38% PEEK, n = 29; 62% Titanium, n = 48). Overall complication rates were similar between the PEEK (24%, n = 7) and Titanium groups (23%, n = 11), P = 0.902. Similarly, implant failure was similar between the 2 groups (7% in PEEK (n = 2), 13% in Titanium (n = 6), P = 0.703). History of radiation was associated with increased rate of infection in patients with Titanium mesh cranioplasty (38% in radiated patients (n = 3), 3% in nonradiated patients (n = 1), P = 0.012) but not PEEK implants (0% infection rate in radiated patients (n = 0), 15% in nonradiated patients (n = 4), P = 1.000). A total of 24 patients (33% response rate) participated in the telephone survey. All PEEK cranioplasty patients who responded to our survey (n = 13) reported good to excellent satisfaction, while 72% of our titanium mesh cohort (n = 8) described good or excellent satisfaction and 27% (n = 3) reported acceptable result.

Conclusion:
Cranial reconstruction is associated with high satisfaction among cranioplasty patients with PEEK or Titanium showing comparable complications, failure, and patient-reported satisfaction rates. Patients with history of radiotherapy demonstrated a higher infection rate when titanium mesh was used.
A Health Economic Evaluation of the World Health Organization Surgical Safety Checklist
Authors: Healey Andy , Søfteland Eirik , Harthug Stig , Haaverstad Rune , Mahesparan Rupavathana , Hjallen Bjørg Merete , Eide Geir Egil , Sevdalis Nick , Haugen Arvid Steinar 
Published: October 2020

Objectives:
To evaluate cost-effectiveness of the WHO Surgical Safety Checklist.

Background:
The clinical effectiveness of surgical checklists is largely understood. Few studies to-date have evaluated the cost-effectiveness of checklist use.

Methods:
An economic evaluation was carried out using data from the only available randomized controlled trial of the checklist. Analyses were based on 3702 procedures. Costs considered included checklist implementation costs and length and cost of hospital stay, costs of warming blanket use, blood transfusions and antibiotics used in the operating room, and the cost of clinical time in the operating room – all calculated for each procedure and its associated admission. Nonparametric bootstrapping was used to simulate an empirical distribution of the mean effect of the checklist on total admission costs and the probability of observing a complication-free admission and to quantify sampling uncertainty around mean cost estimates.

Results:
The overall cost of checklist implementation was calculated to be $900 per 100 admissions. Implementation of the WHO checklist resulted in an additional 5.9 complication-free admissions per 100 admissions and an average of 110 bed-days saved per 100 admissions. Accounting for all costs included in the analysis, for every 100 admissions, use of the WHO checklist was estimated to save $55,899.

Conclusions:
Implementation of the WHO checklist was a cost-effective strategy for improving surgical safety.
Distribution of Residual Disease and Recurrence Patterns in Pathological Responders After Neoadjuvant Chemotherapy for Esophageal Squamous Cell Carcinoma
Authors: Matsuda Satoru , Kawakubo Hirofumi , Okamura Akihiko , Takahashi Keita , Toihata Tasuku , Takemura Ryo , Mayanagi Shuhei , Hirata Kenro , Irino Tomoyuki , Hamamoto Yasuo , Takeuchi Hiroya , FACS  , Watanabe Masayuki , Kitagawa Yuko 
Published: October 2020

Objective:
This study aimed to elucidate the residual disease distribution and recurrence patterns in patients with ESCC responding to NAC.

Summary Background Data:
To appropriately plan a prospective trial for the organ preservation approach which includes additional chemoradiotherapy in patients who responded to NAC, the distribution of residual disease needs to be elucidated. Given that the residual tumor is located in the regional field, chemoradiotherapy can be safely added to eliminate the residual disease.

Methods:
Overall, 483 patients with resectable ESCC who received NAC followed by transthoracic esophagectomy at 2 high-volume centers were reviewed. The recurrence-free survival, overall survival (OS), and residual and recurrent tumor patterns were compared among the pathological responses.

Results:
Compared with nonpathological responders, pathological responders exhibited significantly longer recurrence-free survival [hazard ratio of Grade 1b/2/3 compared with Grade 0; 0.25 (P < 0.001)/0.17 (P < 0.001)/0.16 (P = 0.003)] and OS [hazard ratio of Grade 1b/2/3 compared with Grade 0; 0.26 (P < 0.001)/0.12 (P < 0.001)/0.11 (P = 0.003)]. In terms of the distribution of recurrence, the percentages of solitary recurrence in the regional field out of all recurrence was significantly higher in patients with Grade 1b (60%)/2 (67%)/3 (67%) whereas less than 25% in Grade 0 or 1a.

Conclusions:
It was found that postoperative recurrence in responders occurred in the regional field mostly as a solitary lesion without the distant failure, indicating that the residual tumor cells can be eliminated by additional chemoradiotherapy.
Using Direct-to-Consumer Genetic Testing Results to Accelerate Alzheimer Disease Clinical Trial Recruitment
Authors: Ryan Mary M. , Cox Chelsea G. , Witbracht Megan , Hoang Dan , Gillen Daniel L. , Grill Joshua D. 
Published: October 2020

Introduction:
The apolipoprotein E (APOE) gene is the strongest known genetic risk factor for sporadic Alzheimer disease (AD). APOE can be used as an enrichment strategy or inclusion criterion for AD prevention trials. Personal genomics companies market direct-to-consumer (DTC) genetic tests, including APOE. We assessed DTC APOE testing usage among enrollees of the University of California Irvine Consent-to-Contact Registry, an online recruitment registry, and attitudes toward using this information in clinical trial recruitment.

Methods:
We emailed links to an electronic survey to registry enrollees age 50 years or older. We assessed participants’ use of DTC services, willingness to learn APOE status, and willingness to share genetic information. Logistic regression models assessed relationships between DTC testing usage and demographic characteristics, and with willingness to share results to assist trial recruitment.

Results:
Among 1312 responders (57% response rate), few (7%) had used DTC testing for APOE. Non-Hispanic Asian enrollees were 93% less likely to have used DTC testing, compared with non-Hispanic Whites [95% confidence interval: (0.01, 0.67)]. Willingness to share APOE information for study recruitment was >90% for both users and nonusers.

Conclusions:
Matching participants to trials on the basis of DTC APOE information may be an effective way to streamline AD prevention trial recruitment.
Lewinella aurantiaca sp. nov., a carotenoid pigment-producing bacterium isolated from surface seawater
Authors: Kim Inhyup , Chhetri Geeta , Kim Jiyoun , Kang Minchung , Seo Taegun 
Published: October 2020

A Gram-stain-negative, aerobic, rod-shaped, carotenoid-pigmented, motile-by-gliding bacterium, which was designated as SSH13T, was isolated from a surface seawater sample collected from Sehwa Beach in the Republic of Korea. Strain SSH13T was oxidase-negative, catalase-positive and grew at 2–37 °C (optimum, 30 °C), in the presence of 0.5–6% NaCl and within a pH range of pH 6–10 (optimum, pH 8). The novel isolate required NaCl for growth and grew optimally with approximately 2 % NaCl. Chemotaxonomic and morphological characteristics were consistent with members of the genus

Lewinella

. Furthermore, phylogenetic analysis based on 16S rRNA gene sequencing revealed that strain SSH13T was most closely related to the type strains of the genus

Lewinella

. Strain SSH13T had highest 16S rRNA gene sequence similarities to

Lewinella persica

DSM 23188T (95.3 %) and

Lewinella agarilytica

KCTC 12774T (95.0 %). The major fatty acids of SSH13T were summed feature 3 (C16 : 1
ω7c and/or C16 : 1
ω6c) and iso-C15 : 0. Strain SSH13T contained phosphatidylethanolamine as a major polar lipid. Menaquinone-7 was the predominant respiratory quinone. The average nucleotide identity values between strain SSH13T and

L. persica

T-3T and

L. agarilytica

SST-19T were 72.9 and 72.6 %, respectively. The DNA G+C content of the genomic DNA was 52.8 mol%. The present study aimed to determine the multiple-antibiotic resistance of the novel bacterium. Based on phylogenetic and phenotypic analyses, strain SSH13T is considered to represent a novel species of the genus

Lewinella

, for which the name Lewinella aurantiaca sp. nov. (type strain SSH13T=KACC 21167T=NBRC 113866T) is proposed.
Stay-at-home policy: is it a case of exception fallacy? An internet-based ecological study
Authors: Savaris Ricardo F. , Pumi Guilherme , Dalzochio Jovani , Kunst Rafael 
Published: October 2020

AbstractBackgroundCountries with strict lockdown had a spike on the number of deaths. A recent mathematical model has suggested that staying at home did not play a dominant role in reducing COVID-19 transmission. Comparison between number of deaths and social mobility is difficult due to the non-stationary nature of the COVID-19 data.ObjectiveTo propose a novel approach to assess the association between staying at home values and the reduction/increase in the number of deaths due to COVID-19 in several regions around the world.MethodsIn this ecological study, data fromwww.google.com/covid19/mobility/, ourworldindata.org and covid.saude.gov.br were combined. Countries with >100 deaths and with a Healthcare Access and Quality Index of ≥67 were included. Data were preprocessed and analyzed using the difference between number of deaths/million between 2 regions and the difference between the percentage of staying at home. Analysis was performed using linear regression and residual analysisResultsAfter preprocessing the data, 87 regions around the world were included, yielding 3,741 pairwise comparisons for linear regression analysis. Only 63 (1.6%) comparisons were significant.DiscussionWith our results, we were not able to explain if COVID-19 mortality is reduced by staying as home in ∼98% of the comparisons after epidemiological weeks 9 to 34.
Sustainable Production of the Biofueln-Butanol byRhodopseudomonas palustrisTIE-1
Authors: Bai W. , Ranaivoarisoa T. O. , Singh R. , Rengasamy K. , Bose A. 
Published: October 2020

AbstractAnthropogenic carbon dioxide (CO2) release in the atmosphere from fossil fuel combustion has inspired scientists to study CO2to fuel conversion. Oxygenic phototrophs such as cyanobacteria have been used to produce biofuels using CO2. However, oxygen generation during oxygenic photosynthesis affects biofuel production efficiency. To producen-butanol (biofuel) from CO2, here we introduced ann-butanol biosynthesis pathway into an anoxygenic (non-oxygen evolving) photoautotroph,Rhodopseudomonas palustrisTIE-1 (TIE-1). Using different carbon, nitrogen, and electron sources, we achievedn-butanol production in wild-type TIE-1 and mutants lacking electron-consuming (nitrogen-fixing) or acetyl-CoA-consuming (polyhydroxybutyrate and glycogen synthesis) pathways. The mutant lacking the nitrogen-fixing pathway produced highestn-butanol. Coupled with novel hybrid bioelectrochemical platforms, this mutant producedn-butanol using CO2, solar panel-generated electricity, and light, with high electrical energy conversion efficiency. Overall, this approach showcases TIE-1 as an attractive microbial chassis for carbon-neutraln-butanol bioproduction using sustainable, renewable, and abundant resources.
Comparison between instrumental variable and mediation-based methods for reconstructing causal gene networks in yeast
Authors: Ludl Adriaan-Alexander , Michoel Tom 
Published: October 2020

AbstractCausal gene networks model the flow of information within a cell. Reconstructing causal networks from omics data is challenging because correlation does not imply causation. When genomics and transcriptomics data from a segregating population are combined, genomic variants can be used to orient the direction of causality between gene expression traits. Instrumental variable methods use a local expression quantitative trait locus (eQTL) as a randomized instrument for a gene’s expression level, and assign target genes based on distal eQTL associations. Mediation-based methods additionally require that distal eQTL associations are mediated by the source gene. A detailed comparison between these methods has not yet been conducted, due to the lack of a standardized implementation of different methods, the limited sample size of most multi-omics datasets, and the absence of ground-truth networks for most organisms. Here we used Findr, a software package providing uniform implementations of instrumental variable, mediation, and coexpression-based methods, a recent dataset of 1,012 segregants from a cross between two budding yeast strains, and the YEASTRACT database of known transcriptional interactions to compare causal gene network inference methods. We found that causal inference methods result in a significant overlap with the ground-truth, whereas coexpression did not perform better than random. A subsampling analysis revealed that the performance of mediation saturates at large sample sizes, due to a loss of sensitivity when residual correlations become significant. Instrumental variable methods on the other hand contain false positive predictions, due to genomic linkage between eQTL instruments. Instrumental variable and mediation-based methods also have complementary roles for identifying causal genes underlying transcriptional hotspots. Instrumental variable methods correctly predictedSTB5targets for a hotspot centred on the transcription factorSTB5, whereas mediation failed due to Stb5p auto-regulating its own expression. Mediation suggests a new candidate gene,DNM1, for a hotspot on Chr XII, whereas instrumental variable methods could not distinguish between multiple genes located within the hotspot. In conclusion, causal inference from genomics and transcriptomics data is a powerful approach for reconstructing causal gene networks, which could be further improved by the development of methods to control for residual correlations in mediation analyses and genomic linkage and pleiotropic effects from transcriptional hotspots in instrumental variable analyses.
Auxin guides germ cell specification inArabidopsisanthers
Authors: Zheng Yafeng , Wang Donghui , Ye Sida , Chen Wenqian , Li Guilan , Xu Zhihong , Bai Shunong , Zhao Feng 
Published: October 2020

SummaryGerm cells (GCs) transmit genetic information from one generation to the next. Unlike animal GCs, plant GCs are induced post-embryonically, forming locally from somatic cells. This induction is coordinated with organogenesis and might be guided by positional cues. In angiosperms, male GCs initiate from the internal layers at the four corners of the anther primordia and are gradually enclosed by parietal cell (PC) layers, leading to a concentric GC-PC pattern.1,2However, the underlying mechanism of GC initiation and GC-PC pattern formation is unclear. Auxin affects pattern formation3and anther development.4–11However, whether GC formation involves auxin remains unknown. We report that the auxin distribution in pre-meiotic anthers parallels GC initiation, forming a centripetal gradient between the outer primordial cells and the inner GCs. The auxin biosynthesis genesTRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS 1(TAA1) andTRYPTOPHAN AMINOTRANSFERASE RELATED 2(TAR2)5,12are responsible for this patterning and essential for GC specification.SPOROCYTELESS/NOZZLE(SPL/NZZ, a determinant for GC specification)13–15mediates the effect of auxin on GC specification, modulates auxin homeostasis, and maintains centripetal auxin patterning. Our results reveal that auxin is a key factor guiding GC specification inArabidopsisanthers.
Reducing SAR in 7T brain fMRI by circumventing fat suppression while removing the lipid signal through a parallel acquisition approach
Authors: Seginer Amir , Furman-Haran Edna , Goldberg Ilan , Schmidt Rita 
Published: October 2020

AbstractUltra-high-field functional magnetic resonance imaging (fMRI) offers the way to new insights while increasing the spatial and temporal resolution. However, a crucial concern in 7T human MRI is the increase in power deposition, supervised through the specific absorption rate (SAR). The SAR limitation can restrict the brain coverage or the minimal repetition time of fMRI experiments. fMRI is based on the well-known gradient-echo echo-planar imaging (GRE-EPI) sequence, which offers ultrafast acquisition. Commonly, the GRE-EPI sequence comprises two pulses: fat suppression and excitation. This work provides the means for a significant reduction in the SAR by circumventing the fat-suppression pulse. Without this fat-suppression, however, lipid signal can result in artifacts due to the chemical shift between the lipid and water signals. Our approach exploits a reconstruction similar to the simultaneous-multi-slice (SMS) method to separate the lipid and water images, thus avoiding undesired lipid artifacts in brain images. The lipid-water separation is based on the known spatial shift of the lipid signal, which can be detected by the multi-channel coils sensitivity profiles. Our study shows robust human imaging, offering greater flexibility to reduce the SAR, shorten the repetition time or increase the volume coverage with substantial benefit for brain functional studies.
Tau pathology spreads between anatomically-connected regions of the brain and is modulated by a LRRK2 mutation
Authors: Henderson Michael X. , Cornblath Eli J. , Li Howard L. , Changolkar Lakshmi , Zhang Bin , Brown Hannah J. , Gathagan Ronald J. , Olufemi Modupe F. , Bassett Danielle S. , Trojanowski John Q. , Lee Virginia M.Y. 
Published: October 2020

ABSTRACTTau pathology is a diagnostic feature of Alzheimer’s disease (AD) but is also a prominent feature of Parkinson’s disease (PD), including genetic forms of PD with mutations in leucine-rich repeat kinase 2 (LRRK2). In both diseases, tau pathology is progressive and correlates with cognitive decline. Neuropathological staging studies in humans and mouse models have suggested that tau spreads through the brain, but it is unclear how neuroanatomical connections, spatial proximity, and regional vulnerability contribute to pathology spread. Further, it is unknown how mutations in theLRRK2gene may modulate susceptibility to tau pathology’s initiation or spread. In this study, we used seed-based models of tauopathy to capture spatiotemporal patterns of pathology in mice. Following the injection of AD brain-derived tau into the brains of non-transgenic mice, tau pathology spreads progressively through the brain in a spatiotemporal pattern that is well-explained by anatomical connectivity. We validated and compared network models based on diffusion along anatomical connections to predict tau spread, estimate regional vulnerability to tau pathology, and investigate gene expression patterns related to regional vulnerability. We further investigated tau pathology spread in mice harboring a mutation in LRRK2 and found that while tau pathology spread is still constrained by anatomical connectivity, it spreads preferentially in a retrograde direction to regions that are otherwise resilient in wildtype mice. This study provides a quantitative demonstration that tau pathology spreads along anatomical connections, explores the kinetics of this spread, and provides a platform for investigating the effect of genetic risk factors and treatments on the progression of tauopathies.
Cross-modal orienting of exogenous attention results in visual-cortical facilitation, not suppression
Authors: Keefe Jonathan M. , Pokta Emilia , Störmer Viola S. 
Published: October 2020

AbstractAttention may be oriented exogenously (i.e., involuntarily) to the location of salient stimuli, resulting in improved perception. However, it is unknown whether exogenous attention improves perception by facilitating processing of attended information, suppressing processing of unattended information, or both. To test this question, we measured behavioral performance and cue-elicited neural changes in the electroencephalogram as participants (N = 19) performed a task in which a spatially non-predictive auditory cue preceded a visual target. Critically, this cue was either presented at a peripheral target location or from the center of the screen, allowing us to isolate spatially specific attentional activity. We find that both behavior and attention-mediated changes in visual-cortical activity are enhanced at the location of a cue prior to the onset of a target, but that behavior and neural activity at an unattended target location are equivalent to that following a central cue that does not direct attention (i.e., baseline). These results suggest that exogenous attention operates solely via facilitation of information at an attended location.
Modelling selection response in plant breeding programs using crop models as mechanistic gene-to-phenotype (CGM-G2P) multi-trait link functions
Authors: Cooper M , Powell O , Voss-Fels KP , Messina CD , Gho C , Podlich DW , Technow F , Chapman SC , Beveridge CA , Ortiz-Barientos D , Hammer GL 
Published: October 2020

AbstractPlant breeding programs are designed and operated over multiple cycles to systematically change the genetic makeup of plants to achieve improved trait performance for a Target Population of Environments (TPE). Within each cycle, selection applied to the standing genetic variation within a structured reference population of genotypes (RPG) is the primary mechanism by which breeding programs make the desired genetic changes. Selection operates to change the frequencies of the alleles of the genes controlling trait variation within the RPG. The structure of the RPG and the TPE has important implications for the design of optimal breeding strategies. The breeder’s equation, together with the quantitative genetic theory behind the equation, informs many of the principles for design of breeding programs. The breeder’s equation can take many forms depending on the details of the breeding strategy. Through the genetic changes achieved by selection, the cultivated varieties of crops (cultivars) are improved for use in agriculture. From a breeding perspective, selection for specific trait combinations requires a quantitative link between the effects of the alleles of the genes impacted by selection and the trait phenotypes of plants and their breeding value. This gene-to-phenotype link function provides the G2P map for one to many traits. For complex traits controlled by many genes, the infinitesimal model for trait genetic variation is the dominant G2P model of quantitative genetics. Here we consider motivations and potential benefits of using the hierarchical structure of crop models as CGM-G2P trait link functions in combination with the infinitesimal model for the design and optimisation of selection in breeding programs.